Sodium in PDB 4plg: Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
Protein crystallography data
The structure of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate., PDB code: 4plg
was solved by
J.I.Boucher,
J.R.Jacobowitz,
B.C.Beckett,
S.Classen,
D.L.Theobald,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.53 /
1.19
|
|
Space group
|
C 2 2 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
113.680,
143.260,
91.540,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.7 /
18.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
(pdb code 4plg). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the
Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate., PDB code: 4plg:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Sodium binding site 1 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 1 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na402
b:17.2
occ:1.00
|
H
|
A:GLY20
|
2.1
|
12.2
|
1.0
|
|
HG1
|
A:THR83
|
2.2
|
13.8
|
1.0
|
|
H
|
A:GLY17
|
2.2
|
12.7
|
1.0
|
|
O2N
|
A:NAI409
|
2.8
|
10.8
|
1.0
|
|
OG1
|
A:THR83
|
2.8
|
11.5
|
1.0
|
|
N
|
A:GLY17
|
2.9
|
10.6
|
1.0
|
|
N
|
A:GLY20
|
3.0
|
10.1
|
1.0
|
|
HA3
|
A:GLY17
|
3.1
|
12.2
|
1.0
|
|
HB
|
A:THR83
|
3.2
|
13.3
|
1.0
|
|
H
|
A:ILE19
|
3.2
|
13.0
|
1.0
|
|
CA
|
A:GLY17
|
3.3
|
10.1
|
1.0
|
|
HA3
|
A:GLY20
|
3.3
|
11.5
|
1.0
|
|
C
|
A:GLY17
|
3.3
|
10.6
|
1.0
|
|
H4B
|
A:NAI409
|
3.4
|
15.8
|
1.0
|
|
O5B
|
A:NAI409
|
3.5
|
13.6
|
1.0
|
|
CB
|
A:THR83
|
3.5
|
11.1
|
1.0
|
|
HB
|
A:ILE19
|
3.5
|
11.7
|
1.0
|
|
H52A
|
A:NAI409
|
3.6
|
15.5
|
1.0
|
|
N
|
A:ILE19
|
3.6
|
10.9
|
1.0
|
|
CA
|
A:GLY20
|
3.7
|
9.6
|
1.0
|
|
C
|
A:GLY15
|
3.7
|
10.8
|
1.0
|
|
N
|
A:MET18
|
3.7
|
11.7
|
1.0
|
|
O
|
A:GLY17
|
3.7
|
11.6
|
1.0
|
|
HG21
|
A:THR83
|
3.8
|
13.8
|
1.0
|
|
O
|
A:GLY15
|
3.8
|
10.4
|
1.0
|
|
H
|
A:MET18
|
3.8
|
14.0
|
1.0
|
|
H52N
|
A:NAI409
|
3.9
|
13.2
|
1.0
|
|
N
|
A:SER16
|
3.9
|
10.7
|
1.0
|
|
C
|
A:SER16
|
3.9
|
10.9
|
1.0
|
|
C5B
|
A:NAI409
|
3.9
|
12.9
|
1.0
|
|
HA3
|
A:GLY15
|
4.0
|
12.5
|
1.0
|
|
C
|
A:ILE19
|
4.0
|
9.8
|
1.0
|
|
CA
|
A:ILE19
|
4.1
|
9.9
|
1.0
|
|
PN
|
A:NAI409
|
4.1
|
11.5
|
1.0
|
|
C4B
|
A:NAI409
|
4.1
|
13.2
|
1.0
|
|
HA
|
A:SER16
|
4.1
|
12.6
|
1.0
|
|
H
|
A:SER16
|
4.2
|
12.9
|
1.0
|
|
CG2
|
A:THR83
|
4.2
|
11.5
|
1.0
|
|
HA2
|
A:GLY20
|
4.2
|
11.5
|
1.0
|
|
HA2
|
A:GLY17
|
4.2
|
12.2
|
1.0
|
|
CA
|
A:SER16
|
4.2
|
10.5
|
1.0
|
|
CB
|
A:ILE19
|
4.3
|
9.7
|
1.0
|
|
H
|
A:GLY21
|
4.4
|
11.5
|
1.0
|
|
CA
|
A:GLY15
|
4.4
|
10.4
|
1.0
|
|
C
|
A:MET18
|
4.4
|
11.5
|
1.0
|
|
H51N
|
A:NAI409
|
4.4
|
13.2
|
1.0
|
|
O3
|
A:NAI409
|
4.5
|
12.6
|
1.0
|
|
PA
|
A:NAI409
|
4.5
|
12.2
|
1.0
|
|
O
|
A:THR83
|
4.5
|
11.4
|
1.0
|
|
C5D
|
A:NAI409
|
4.6
|
11.0
|
1.0
|
|
O2A
|
A:NAI409
|
4.6
|
12.7
|
1.0
|
|
CA
|
A:MET18
|
4.7
|
11.1
|
1.0
|
|
HA2
|
A:GLY15
|
4.7
|
12.5
|
1.0
|
|
NA
|
A:NA403
|
4.7
|
17.0
|
1.0
|
|
C
|
A:THR83
|
4.7
|
11.1
|
1.0
|
|
CA
|
A:THR83
|
4.8
|
10.2
|
1.0
|
|
HG23
|
A:THR83
|
4.8
|
13.8
|
1.0
|
|
C
|
A:GLY20
|
4.8
|
10.0
|
1.0
|
|
HG22
|
A:THR83
|
4.9
|
13.8
|
1.0
|
|
O5D
|
A:NAI409
|
4.9
|
11.8
|
1.0
|
|
HG13
|
A:ILE19
|
4.9
|
13.0
|
1.0
|
|
N
|
A:GLY21
|
4.9
|
9.6
|
1.0
|
|
O
|
A:SER16
|
5.0
|
11.6
|
1.0
|
|
H51A
|
A:NAI409
|
5.0
|
15.5
|
1.0
|
|
O4B
|
A:NAI409
|
5.0
|
13.7
|
1.0
|
|
Sodium binding site 2 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 2 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:17.0
occ:1.00
|
OG1
|
A:THR83
|
2.8
|
11.5
|
1.0
|
|
HB3
|
A:LEU13
|
2.8
|
12.6
|
1.0
|
|
O
|
A:GLY15
|
2.8
|
10.4
|
1.0
|
|
HG1
|
A:THR83
|
2.8
|
13.8
|
1.0
|
|
HG23
|
A:THR83
|
2.9
|
13.8
|
1.0
|
|
HE1
|
A:MET23
|
3.0
|
13.5
|
1.0
|
|
O
|
A:ILE81
|
3.0
|
10.1
|
1.0
|
|
H
|
A:THR83
|
3.0
|
12.7
|
1.0
|
|
HA2
|
A:GLY20
|
3.2
|
11.5
|
1.0
|
|
HE2
|
A:MET23
|
3.3
|
13.5
|
1.0
|
|
HE3
|
A:MET23
|
3.3
|
13.5
|
1.0
|
|
CE
|
A:MET23
|
3.4
|
11.2
|
1.0
|
|
HA
|
A:LEU13
|
3.4
|
12.3
|
1.0
|
|
HA3
|
A:GLY20
|
3.4
|
11.5
|
1.0
|
|
O
|
A:ILE14
|
3.4
|
11.6
|
1.0
|
|
H
|
A:ILE14
|
3.4
|
13.2
|
1.0
|
|
CG2
|
A:THR83
|
3.5
|
11.5
|
1.0
|
|
N
|
A:ILE14
|
3.5
|
11.0
|
1.0
|
|
HG21
|
A:THR83
|
3.5
|
13.8
|
1.0
|
|
C
|
A:LEU13
|
3.6
|
11.2
|
1.0
|
|
N
|
A:THR83
|
3.6
|
10.5
|
1.0
|
|
CB
|
A:LEU13
|
3.6
|
10.5
|
1.0
|
|
CB
|
A:THR83
|
3.6
|
11.1
|
1.0
|
|
C
|
A:ILE14
|
3.6
|
10.8
|
1.0
|
|
CA
|
A:LEU13
|
3.7
|
10.2
|
1.0
|
|
HA3
|
A:GLY15
|
3.7
|
12.5
|
1.0
|
|
C
|
A:GLY15
|
3.7
|
10.8
|
1.0
|
|
CA
|
A:GLY20
|
3.8
|
9.6
|
1.0
|
|
C
|
A:ILE81
|
3.9
|
10.4
|
1.0
|
|
HA
|
A:ILE82
|
3.9
|
12.3
|
1.0
|
|
HD22
|
A:LEU13
|
4.0
|
12.7
|
1.0
|
|
N
|
A:GLY15
|
4.0
|
10.8
|
1.0
|
|
CA
|
A:GLY15
|
4.0
|
10.4
|
1.0
|
|
HB
|
A:ILE81
|
4.1
|
13.0
|
1.0
|
|
HB2
|
A:LEU13
|
4.1
|
12.6
|
1.0
|
|
CA
|
A:THR83
|
4.2
|
10.2
|
1.0
|
|
CA
|
A:ILE14
|
4.3
|
11.1
|
1.0
|
|
O
|
A:LEU13
|
4.3
|
11.3
|
1.0
|
|
HG22
|
A:ILE81
|
4.3
|
12.6
|
1.0
|
|
C
|
A:ILE82
|
4.3
|
11.2
|
1.0
|
|
HG22
|
A:THR83
|
4.4
|
13.8
|
1.0
|
|
N
|
A:GLY20
|
4.4
|
10.1
|
1.0
|
|
HB
|
A:THR83
|
4.4
|
13.3
|
1.0
|
|
CA
|
A:ILE82
|
4.4
|
10.2
|
1.0
|
|
H
|
A:GLY20
|
4.5
|
12.2
|
1.0
|
|
N
|
A:ILE82
|
4.5
|
10.4
|
1.0
|
|
CD2
|
A:LEU13
|
4.6
|
10.6
|
1.0
|
|
CG
|
A:LEU13
|
4.6
|
10.2
|
1.0
|
|
H
|
A:GLY15
|
4.6
|
12.9
|
1.0
|
|
HD23
|
A:LEU13
|
4.6
|
12.7
|
1.0
|
|
NA
|
A:NA402
|
4.7
|
17.2
|
1.0
|
|
HD13
|
A:LEU13
|
4.7
|
13.6
|
1.0
|
|
CB
|
A:ILE81
|
4.8
|
10.8
|
1.0
|
|
HA
|
A:ILE14
|
4.9
|
13.3
|
1.0
|
|
H
|
A:ALA84
|
4.9
|
13.7
|
1.0
|
|
HA
|
A:SER16
|
4.9
|
12.6
|
1.0
|
|
HA
|
A:THR83
|
4.9
|
12.2
|
1.0
|
|
CA
|
A:ILE81
|
5.0
|
10.0
|
1.0
|
|
N
|
A:SER16
|
5.0
|
10.7
|
1.0
|
|
CG2
|
A:ILE81
|
5.0
|
10.5
|
1.0
|
|
C
|
A:GLY20
|
5.0
|
10.0
|
1.0
|
|
HA2
|
A:GLY15
|
5.0
|
12.5
|
1.0
|
|
HD12
|
A:ILE129
|
5.0
|
15.1
|
1.0
|
|
Sodium binding site 3 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 3 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:18.2
occ:1.00
|
H
|
A:VAL157
|
2.2
|
12.7
|
1.0
|
|
H
|
A:ALA155
|
2.2
|
12.4
|
1.0
|
|
HA
|
A:MET154
|
2.6
|
12.8
|
1.0
|
|
HG23
|
A:VAL157
|
2.7
|
13.8
|
1.0
|
|
O
|
A:VAL265
|
2.7
|
11.7
|
1.0
|
|
HA
|
A:CYS266
|
2.8
|
15.2
|
1.0
|
|
H
|
A:GLY156
|
3.0
|
13.8
|
1.0
|
|
N
|
A:ALA155
|
3.0
|
10.4
|
1.0
|
|
N
|
A:VAL157
|
3.0
|
10.6
|
1.0
|
|
HB
|
A:VAL157
|
3.1
|
12.7
|
1.0
|
|
HG2
|
A:MET154
|
3.2
|
12.9
|
1.0
|
|
N
|
A:GLY156
|
3.3
|
11.5
|
1.0
|
|
SD
|
A:MET252
|
3.4
|
12.3
|
1.0
|
|
CG2
|
A:VAL157
|
3.4
|
11.5
|
1.0
|
|
CA
|
A:MET154
|
3.5
|
10.7
|
1.0
|
|
CB
|
A:VAL157
|
3.6
|
10.6
|
1.0
|
|
CA
|
A:CYS266
|
3.6
|
12.7
|
1.0
|
|
HG21
|
A:VAL157
|
3.7
|
13.8
|
1.0
|
|
C
|
A:MET154
|
3.7
|
10.8
|
1.0
|
|
C
|
A:ALA155
|
3.7
|
11.3
|
1.0
|
|
C
|
A:VAL265
|
3.7
|
11.3
|
1.0
|
|
SG
|
A:CYS266
|
3.8
|
13.7
|
1.0
|
|
O
|
A:GLY153
|
3.9
|
12.1
|
1.0
|
|
CA
|
A:VAL157
|
3.9
|
10.7
|
1.0
|
|
C
|
A:GLY156
|
3.9
|
11.4
|
1.0
|
|
HB3
|
A:CYS266
|
3.9
|
16.1
|
1.0
|
|
CA
|
A:GLY156
|
3.9
|
11.3
|
1.0
|
|
HA3
|
A:GLY156
|
3.9
|
13.6
|
1.0
|
|
CB
|
A:CYS266
|
4.0
|
13.4
|
1.0
|
|
CA
|
A:ALA155
|
4.0
|
10.4
|
1.0
|
|
CG
|
A:MET154
|
4.0
|
10.8
|
1.0
|
|
HE1
|
A:MET252
|
4.0
|
15.3
|
1.0
|
|
HE3
|
A:MET252
|
4.1
|
15.3
|
1.0
|
|
CE
|
A:MET252
|
4.1
|
12.8
|
1.0
|
|
N
|
A:CYS266
|
4.2
|
11.9
|
1.0
|
|
HG22
|
A:VAL157
|
4.2
|
13.8
|
1.0
|
|
H
|
A:LEU158
|
4.2
|
12.7
|
1.0
|
|
CB
|
A:MET154
|
4.2
|
11.8
|
1.0
|
|
HA
|
A:VAL157
|
4.5
|
12.8
|
1.0
|
|
HG2
|
A:MET252
|
4.5
|
13.1
|
1.0
|
|
O
|
A:ALA155
|
4.5
|
11.1
|
1.0
|
|
SD
|
A:MET154
|
4.5
|
12.0
|
1.0
|
|
N
|
A:MET154
|
4.5
|
10.2
|
1.0
|
|
H
|
A:SER267
|
4.5
|
14.0
|
1.0
|
|
CG
|
A:MET252
|
4.5
|
10.9
|
1.0
|
|
HA
|
A:ALA155
|
4.6
|
12.5
|
1.0
|
|
O
|
A:HOH639
|
4.6
|
13.2
|
1.0
|
|
HB2
|
A:MET154
|
4.6
|
14.2
|
1.0
|
|
C
|
A:GLY153
|
4.6
|
10.4
|
1.0
|
|
HG3
|
A:MET252
|
4.6
|
13.1
|
1.0
|
|
HG
|
A:CYS266
|
4.7
|
16.4
|
1.0
|
|
HB3
|
A:SER248
|
4.7
|
13.9
|
1.0
|
|
HG3
|
A:MET154
|
4.8
|
12.9
|
1.0
|
|
C
|
A:CYS266
|
4.8
|
11.9
|
1.0
|
|
HA2
|
A:GLY156
|
4.8
|
13.6
|
1.0
|
|
HB3
|
A:LEU264
|
4.9
|
17.9
|
1.0
|
|
N
|
A:LEU158
|
4.9
|
10.6
|
1.0
|
|
HB3
|
A:ALA155
|
4.9
|
13.6
|
1.0
|
|
HB2
|
A:CYS266
|
4.9
|
16.1
|
1.0
|
|
O
|
A:MET154
|
4.9
|
12.0
|
1.0
|
|
C
|
A:VAL157
|
5.0
|
10.6
|
1.0
|
|
Sodium binding site 4 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 4 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na405
b:18.5
occ:1.00
|
HA3
|
A:GLY282
|
2.6
|
15.3
|
1.0
|
|
O
|
A:HOH668
|
2.7
|
17.1
|
1.0
|
|
HA
|
A:ILE183
|
2.7
|
15.9
|
1.0
|
|
O
|
A:HOH639
|
2.8
|
13.2
|
1.0
|
|
O
|
A:VAL182
|
2.8
|
13.1
|
1.0
|
|
HG12
|
A:VAL265
|
2.9
|
14.7
|
1.0
|
|
HA2
|
A:GLY156
|
3.0
|
13.6
|
1.0
|
|
HG11
|
A:VAL265
|
3.0
|
14.7
|
1.0
|
|
HA3
|
A:GLY156
|
3.1
|
13.6
|
1.0
|
|
CG1
|
A:VAL265
|
3.4
|
12.3
|
1.0
|
|
CA
|
A:GLY156
|
3.4
|
11.3
|
1.0
|
|
CA
|
A:GLY282
|
3.5
|
12.8
|
1.0
|
|
CA
|
A:ILE183
|
3.5
|
13.2
|
1.0
|
|
O
|
A:GLY184
|
3.5
|
13.4
|
1.0
|
|
O
|
A:HOH635
|
3.7
|
13.7
|
1.0
|
|
C
|
A:ILE183
|
3.7
|
13.3
|
1.0
|
|
C
|
A:VAL182
|
3.7
|
13.0
|
1.0
|
|
HA2
|
A:GLY282
|
3.7
|
15.3
|
1.0
|
|
H
|
A:GLY156
|
3.8
|
13.8
|
1.0
|
|
N
|
A:GLY156
|
3.8
|
11.5
|
1.0
|
|
H
|
A:GLY184
|
3.9
|
15.2
|
1.0
|
|
N
|
A:GLY184
|
3.9
|
12.7
|
1.0
|
|
HG13
|
A:VAL265
|
3.9
|
14.7
|
1.0
|
|
N
|
A:ILE183
|
4.0
|
13.3
|
1.0
|
|
C
|
A:GLY282
|
4.0
|
12.6
|
1.0
|
|
HG12
|
A:VAL182
|
4.1
|
15.8
|
1.0
|
|
O
|
A:ILE183
|
4.3
|
13.6
|
1.0
|
|
HB3
|
A:ALA155
|
4.3
|
13.6
|
1.0
|
|
O
|
A:GLY282
|
4.3
|
12.4
|
1.0
|
|
H
|
A:GLY282
|
4.4
|
15.7
|
1.0
|
|
C
|
A:GLY184
|
4.4
|
12.1
|
1.0
|
|
HB
|
A:VAL265
|
4.5
|
14.7
|
1.0
|
|
N
|
A:GLY282
|
4.5
|
13.1
|
1.0
|
|
HB2
|
A:ASP159
|
4.5
|
14.1
|
1.0
|
|
HB
|
A:VAL182
|
4.6
|
15.4
|
1.0
|
|
OD2
|
A:ASP159
|
4.6
|
13.8
|
1.0
|
|
CB
|
A:VAL265
|
4.6
|
12.2
|
1.0
|
|
HG22
|
A:ILE183
|
4.6
|
15.5
|
1.0
|
|
C
|
A:ALA155
|
4.7
|
11.3
|
1.0
|
|
N
|
A:VAL283
|
4.7
|
12.3
|
1.0
|
|
CA
|
A:GLY184
|
4.7
|
12.9
|
1.0
|
|
CB
|
A:ILE183
|
4.7
|
13.3
|
1.0
|
|
HB
|
A:ILE183
|
4.8
|
16.0
|
1.0
|
|
H
|
A:ILE183
|
4.8
|
15.9
|
1.0
|
|
C
|
A:GLY156
|
4.8
|
11.4
|
1.0
|
|
H
|
A:VAL283
|
4.9
|
14.7
|
1.0
|
|
HB1
|
A:ALA155
|
4.9
|
13.6
|
1.0
|
|
CG1
|
A:VAL182
|
4.9
|
13.2
|
1.0
|
|
CA
|
A:VAL182
|
5.0
|
12.7
|
1.0
|
|
Sodium binding site 5 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 5 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na406
b:19.1
occ:1.00
|
H
|
A:ALA241
|
2.0
|
13.0
|
1.0
|
|
HN1
|
A:OXM401
|
2.6
|
25.4
|
1.0
|
|
HB2
|
A:SER240
|
2.6
|
15.4
|
1.0
|
|
HB2
|
A:ALA241
|
2.8
|
13.3
|
1.0
|
|
O2
|
A:OXM401
|
2.9
|
13.3
|
1.0
|
|
HA2
|
A:GLY229
|
2.9
|
16.2
|
1.0
|
|
N
|
A:ALA241
|
2.9
|
10.9
|
1.0
|
|
O
|
A:GLY229
|
3.0
|
13.5
|
1.0
|
|
HB
|
A:ILE232
|
3.0
|
14.9
|
1.0
|
|
HG23
|
A:VAL233
|
3.1
|
17.8
|
1.0
|
|
HB3
|
A:ALA241
|
3.1
|
13.3
|
1.0
|
|
CB
|
A:ALA241
|
3.3
|
11.1
|
1.0
|
|
CB
|
A:SER240
|
3.4
|
12.8
|
1.0
|
|
HG22
|
A:ILE232
|
3.5
|
15.7
|
1.0
|
|
N1
|
A:OXM401
|
3.6
|
21.2
|
1.0
|
|
CA
|
A:GLY229
|
3.6
|
13.5
|
1.0
|
|
HB3
|
A:SER240
|
3.6
|
15.4
|
1.0
|
|
HA
|
A:SER240
|
3.6
|
13.0
|
1.0
|
|
C
|
A:GLY229
|
3.6
|
13.3
|
1.0
|
|
HG21
|
A:ILE232
|
3.6
|
15.7
|
1.0
|
|
HH22
|
A:ARG162
|
3.7
|
14.4
|
1.0
|
|
CA
|
A:ALA241
|
3.7
|
10.6
|
1.0
|
|
HA3
|
A:GLY229
|
3.8
|
16.2
|
1.0
|
|
H
|
A:VAL233
|
3.8
|
15.2
|
1.0
|
|
C2
|
A:OXM401
|
3.8
|
15.5
|
1.0
|
|
CA
|
A:SER240
|
3.8
|
10.8
|
1.0
|
|
C
|
A:SER240
|
3.8
|
9.8
|
1.0
|
|
CB
|
A:ILE232
|
3.8
|
12.4
|
1.0
|
|
CG2
|
A:ILE232
|
3.8
|
13.1
|
1.0
|
|
CG2
|
A:VAL233
|
4.0
|
14.9
|
1.0
|
|
HG22
|
A:VAL233
|
4.1
|
17.8
|
1.0
|
|
C1
|
A:OXM401
|
4.2
|
17.3
|
1.0
|
|
HB1
|
A:ALA241
|
4.2
|
13.3
|
1.0
|
|
N
|
A:VAL233
|
4.2
|
12.7
|
1.0
|
|
HA
|
A:ALA241
|
4.2
|
12.7
|
1.0
|
|
HD12
|
A:ILE232
|
4.3
|
15.9
|
1.0
|
|
HN2
|
A:OXM401
|
4.3
|
25.4
|
1.0
|
|
NH2
|
A:ARG162
|
4.3
|
12.0
|
1.0
|
|
HG21
|
A:VAL233
|
4.4
|
17.8
|
1.0
|
|
H5N
|
A:NAI409
|
4.5
|
18.1
|
1.0
|
|
HH21
|
A:ARG162
|
4.5
|
14.4
|
1.0
|
|
OG
|
A:SER240
|
4.6
|
13.3
|
1.0
|
|
H
|
A:ILE232
|
4.6
|
15.5
|
1.0
|
|
HD13
|
A:ILE232
|
4.7
|
15.9
|
1.0
|
|
C
|
A:ILE232
|
4.7
|
13.4
|
1.0
|
|
HG
|
A:SER240
|
4.7
|
16.0
|
1.0
|
|
O3
|
A:OXM401
|
4.7
|
17.4
|
1.0
|
|
CA
|
A:ILE232
|
4.8
|
12.6
|
1.0
|
|
HH2
|
A:TRP97
|
4.8
|
19.2
|
1.0
|
|
CD1
|
A:ILE232
|
4.8
|
13.2
|
1.0
|
|
HG23
|
A:ILE232
|
4.8
|
15.7
|
1.0
|
|
HA
|
A:VAL233
|
4.8
|
15.6
|
1.0
|
|
C
|
A:ALA241
|
4.9
|
9.6
|
1.0
|
|
O
|
A:ALA228
|
4.9
|
13.1
|
1.0
|
|
N
|
A:GLY229
|
4.9
|
12.7
|
1.0
|
|
CG1
|
A:ILE232
|
4.9
|
13.3
|
1.0
|
|
N
|
A:GLY230
|
4.9
|
12.9
|
1.0
|
|
CA
|
A:VAL233
|
4.9
|
13.0
|
1.0
|
|
CB
|
A:VAL233
|
5.0
|
13.4
|
1.0
|
|
O
|
A:ALA241
|
5.0
|
11.6
|
1.0
|
|
CH2
|
A:TRP97
|
5.0
|
16.0
|
1.0
|
|
O
|
A:SER240
|
5.0
|
11.2
|
1.0
|
|
Sodium binding site 6 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 6 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 6 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na407
b:19.3
occ:1.00
|
HH11
|
A:ARG162
|
2.1
|
14.7
|
1.0
|
|
OD1
|
A:ASP159
|
2.6
|
13.1
|
1.0
|
|
NA
|
A:NA408
|
2.8
|
19.9
|
1.0
|
|
HE1
|
A:MET190
|
2.8
|
17.1
|
1.0
|
|
O
|
A:THR225
|
2.8
|
13.9
|
1.0
|
|
NH1
|
A:ARG162
|
2.9
|
12.2
|
1.0
|
|
HD3
|
A:ARG162
|
2.9
|
14.1
|
1.0
|
|
HB3
|
A:ALA228
|
2.9
|
16.7
|
1.0
|
|
HD2
|
A:ARG162
|
3.0
|
14.1
|
1.0
|
|
HH12
|
A:ARG162
|
3.2
|
14.7
|
1.0
|
|
HA
|
A:ASP159
|
3.3
|
14.0
|
1.0
|
|
CD
|
A:ARG162
|
3.4
|
11.8
|
1.0
|
|
CE
|
A:MET190
|
3.6
|
14.2
|
1.0
|
|
CG
|
A:ASP159
|
3.7
|
12.9
|
1.0
|
|
SD
|
A:MET190
|
3.8
|
13.8
|
1.0
|
|
CB
|
A:ALA228
|
3.9
|
13.9
|
1.0
|
|
CZ
|
A:ARG162
|
3.9
|
11.5
|
1.0
|
|
H
|
A:GLY229
|
3.9
|
15.2
|
1.0
|
|
H
|
A:ALA228
|
3.9
|
16.1
|
1.0
|
|
HE1
|
A:HIS186
|
4.0
|
16.5
|
1.0
|
|
C
|
A:THR225
|
4.0
|
14.0
|
1.0
|
|
HE3
|
A:MET190
|
4.0
|
17.1
|
1.0
|
|
HG22
|
A:THR225
|
4.1
|
17.6
|
1.0
|
|
NE
|
A:ARG162
|
4.1
|
10.7
|
1.0
|
|
CA
|
A:ASP159
|
4.1
|
11.7
|
1.0
|
|
HB2
|
A:ALA228
|
4.1
|
16.7
|
1.0
|
|
HB3
|
A:ASP159
|
4.2
|
14.1
|
1.0
|
|
HB2
|
A:ARG162
|
4.2
|
14.8
|
1.0
|
|
HG23
|
A:THR225
|
4.2
|
17.6
|
1.0
|
|
CB
|
A:ASP159
|
4.2
|
11.8
|
1.0
|
|
HH22
|
A:ARG99
|
4.2
|
17.9
|
1.0
|
|
HE2
|
A:MET190
|
4.4
|
17.1
|
1.0
|
|
HB1
|
A:ALA228
|
4.4
|
16.7
|
1.0
|
|
HA
|
A:LYS226
|
4.4
|
17.4
|
1.0
|
|
O3
|
A:OXM401
|
4.5
|
17.4
|
1.0
|
|
N
|
A:GLY229
|
4.5
|
12.7
|
1.0
|
|
HA
|
A:THR225
|
4.5
|
16.0
|
1.0
|
|
N
|
A:ALA228
|
4.6
|
13.5
|
1.0
|
|
O
|
A:LYS226
|
4.6
|
15.1
|
1.0
|
|
HH21
|
A:ARG99
|
4.6
|
17.9
|
1.0
|
|
CG2
|
A:THR225
|
4.6
|
14.7
|
1.0
|
|
HG
|
A:LEU158
|
4.6
|
12.2
|
1.0
|
|
OD2
|
A:ASP159
|
4.6
|
13.8
|
1.0
|
|
CG
|
A:ARG162
|
4.6
|
12.3
|
1.0
|
|
NH2
|
A:ARG99
|
4.7
|
14.9
|
1.0
|
|
CA
|
A:ALA228
|
4.7
|
12.6
|
1.0
|
|
CE1
|
A:HIS186
|
4.7
|
13.8
|
1.0
|
|
CB
|
A:ARG162
|
4.8
|
12.3
|
1.0
|
|
HB3
|
A:ARG162
|
4.8
|
14.8
|
1.0
|
|
C
|
A:LYS226
|
4.8
|
14.0
|
1.0
|
|
CA
|
A:THR225
|
4.8
|
13.3
|
1.0
|
|
N
|
A:ASP159
|
4.9
|
11.7
|
1.0
|
|
N
|
A:LYS226
|
4.9
|
14.2
|
1.0
|
|
CA
|
A:LYS226
|
4.9
|
14.5
|
1.0
|
|
HE
|
A:ARG162
|
4.9
|
12.8
|
1.0
|
|
Sodium binding site 7 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 7 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 7 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na408
b:19.9
occ:1.00
|
H
|
A:GLY229
|
2.1
|
15.2
|
1.0
|
|
HH22
|
A:ARG99
|
2.1
|
17.9
|
1.0
|
|
NA
|
A:NA407
|
2.8
|
19.3
|
1.0
|
|
O
|
A:LYS226
|
2.8
|
15.1
|
1.0
|
|
NH2
|
A:ARG99
|
2.9
|
14.9
|
1.0
|
|
N
|
A:GLY229
|
2.9
|
12.7
|
1.0
|
|
H
|
A:ALA228
|
3.1
|
16.1
|
1.0
|
|
HE1
|
A:MET190
|
3.1
|
17.1
|
1.0
|
|
HH21
|
A:ARG99
|
3.2
|
17.9
|
1.0
|
|
HA3
|
A:GLY229
|
3.3
|
16.2
|
1.0
|
|
HB3
|
A:ALA228
|
3.4
|
16.7
|
1.0
|
|
N
|
A:ALA228
|
3.4
|
13.5
|
1.0
|
|
O
|
A:HOH653
|
3.4
|
18.6
|
1.0
|
|
HE3
|
A:MET190
|
3.5
|
17.1
|
1.0
|
|
HH11
|
A:ARG162
|
3.5
|
14.7
|
1.0
|
|
O
|
A:THR225
|
3.5
|
13.9
|
1.0
|
|
HH12
|
A:ARG162
|
3.5
|
14.7
|
1.0
|
|
C
|
A:LYS226
|
3.6
|
14.0
|
1.0
|
|
CA
|
A:GLY229
|
3.7
|
13.5
|
1.0
|
|
HH12
|
A:ARG99
|
3.7
|
16.4
|
1.0
|
|
O
|
A:HOH649
|
3.7
|
17.7
|
1.0
|
|
CE
|
A:MET190
|
3.7
|
14.2
|
1.0
|
|
NH1
|
A:ARG162
|
3.8
|
12.2
|
1.0
|
|
C
|
A:ALA228
|
3.9
|
12.9
|
1.0
|
|
CA
|
A:ALA228
|
4.0
|
12.6
|
1.0
|
|
C
|
A:ASN227
|
4.0
|
13.8
|
1.0
|
|
CZ
|
A:ARG99
|
4.0
|
14.0
|
1.0
|
|
O3
|
A:OXM401
|
4.1
|
17.4
|
1.0
|
|
CB
|
A:ALA228
|
4.1
|
13.9
|
1.0
|
|
H
|
A:GLY230
|
4.1
|
15.5
|
1.0
|
|
HA
|
A:LYS226
|
4.2
|
17.4
|
1.0
|
|
NH1
|
A:ARG99
|
4.2
|
13.7
|
1.0
|
|
HA
|
A:ASN227
|
4.2
|
18.2
|
1.0
|
|
HA2
|
A:GLY229
|
4.3
|
16.2
|
1.0
|
|
N
|
A:ASN227
|
4.3
|
14.5
|
1.0
|
|
CA
|
A:ASN227
|
4.4
|
15.2
|
1.0
|
|
CA
|
A:LYS226
|
4.5
|
14.5
|
1.0
|
|
HE2
|
A:MET190
|
4.5
|
17.1
|
1.0
|
|
OD1
|
A:ASP159
|
4.6
|
13.1
|
1.0
|
|
O
|
A:ASN227
|
4.6
|
13.9
|
1.0
|
|
HB2
|
A:ALA228
|
4.6
|
16.7
|
1.0
|
|
C
|
A:THR225
|
4.6
|
14.0
|
1.0
|
|
SD
|
A:MET190
|
4.7
|
13.8
|
1.0
|
|
HE1
|
A:HIS186
|
4.7
|
16.5
|
1.0
|
|
N
|
A:GLY230
|
4.7
|
12.9
|
1.0
|
|
C
|
A:GLY229
|
4.8
|
13.3
|
1.0
|
|
HD3
|
A:ARG162
|
4.8
|
14.1
|
1.0
|
|
HB1
|
A:ALA228
|
4.8
|
16.7
|
1.0
|
|
HA
|
A:ALA228
|
4.9
|
15.1
|
1.0
|
|
CZ
|
A:ARG162
|
4.9
|
11.5
|
1.0
|
|
C2
|
A:OXM401
|
5.0
|
15.5
|
1.0
|
|
H
|
A:ASN227
|
5.0
|
17.4
|
1.0
|
|
Sodium binding site 8 out
of 8 in 4plg
Go back to
Sodium Binding Sites List in 4plg
Sodium binding site 8 out
of 8 in the Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate.
 Mono view
 Stereo pair view
|
|
A full contact list of Sodium with other atoms in the Na binding
site number 8 of Crystal Structure of Ancestral Apicomplexan Lactate Dehydrogenase with Oxamate. within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na402
b:27.1
occ:1.00
|
HZ3
|
B:LYS150
|
2.3
|
27.1
|
1.0
|
|
O
|
B:PRO122
|
2.7
|
22.1
|
1.0
|
|
HA
|
B:ASN123
|
2.8
|
24.5
|
1.0
|
|
HG
|
B:LEU146
|
2.8
|
28.8
|
1.0
|
|
O
|
B:ALA124
|
2.9
|
17.6
|
1.0
|
|
HG3
|
B:LYS150
|
2.9
|
22.6
|
1.0
|
|
HD2
|
B:PRO147
|
2.9
|
24.4
|
1.0
|
|
HB3
|
B:LYS150
|
3.0
|
21.5
|
1.0
|
|
NZ
|
B:LYS150
|
3.0
|
22.6
|
1.0
|
|
HZ1
|
B:LYS150
|
3.0
|
27.1
|
1.0
|
|
HE2
|
B:LYS150
|
3.2
|
26.1
|
1.0
|
|
HD23
|
B:LEU146
|
3.2
|
28.6
|
1.0
|
|
HB2
|
B:LYS150
|
3.3
|
21.5
|
1.0
|
|
C
|
B:ASN123
|
3.3
|
18.7
|
1.0
|
|
O
|
B:HOH789
|
3.3
|
43.6
|
1.0
|
|
HD21
|
B:LEU146
|
3.4
|
28.6
|
1.0
|
|
CB
|
B:LYS150
|
3.4
|
17.9
|
1.0
|
|
CA
|
B:ASN123
|
3.4
|
20.4
|
1.0
|
|
CG
|
B:LYS150
|
3.5
|
18.8
|
1.0
|
|
CE
|
B:LYS150
|
3.5
|
21.8
|
1.0
|
|
CD2
|
B:LEU146
|
3.6
|
23.9
|
1.0
|
|
O
|
B:ASN123
|
3.6
|
18.8
|
1.0
|
|
CG
|
B:LEU146
|
3.6
|
24.0
|
1.0
|
|
N
|
B:ALA124
|
3.6
|
18.0
|
1.0
|
|
C
|
B:PRO122
|
3.7
|
21.4
|
1.0
|
|
HZ2
|
B:LYS150
|
3.7
|
27.1
|
1.0
|
|
CD
|
B:PRO147
|
3.8
|
20.4
|
1.0
|
|
C
|
B:ALA124
|
3.8
|
17.2
|
1.0
|
|
HD3
|
B:PRO147
|
3.8
|
24.4
|
1.0
|
|
H
|
B:ALA124
|
3.8
|
21.6
|
1.0
|
|
N
|
B:ASN123
|
4.0
|
20.6
|
1.0
|
|
HG2
|
B:PRO147
|
4.0
|
25.9
|
1.0
|
|
CD
|
B:LYS150
|
4.2
|
20.1
|
1.0
|
|
HB3
|
B:LEU146
|
4.3
|
26.9
|
1.0
|
|
CA
|
B:ALA124
|
4.3
|
17.9
|
1.0
|
|
O
|
B:HOH626
|
4.3
|
24.4
|
1.0
|
|
HG2
|
B:LYS150
|
4.4
|
22.6
|
1.0
|
|
HE3
|
B:LYS150
|
4.4
|
26.1
|
1.0
|
|
CG
|
B:PRO147
|
4.4
|
21.6
|
1.0
|
|
HD11
|
B:LEU146
|
4.5
|
30.0
|
1.0
|
|
CB
|
B:LEU146
|
4.5
|
22.5
|
1.0
|
|
HD22
|
B:LEU146
|
4.5
|
28.6
|
1.0
|
|
HA
|
B:LEU146
|
4.6
|
25.8
|
1.0
|
|
CD1
|
B:LEU146
|
4.6
|
25.0
|
1.0
|
|
HA
|
B:PHE125
|
4.7
|
18.7
|
1.0
|
|
CB
|
B:ASN123
|
4.7
|
21.8
|
1.0
|
|
HD3
|
B:LYS150
|
4.8
|
24.1
|
1.0
|
|
H
|
B:ASN123
|
4.8
|
24.8
|
1.0
|
|
N
|
B:PHE125
|
4.8
|
16.0
|
1.0
|
|
HD2
|
B:LYS150
|
4.8
|
24.1
|
1.0
|
|
CA
|
B:LYS150
|
4.9
|
16.6
|
1.0
|
|
HA
|
B:ALA124
|
4.9
|
21.4
|
1.0
|
|
N
|
B:PRO147
|
4.9
|
19.1
|
1.0
|
|
HD12
|
B:LEU146
|
5.0
|
30.0
|
1.0
|
|
HA
|
B:PRO122
|
5.0
|
25.4
|
1.0
|
|
CA
|
B:PRO122
|
5.0
|
21.2
|
1.0
|
|
Reference:
J.I.Boucher,
J.R.Jacobowitz,
B.C.Beckett,
S.Classen,
D.L.Theobald.
An Atomic-Resolution View of Neofunctionalization in the Evolution of Apicomplexan Lactate Dehydrogenases. Elife V. 3 02304 2014.
ISSN: ESSN 2050-084X
PubMed: 24966208
DOI: 10.7554/ELIFE.02304
Page generated: Mon Oct 7 17:44:33 2024
|
