Sodium in PDB 8xpc: Crystal Structure of Tris-Bound Tsabgl (Data I)
Enzymatic activity of Crystal Structure of Tris-Bound Tsabgl (Data I)
All present enzymatic activity of Crystal Structure of Tris-Bound Tsabgl (Data I):
3.2.1.21;
Protein crystallography data
The structure of Crystal Structure of Tris-Bound Tsabgl (Data I), PDB code: 8xpc
was solved by
K.H.Nam,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.44 /
1.55
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.752,
71.023,
98.873,
90,
90,
90
|
R / Rfree (%)
|
14.9 /
16.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Tris-Bound Tsabgl (Data I)
(pdb code 8xpc). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of Tris-Bound Tsabgl (Data I), PDB code: 8xpc:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 8xpc
Go back to
Sodium Binding Sites List in 8xpc
Sodium binding site 1 out
of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data I)
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 Tris-Bound Tsabgl (Data I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:14.8
occ:1.00
|
O
|
A:GLY49
|
2.6
|
8.3
|
1.0
|
O
|
A:HOH761
|
2.7
|
8.5
|
1.0
|
O
|
A:TYR17
|
2.8
|
7.4
|
1.0
|
N
|
A:GLY21
|
2.9
|
8.6
|
1.0
|
CA
|
A:GLY21
|
3.5
|
9.2
|
1.0
|
C
|
A:TYR17
|
3.5
|
9.8
|
1.0
|
C
|
A:GLY49
|
3.6
|
8.9
|
1.0
|
CA
|
A:TYR17
|
3.7
|
9.6
|
1.0
|
CD1
|
A:TYR17
|
3.8
|
9.5
|
1.0
|
N
|
A:GLU20
|
3.8
|
7.5
|
1.0
|
O
|
A:SER16
|
3.8
|
7.3
|
1.0
|
CA
|
A:GLY49
|
3.9
|
6.9
|
1.0
|
CB
|
A:ALA52
|
3.9
|
11.3
|
1.0
|
C
|
A:GLU20
|
4.0
|
7.8
|
1.0
|
O
|
A:GLY21
|
4.1
|
8.1
|
1.0
|
CE1
|
A:TYR17
|
4.2
|
12.8
|
1.0
|
C
|
A:GLY21
|
4.2
|
7.1
|
1.0
|
CG
|
A:TYR17
|
4.3
|
8.7
|
1.0
|
CA
|
A:GLU20
|
4.3
|
6.9
|
1.0
|
CB
|
A:GLU20
|
4.4
|
6.7
|
1.0
|
C
|
A:VAL19
|
4.6
|
7.6
|
1.0
|
CB
|
A:TYR17
|
4.6
|
6.5
|
1.0
|
N
|
A:GLN18
|
4.6
|
7.4
|
1.0
|
N
|
A:VAL19
|
4.7
|
7.7
|
1.0
|
C
|
A:SER16
|
4.7
|
8.9
|
1.0
|
O
|
A:HOH733
|
4.7
|
10.7
|
1.0
|
N
|
A:TYR17
|
4.7
|
6.2
|
1.0
|
N
|
A:ASP50
|
4.9
|
8.6
|
1.0
|
CZ
|
A:TYR17
|
4.9
|
8.9
|
1.0
|
C
|
A:GLN18
|
4.9
|
10.3
|
1.0
|
CD2
|
A:TYR17
|
4.9
|
9.1
|
1.0
|
|
Sodium binding site 2 out
of 5 in 8xpc
Go back to
Sodium Binding Sites List in 8xpc
Sodium binding site 2 out
of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data I)
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 Tris-Bound Tsabgl (Data I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:20.4
occ:1.00
|
O
|
A:HOH1150
|
2.7
|
27.4
|
1.0
|
O
|
A:SER46
|
2.8
|
11.8
|
1.0
|
O
|
A:SER37
|
2.8
|
11.9
|
0.6
|
O
|
A:SER37
|
2.9
|
11.9
|
0.4
|
ND2
|
A:ASN48
|
3.0
|
14.9
|
1.0
|
C
|
A:SER37
|
3.5
|
9.5
|
0.6
|
C
|
A:SER37
|
3.5
|
9.6
|
0.4
|
C
|
A:SER46
|
3.6
|
12.9
|
1.0
|
CB
|
A:ASN48
|
3.7
|
8.9
|
1.0
|
CG
|
A:ASN48
|
3.8
|
11.0
|
1.0
|
CA
|
A:ARG38
|
3.8
|
10.9
|
1.0
|
CG
|
A:ARG38
|
3.9
|
13.4
|
1.0
|
O
|
A:HIS47
|
4.0
|
10.8
|
1.0
|
N
|
A:ARG38
|
4.0
|
10.7
|
1.0
|
CB
|
A:SER46
|
4.0
|
20.1
|
1.0
|
CA
|
A:SER46
|
4.1
|
12.2
|
1.0
|
C
|
A:HIS47
|
4.2
|
10.5
|
1.0
|
OG
|
A:SER37
|
4.3
|
11.0
|
0.6
|
CB
|
A:SER37
|
4.3
|
10.5
|
0.4
|
CB
|
A:SER37
|
4.4
|
10.6
|
0.6
|
CB
|
A:ARG38
|
4.5
|
12.2
|
1.0
|
N
|
A:ASN48
|
4.5
|
8.1
|
1.0
|
CA
|
A:SER37
|
4.6
|
9.5
|
0.4
|
CA
|
A:SER37
|
4.6
|
9.5
|
0.6
|
N
|
A:HIS47
|
4.6
|
10.2
|
1.0
|
CA
|
A:ASN48
|
4.7
|
7.8
|
1.0
|
O
|
A:HOH969
|
4.7
|
36.6
|
1.0
|
CA
|
A:HIS47
|
4.9
|
8.8
|
1.0
|
OD1
|
A:ASN48
|
5.0
|
10.5
|
1.0
|
|
Sodium binding site 3 out
of 5 in 8xpc
Go back to
Sodium Binding Sites List in 8xpc
Sodium binding site 3 out
of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data I)
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 Tris-Bound Tsabgl (Data I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na504
b:23.1
occ:1.00
|
O
|
A:HOH672
|
2.9
|
22.8
|
1.0
|
O
|
A:HOH867
|
2.9
|
38.5
|
1.0
|
N
|
A:LEU286
|
2.9
|
10.5
|
1.0
|
CE
|
A:MET345
|
3.2
|
22.2
|
1.0
|
O
|
A:HOH919
|
3.5
|
32.1
|
1.0
|
CE1
|
A:PHE253
|
3.5
|
10.2
|
1.0
|
CB
|
A:LEU286
|
3.6
|
8.7
|
1.0
|
CA
|
A:LYS285
|
3.7
|
8.1
|
1.0
|
CD1
|
A:PHE253
|
3.7
|
13.1
|
1.0
|
C
|
A:LYS285
|
3.8
|
11.0
|
1.0
|
CG
|
A:LEU286
|
3.8
|
9.5
|
1.0
|
CA
|
A:LEU286
|
3.8
|
8.6
|
1.0
|
CD
|
A:LYS285
|
3.9
|
13.3
|
1.0
|
O
|
A:GLN284
|
3.9
|
12.0
|
1.0
|
O
|
A:LEU286
|
4.2
|
11.5
|
1.0
|
O
|
A:HOH789
|
4.4
|
34.2
|
1.0
|
CD1
|
A:LEU286
|
4.4
|
9.0
|
1.0
|
SD
|
A:MET345
|
4.4
|
17.4
|
1.0
|
C
|
A:LEU286
|
4.5
|
10.1
|
1.0
|
CE
|
A:LYS285
|
4.5
|
18.4
|
1.0
|
CG
|
A:LYS285
|
4.5
|
12.7
|
1.0
|
N
|
A:LYS285
|
4.6
|
10.7
|
1.0
|
C
|
A:GLN284
|
4.6
|
10.6
|
1.0
|
NZ
|
A:LYS285
|
4.6
|
24.1
|
1.0
|
CB
|
A:LYS285
|
4.6
|
12.2
|
1.0
|
O
|
A:HOH842
|
4.7
|
36.1
|
1.0
|
CZ
|
A:PHE253
|
4.7
|
11.5
|
1.0
|
O
|
A:LEU252
|
4.8
|
10.3
|
1.0
|
O
|
A:LYS285
|
4.9
|
10.9
|
1.0
|
O
|
A:HOH734
|
5.0
|
11.8
|
1.0
|
|
Sodium binding site 4 out
of 5 in 8xpc
Go back to
Sodium Binding Sites List in 8xpc
Sodium binding site 4 out
of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data I)
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 Tris-Bound Tsabgl (Data I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na505
b:30.4
occ:1.00
|
O
|
A:HOH977
|
2.2
|
35.5
|
1.0
|
O
|
A:ASP287
|
2.9
|
10.7
|
1.0
|
O
|
A:HOH649
|
3.2
|
25.3
|
1.0
|
C
|
A:ASP287
|
3.6
|
9.5
|
1.0
|
CG
|
A:PRO346
|
3.8
|
12.8
|
1.0
|
CB
|
A:PHE288
|
3.8
|
8.2
|
1.0
|
CB
|
A:ASP287
|
3.8
|
10.7
|
1.0
|
CB
|
A:PRO346
|
3.9
|
11.4
|
1.0
|
CG
|
A:LYS214
|
4.1
|
18.4
|
1.0
|
CD2
|
A:PHE288
|
4.1
|
9.8
|
1.0
|
CD
|
A:LYS214
|
4.1
|
27.6
|
1.0
|
O
|
A:HOH787
|
4.2
|
21.0
|
1.0
|
CB
|
A:LYS214
|
4.2
|
9.7
|
1.0
|
CA
|
A:ASP287
|
4.2
|
9.2
|
1.0
|
N
|
A:PHE288
|
4.3
|
8.5
|
1.0
|
CG
|
A:PHE288
|
4.4
|
8.7
|
1.0
|
CA
|
A:PHE288
|
4.5
|
7.1
|
1.0
|
CD
|
A:PRO346
|
4.6
|
10.8
|
1.0
|
O
|
A:HOH792
|
4.8
|
28.4
|
1.0
|
CE
|
A:LYS214
|
4.8
|
31.5
|
1.0
|
CE1
|
A:TYR348
|
4.8
|
12.2
|
1.0
|
OH
|
A:TYR348
|
4.9
|
14.6
|
1.0
|
|
Sodium binding site 5 out
of 5 in 8xpc
Go back to
Sodium Binding Sites List in 8xpc
Sodium binding site 5 out
of 5 in the Crystal Structure of Tris-Bound Tsabgl (Data I)
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 Tris-Bound Tsabgl (Data I) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na506
b:26.1
occ:1.00
|
N
|
A:GLU328
|
3.0
|
9.2
|
1.0
|
CB
|
A:GLU328
|
3.3
|
17.6
|
1.0
|
N
|
A:PRO327
|
3.4
|
9.1
|
1.0
|
CD
|
A:PRO327
|
3.4
|
10.0
|
1.0
|
CG
|
A:GLU328
|
3.5
|
27.6
|
1.0
|
CD1
|
A:TYR326
|
3.5
|
12.7
|
1.0
|
CE1
|
A:TYR326
|
3.6
|
16.5
|
1.0
|
C
|
A:TYR326
|
3.6
|
10.7
|
1.0
|
CG
|
A:TYR326
|
3.7
|
10.2
|
1.0
|
CA
|
A:GLU328
|
3.7
|
11.1
|
1.0
|
CA
|
A:TYR326
|
3.8
|
9.8
|
1.0
|
CZ
|
A:TYR326
|
3.9
|
19.6
|
1.0
|
CG
|
A:PRO327
|
3.9
|
13.5
|
1.0
|
C
|
A:PRO327
|
4.0
|
9.1
|
1.0
|
CD2
|
A:TYR326
|
4.0
|
11.8
|
1.0
|
OE2
|
A:GLU328
|
4.1
|
51.3
|
1.0
|
CE2
|
A:TYR326
|
4.1
|
12.8
|
1.0
|
CA
|
A:PRO327
|
4.1
|
9.0
|
1.0
|
CD
|
A:GLU328
|
4.2
|
44.5
|
1.0
|
O
|
A:TYR326
|
4.2
|
10.9
|
1.0
|
CB
|
A:TYR326
|
4.4
|
11.1
|
1.0
|
O
|
A:HOH1102
|
4.5
|
30.6
|
1.0
|
CB
|
A:PRO327
|
4.5
|
9.4
|
1.0
|
OH
|
A:TYR326
|
4.7
|
18.5
|
1.0
|
C
|
A:GLU328
|
4.8
|
10.7
|
1.0
|
N
|
A:SER329
|
4.9
|
8.9
|
1.0
|
|
Reference:
K.H.Nam,
K.H.Nam.
N/A N/A.
Page generated: Wed Oct 9 14:22:59 2024
|