Sodium in PDB 8d88: Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
Enzymatic activity of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
All present enzymatic activity of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine:
4.1.1.116;
Protein crystallography data
The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine, PDB code: 8d88
was solved by
R.S.Phillips,
K.N.Nguyen Hoang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.28 /
1.41
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
141.24,
50.49,
139.32,
90,
117.26,
90
|
R / Rfree (%)
|
17.5 /
19.5
|
Other elements in 8d88:
The structure of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
(pdb code 8d88). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine, PDB code: 8d88:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 8d88
Go back to
Sodium Binding Sites List in 8d88
Sodium binding site 1 out
of 4 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na507
b:30.1
occ:1.00
|
O
|
A:HOH1003
|
2.3
|
50.8
|
1.0
|
O
|
A:VAL210
|
2.3
|
24.8
|
1.0
|
O
|
A:MET207
|
2.3
|
30.5
|
1.0
|
O
|
A:ILE204
|
2.4
|
26.4
|
1.0
|
O
|
A:LEU205
|
2.9
|
38.5
|
1.0
|
C
|
A:LEU205
|
3.4
|
32.6
|
1.0
|
C
|
A:MET207
|
3.4
|
33.4
|
1.0
|
C
|
A:VAL210
|
3.5
|
24.1
|
1.0
|
C
|
A:ILE204
|
3.5
|
27.2
|
1.0
|
N
|
A:MET207
|
3.7
|
27.4
|
1.0
|
CA
|
A:LEU205
|
3.7
|
29.6
|
1.0
|
O
|
A:HOH1050
|
3.9
|
58.4
|
0.9
|
CA
|
A:MET207
|
4.0
|
28.1
|
1.0
|
O
|
A:HOH891
|
4.0
|
37.8
|
1.0
|
N
|
A:LEU205
|
4.1
|
29.5
|
1.0
|
N
|
A:VAL210
|
4.2
|
24.8
|
1.0
|
CB
|
A:MET207
|
4.2
|
25.5
|
1.0
|
CA
|
A:VAL210
|
4.3
|
24.1
|
1.0
|
N
|
A:ALA206
|
4.3
|
31.2
|
1.0
|
O
|
A:HOH1000
|
4.3
|
44.0
|
0.8
|
C
|
A:ALA206
|
4.4
|
34.5
|
1.0
|
CG2
|
A:ILE204
|
4.5
|
23.6
|
1.0
|
N
|
A:HIS211
|
4.5
|
25.6
|
1.0
|
N
|
A:PRO208
|
4.6
|
25.8
|
1.0
|
CB
|
A:VAL210
|
4.6
|
24.4
|
1.0
|
CA
|
A:HIS211
|
4.7
|
27.4
|
1.0
|
CA
|
A:ILE204
|
4.7
|
25.8
|
1.0
|
C
|
A:PRO208
|
4.8
|
28.3
|
1.0
|
CA
|
A:PRO208
|
4.8
|
27.3
|
1.0
|
CA
|
A:ALA206
|
4.9
|
32.1
|
1.0
|
|
Sodium binding site 2 out
of 4 in 8d88
Go back to
Sodium Binding Sites List in 8d88
Sodium binding site 2 out
of 4 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na508
b:34.8
occ:1.00
|
O
|
A:HOH1010
|
2.4
|
45.6
|
1.0
|
O
|
A:HOH758
|
2.4
|
35.6
|
1.0
|
OE1
|
A:GLU322
|
2.4
|
37.7
|
1.0
|
O
|
A:HOH903
|
2.5
|
33.4
|
1.0
|
OG1
|
A:THR46
|
2.5
|
24.9
|
1.0
|
O
|
B:HOH685
|
2.5
|
42.8
|
1.0
|
CD
|
A:GLU322
|
3.4
|
50.6
|
1.0
|
O
|
A:HOH691
|
3.6
|
41.2
|
1.0
|
CB
|
A:THR46
|
3.7
|
24.0
|
1.0
|
N
|
A:THR46
|
3.7
|
31.3
|
1.0
|
CB
|
A:GLU322
|
3.9
|
25.5
|
1.0
|
CG2
|
A:THR46
|
4.0
|
27.4
|
1.0
|
OD2
|
A:ASP348
|
4.1
|
23.6
|
1.0
|
OE2
|
A:GLU322
|
4.1
|
41.9
|
1.0
|
NZ
|
B:LYS127
|
4.2
|
35.2
|
1.0
|
CG
|
A:GLU322
|
4.2
|
28.2
|
1.0
|
CA
|
A:THR46
|
4.3
|
29.1
|
1.0
|
O
|
A:THR46
|
4.6
|
27.3
|
1.0
|
O
|
A:HOH917
|
4.6
|
47.0
|
1.0
|
C
|
A:PRO45
|
4.8
|
32.5
|
1.0
|
O
|
A:ALA41
|
4.8
|
35.8
|
1.0
|
C
|
A:THR46
|
4.8
|
24.4
|
1.0
|
CA
|
A:PRO45
|
4.8
|
35.6
|
1.0
|
|
Sodium binding site 3 out
of 4 in 8d88
Go back to
Sodium Binding Sites List in 8d88
Sodium binding site 3 out
of 4 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na507
b:30.2
occ:1.00
|
O
|
B:HOH1002
|
2.3
|
56.9
|
1.0
|
O
|
B:VAL210
|
2.3
|
28.7
|
1.0
|
O
|
B:MET207
|
2.4
|
33.3
|
1.0
|
O
|
B:ILE204
|
2.5
|
30.3
|
1.0
|
O
|
B:LEU205
|
2.8
|
38.3
|
1.0
|
C
|
B:LEU205
|
3.3
|
34.7
|
1.0
|
C
|
B:MET207
|
3.4
|
32.4
|
1.0
|
C
|
B:VAL210
|
3.6
|
25.9
|
1.0
|
N
|
B:MET207
|
3.6
|
31.4
|
1.0
|
C
|
B:ILE204
|
3.6
|
31.1
|
1.0
|
CA
|
B:LEU205
|
3.6
|
32.7
|
1.0
|
CA
|
B:MET207
|
3.9
|
27.8
|
1.0
|
O
|
B:HOH871
|
3.9
|
43.5
|
1.0
|
O
|
B:HOH1024
|
4.1
|
52.9
|
1.0
|
N
|
B:LEU205
|
4.1
|
34.4
|
1.0
|
CB
|
B:MET207
|
4.1
|
29.7
|
1.0
|
N
|
B:ALA206
|
4.2
|
35.7
|
1.0
|
N
|
B:VAL210
|
4.3
|
27.4
|
1.0
|
C
|
B:ALA206
|
4.3
|
34.5
|
1.0
|
CA
|
B:VAL210
|
4.4
|
27.7
|
1.0
|
N
|
B:HIS211
|
4.5
|
25.0
|
1.0
|
CG2
|
B:ILE204
|
4.6
|
27.0
|
1.0
|
N
|
B:PRO208
|
4.6
|
30.5
|
1.0
|
CB
|
B:VAL210
|
4.7
|
28.6
|
1.0
|
CA
|
B:HIS211
|
4.7
|
26.1
|
1.0
|
CA
|
B:ALA206
|
4.8
|
38.7
|
1.0
|
CA
|
B:ILE204
|
4.8
|
31.1
|
1.0
|
CA
|
B:PRO208
|
4.9
|
30.6
|
1.0
|
C
|
B:PRO208
|
4.9
|
30.3
|
1.0
|
|
Sodium binding site 4 out
of 4 in 8d88
Go back to
Sodium Binding Sites List in 8d88
Sodium binding site 4 out
of 4 in the Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Y430F D-Ornithine/D-Lysine Decarboxylase Complex with D- Lysine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na508
b:35.1
occ:1.00
|
O
|
B:HOH1030
|
2.4
|
44.3
|
1.0
|
OE1
|
B:GLU322
|
2.4
|
35.3
|
1.0
|
O
|
B:HOH769
|
2.4
|
36.1
|
1.0
|
OG1
|
B:THR46
|
2.5
|
20.7
|
1.0
|
O
|
A:HOH708
|
2.5
|
43.4
|
1.0
|
O
|
B:HOH950
|
2.5
|
32.5
|
1.0
|
CD
|
B:GLU322
|
3.4
|
45.1
|
1.0
|
O
|
B:HOH745
|
3.6
|
39.5
|
1.0
|
CB
|
B:THR46
|
3.7
|
18.9
|
1.0
|
N
|
B:THR46
|
3.7
|
25.1
|
1.0
|
CB
|
B:GLU322
|
3.9
|
19.6
|
1.0
|
CG2
|
B:THR46
|
4.1
|
23.1
|
1.0
|
OE2
|
B:GLU322
|
4.1
|
36.5
|
1.0
|
NZ
|
A:LYS127
|
4.2
|
32.1
|
1.0
|
OD2
|
B:ASP348
|
4.2
|
20.8
|
1.0
|
CA
|
B:THR46
|
4.3
|
23.0
|
1.0
|
CG
|
B:GLU322
|
4.3
|
20.9
|
1.0
|
O
|
B:HOH717
|
4.5
|
56.9
|
1.0
|
O
|
B:THR46
|
4.6
|
24.2
|
1.0
|
O
|
B:HOH927
|
4.6
|
50.0
|
1.0
|
O
|
B:HOH1042
|
4.6
|
60.0
|
1.0
|
C
|
B:PRO45
|
4.7
|
26.4
|
1.0
|
O
|
B:ALA41
|
4.8
|
31.2
|
1.0
|
CA
|
B:PRO45
|
4.8
|
31.4
|
1.0
|
C
|
B:THR46
|
4.8
|
22.6
|
1.0
|
|
Reference:
R.S.Phillips,
K.N.Nguyen Hoang.
The Y430F Mutant of Salmonella D-Ornithine/D-Lysine Decarboxylase Has Altered Stereospecificity and A Putrescine Allosteric Activation Site. Arch.Biochem.Biophys. V. 731 09429 2022.
ISSN: ESSN 1096-0384
PubMed: 36265649
DOI: 10.1016/J.ABB.2022.109429
Page generated: Wed Oct 9 11:26:13 2024
|