Sodium in PDB 6sss: Crystal Structure of Human Microsomal Glutathione S-Transferase 2
Enzymatic activity of Crystal Structure of Human Microsomal Glutathione S-Transferase 2
All present enzymatic activity of Crystal Structure of Human Microsomal Glutathione S-Transferase 2:
2.5.1.18;
Protein crystallography data
The structure of Crystal Structure of Human Microsomal Glutathione S-Transferase 2, PDB code: 6sss
was solved by
M.Thulasingam,
E.Nji,
J.Z.Haeggstrom,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.33 /
2.50
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.886,
72.162,
72.692,
67.93,
86.71,
86.86
|
R / Rfree (%)
|
21.8 /
26.7
|
Other elements in 6sss:
The structure of Crystal Structure of Human Microsomal Glutathione S-Transferase 2 also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
(pdb code 6sss). 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 Human Microsomal Glutathione S-Transferase 2, PDB code: 6sss:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 6sss
Go back to
Sodium Binding Sites List in 6sss
Sodium binding site 1 out
of 5 in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
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 Human Microsomal Glutathione S-Transferase 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na202
b:55.6
occ:1.00
|
HE21
|
A:GLN18
|
2.5
|
56.4
|
1.0
|
HE1
|
A:TRP95
|
2.7
|
72.8
|
1.0
|
ND1
|
A:HIS91
|
2.7
|
58.1
|
1.0
|
HE1
|
A:PHE22
|
2.8
|
62.1
|
1.0
|
HE2
|
A:TYR21
|
3.1
|
96.0
|
1.0
|
HD2
|
A:TYR21
|
3.2
|
89.8
|
1.0
|
NE2
|
A:GLN18
|
3.3
|
47.0
|
1.0
|
HA
|
A:HIS91
|
3.3
|
57.5
|
1.0
|
HB2
|
A:HIS91
|
3.4
|
64.9
|
1.0
|
NE1
|
A:TRP95
|
3.4
|
60.7
|
1.0
|
HG3
|
A:GLN18
|
3.5
|
52.4
|
1.0
|
CE1
|
A:PHE22
|
3.5
|
51.8
|
1.0
|
CE1
|
A:HIS91
|
3.6
|
60.0
|
1.0
|
HZ
|
A:PHE22
|
3.7
|
63.8
|
1.0
|
HE22
|
A:GLN18
|
3.7
|
56.4
|
1.0
|
CG
|
A:HIS91
|
3.7
|
54.5
|
1.0
|
HE1
|
A:HIS91
|
3.7
|
72.0
|
1.0
|
CE2
|
A:TYR21
|
3.8
|
80.0
|
1.0
|
CD2
|
A:TYR21
|
3.8
|
74.8
|
1.0
|
CB
|
A:HIS91
|
3.9
|
54.1
|
1.0
|
CZ
|
A:PHE22
|
4.0
|
53.2
|
1.0
|
CA
|
A:HIS91
|
4.1
|
48.0
|
1.0
|
HD1
|
A:TRP95
|
4.1
|
71.1
|
1.0
|
CD1
|
A:TRP95
|
4.2
|
59.3
|
1.0
|
CD
|
A:GLN18
|
4.3
|
45.4
|
1.0
|
CG
|
A:GLN18
|
4.3
|
43.7
|
1.0
|
HZ2
|
A:TRP95
|
4.4
|
71.3
|
1.0
|
CE2
|
A:TRP95
|
4.4
|
58.3
|
1.0
|
CD1
|
A:PHE22
|
4.5
|
49.9
|
1.0
|
HD1
|
A:PHE22
|
4.6
|
59.9
|
1.0
|
NE2
|
A:HIS91
|
4.8
|
58.2
|
1.0
|
CZ2
|
A:TRP95
|
4.8
|
59.5
|
1.0
|
HG2
|
A:GLN18
|
4.8
|
52.4
|
1.0
|
HB3
|
A:HIS91
|
4.8
|
64.9
|
1.0
|
CD2
|
A:HIS91
|
4.8
|
51.9
|
1.0
|
HB3
|
A:PHE94
|
4.9
|
49.3
|
1.0
|
O
|
A:HIS91
|
5.0
|
46.7
|
1.0
|
HD2
|
A:PHE94
|
5.0
|
51.8
|
1.0
|
|
Sodium binding site 2 out
of 5 in 6sss
Go back to
Sodium Binding Sites List in 6sss
Sodium binding site 2 out
of 5 in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
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 Human Microsomal Glutathione S-Transferase 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na202
b:44.6
occ:1.00
|
HG2
|
B:PRO61
|
2.2
|
35.3
|
1.0
|
HG13
|
C:VAL57
|
2.6
|
50.0
|
1.0
|
O
|
C:VAL57
|
2.8
|
53.5
|
1.0
|
HD3
|
C:PRO61
|
2.8
|
44.1
|
1.0
|
HG3
|
C:PRO61
|
3.0
|
44.0
|
1.0
|
CG
|
B:PRO61
|
3.1
|
29.4
|
1.0
|
HG12
|
C:VAL57
|
3.3
|
50.0
|
1.0
|
HB3
|
C:TYR60
|
3.3
|
45.6
|
1.0
|
HG3
|
B:PRO61
|
3.3
|
35.3
|
1.0
|
CG1
|
C:VAL57
|
3.4
|
41.7
|
1.0
|
CG
|
C:PRO61
|
3.5
|
36.6
|
1.0
|
HG2
|
C:PRO61
|
3.5
|
44.0
|
1.0
|
CD
|
C:PRO61
|
3.6
|
36.7
|
1.0
|
C
|
C:VAL57
|
3.7
|
50.0
|
1.0
|
HA
|
C:VAL57
|
3.8
|
58.2
|
1.0
|
HD2
|
B:PRO61
|
3.8
|
37.4
|
1.0
|
CD
|
B:PRO61
|
3.8
|
31.2
|
1.0
|
HD2
|
C:TYR60
|
3.9
|
41.7
|
1.0
|
HD3
|
B:PRO61
|
4.0
|
37.4
|
1.0
|
HG11
|
C:VAL57
|
4.0
|
50.0
|
1.0
|
HA
|
B:GLU58
|
4.1
|
50.7
|
1.0
|
HB2
|
B:PRO61
|
4.1
|
33.6
|
1.0
|
HD2
|
C:PRO61
|
4.1
|
44.1
|
1.0
|
CB
|
B:PRO61
|
4.1
|
28.0
|
1.0
|
CA
|
C:VAL57
|
4.1
|
48.5
|
1.0
|
CB
|
C:TYR60
|
4.3
|
38.0
|
1.0
|
O
|
B:VAL57
|
4.3
|
40.7
|
1.0
|
CB
|
C:VAL57
|
4.3
|
46.8
|
1.0
|
HB3
|
B:PRO61
|
4.4
|
33.6
|
1.0
|
HB2
|
C:TYR60
|
4.5
|
45.6
|
1.0
|
H
|
C:TYR60
|
4.5
|
46.3
|
1.0
|
HG22
|
C:VAL57
|
4.5
|
56.4
|
1.0
|
HA
|
C:GLU58
|
4.6
|
57.3
|
1.0
|
N
|
C:PRO61
|
4.6
|
31.8
|
1.0
|
HG12
|
B:VAL57
|
4.7
|
55.2
|
1.0
|
CD2
|
C:TYR60
|
4.7
|
34.8
|
1.0
|
HG3
|
A:PRO61
|
4.7
|
38.5
|
1.0
|
N
|
C:GLU58
|
4.8
|
49.3
|
1.0
|
HG2
|
A:PRO61
|
4.8
|
38.5
|
1.0
|
O
|
B:GLU58
|
4.9
|
47.7
|
1.0
|
HG13
|
B:VAL57
|
4.9
|
55.2
|
1.0
|
CB
|
C:PRO61
|
4.9
|
28.6
|
1.0
|
CA
|
B:GLU58
|
5.0
|
42.3
|
1.0
|
CG
|
C:TYR60
|
5.0
|
39.4
|
1.0
|
|
Sodium binding site 3 out
of 5 in 6sss
Go back to
Sodium Binding Sites List in 6sss
Sodium binding site 3 out
of 5 in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
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 Human Microsomal Glutathione S-Transferase 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na202
b:45.7
occ:1.00
|
HE21
|
D:GLN18
|
2.4
|
59.2
|
1.0
|
ND1
|
D:HIS91
|
2.6
|
65.5
|
1.0
|
HE1
|
D:TRP95
|
2.9
|
71.8
|
1.0
|
HA
|
D:HIS91
|
3.1
|
50.1
|
1.0
|
NE2
|
D:GLN18
|
3.2
|
49.4
|
1.0
|
HB2
|
D:HIS91
|
3.2
|
54.5
|
1.0
|
HE22
|
D:GLN18
|
3.4
|
59.2
|
1.0
|
HE1
|
D:PHE22
|
3.4
|
52.4
|
1.0
|
CG
|
D:HIS91
|
3.5
|
57.1
|
1.0
|
CE1
|
D:HIS91
|
3.6
|
66.3
|
1.0
|
NE1
|
D:TRP95
|
3.6
|
59.8
|
1.0
|
CB
|
D:HIS91
|
3.7
|
45.4
|
1.0
|
HE1
|
D:HIS91
|
3.7
|
79.5
|
1.0
|
HG3
|
D:GLN18
|
3.8
|
53.0
|
1.0
|
CA
|
D:HIS91
|
3.9
|
41.7
|
1.0
|
HD1
|
D:TRP95
|
4.0
|
70.5
|
1.0
|
HZ
|
D:PHE22
|
4.0
|
48.2
|
1.0
|
CE1
|
D:PHE22
|
4.0
|
43.7
|
1.0
|
CD1
|
D:TRP95
|
4.2
|
58.7
|
1.0
|
CD
|
D:GLN18
|
4.3
|
47.4
|
1.0
|
CZ
|
D:PHE22
|
4.3
|
40.2
|
1.0
|
CG
|
D:GLN18
|
4.5
|
44.2
|
1.0
|
HB3
|
D:HIS91
|
4.6
|
54.5
|
1.0
|
CD2
|
D:HIS91
|
4.7
|
59.4
|
1.0
|
NE2
|
D:HIS91
|
4.7
|
62.3
|
1.0
|
CE2
|
D:TRP95
|
4.8
|
61.7
|
1.0
|
N
|
D:HIS91
|
4.8
|
40.6
|
1.0
|
O
|
D:HIS91
|
4.8
|
41.1
|
1.0
|
C
|
D:HIS91
|
4.8
|
41.6
|
1.0
|
HZ2
|
D:TRP95
|
5.0
|
78.7
|
1.0
|
|
Sodium binding site 4 out
of 5 in 6sss
Go back to
Sodium Binding Sites List in 6sss
Sodium binding site 4 out
of 5 in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
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 Human Microsomal Glutathione S-Transferase 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na202
b:60.5
occ:1.00
|
ND1
|
E:HIS91
|
2.7
|
52.0
|
1.0
|
HE21
|
E:GLN18
|
2.8
|
66.3
|
1.0
|
HE1
|
E:TRP95
|
2.8
|
87.8
|
1.0
|
HE1
|
E:PHE22
|
2.9
|
60.5
|
1.0
|
HA
|
E:HIS91
|
3.3
|
56.6
|
1.0
|
NE2
|
E:GLN18
|
3.4
|
55.2
|
1.0
|
HG3
|
E:GLN18
|
3.4
|
49.2
|
1.0
|
NE1
|
E:TRP95
|
3.5
|
73.2
|
1.0
|
HD2
|
E:TYR21
|
3.5
|
84.6
|
1.0
|
CE1
|
E:PHE22
|
3.6
|
50.4
|
1.0
|
HB2
|
E:HIS91
|
3.6
|
60.6
|
1.0
|
CE1
|
E:HIS91
|
3.6
|
53.6
|
1.0
|
HE2
|
E:TYR21
|
3.6
|
91.5
|
1.0
|
HE1
|
E:HIS91
|
3.7
|
64.3
|
1.0
|
HE22
|
E:GLN18
|
3.7
|
66.3
|
1.0
|
CG
|
E:HIS91
|
3.8
|
51.9
|
1.0
|
HZ
|
E:PHE22
|
3.9
|
60.9
|
1.0
|
CB
|
E:HIS91
|
4.0
|
50.5
|
1.0
|
CD2
|
E:TYR21
|
4.0
|
70.5
|
1.0
|
CE2
|
E:TYR21
|
4.0
|
76.2
|
1.0
|
CD
|
E:GLN18
|
4.1
|
50.1
|
1.0
|
CA
|
E:HIS91
|
4.1
|
47.2
|
1.0
|
CG
|
E:GLN18
|
4.1
|
41.0
|
1.0
|
CZ
|
E:PHE22
|
4.2
|
50.7
|
1.0
|
HD1
|
E:TRP95
|
4.2
|
89.1
|
1.0
|
CD1
|
E:TRP95
|
4.2
|
74.3
|
1.0
|
CE2
|
E:TRP95
|
4.4
|
68.7
|
1.0
|
HZ2
|
E:TRP95
|
4.5
|
83.2
|
1.0
|
CD1
|
E:PHE22
|
4.5
|
49.1
|
1.0
|
HD2
|
E:PHE94
|
4.6
|
49.3
|
1.0
|
HD1
|
E:PHE22
|
4.6
|
59.0
|
1.0
|
HG2
|
E:GLN18
|
4.6
|
49.2
|
1.0
|
HB3
|
E:PHE94
|
4.7
|
43.6
|
1.0
|
NE2
|
E:HIS91
|
4.8
|
54.8
|
1.0
|
CZ2
|
E:TRP95
|
4.8
|
69.4
|
1.0
|
CD2
|
E:HIS91
|
4.9
|
53.1
|
1.0
|
HB3
|
E:HIS91
|
4.9
|
60.6
|
1.0
|
O
|
E:HIS91
|
4.9
|
43.5
|
1.0
|
OE1
|
E:GLN18
|
5.0
|
51.5
|
1.0
|
|
Sodium binding site 5 out
of 5 in 6sss
Go back to
Sodium Binding Sites List in 6sss
Sodium binding site 5 out
of 5 in the Crystal Structure of Human Microsomal Glutathione S-Transferase 2
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 Human Microsomal Glutathione S-Transferase 2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Na203
b:34.9
occ:1.00
|
HE21
|
F:GLN18
|
2.2
|
38.3
|
1.0
|
NE2
|
F:GLN18
|
3.0
|
31.9
|
1.0
|
HB2
|
F:SER15
|
3.2
|
36.0
|
1.0
|
HE22
|
F:GLN18
|
3.3
|
38.3
|
1.0
|
HB3
|
F:GLN18
|
3.4
|
43.7
|
1.0
|
HG12
|
F:ILE87
|
3.5
|
35.4
|
1.0
|
HA
|
F:SER15
|
3.5
|
35.2
|
1.0
|
HA
|
F:ILE87
|
3.7
|
40.4
|
1.0
|
HE1
|
F:TYR86
|
3.7
|
48.1
|
1.0
|
HG2
|
F:GLN19
|
3.8
|
34.9
|
1.0
|
HG3
|
F:ARG90
|
3.8
|
44.8
|
1.0
|
HE1
|
F:TYR60
|
3.8
|
37.0
|
1.0
|
O
|
F:SER15
|
3.8
|
26.2
|
1.0
|
HG2
|
F:GLN18
|
3.9
|
49.3
|
1.0
|
HG23
|
F:ILE87
|
4.0
|
37.1
|
1.0
|
HB2
|
F:ARG90
|
4.0
|
44.8
|
1.0
|
HD1
|
F:TYR60
|
4.0
|
34.0
|
1.0
|
CB
|
F:SER15
|
4.0
|
30.0
|
1.0
|
CD
|
F:GLN18
|
4.1
|
38.6
|
1.0
|
CA
|
F:SER15
|
4.1
|
29.3
|
1.0
|
CB
|
F:GLN18
|
4.2
|
36.4
|
1.0
|
CG
|
F:GLN18
|
4.2
|
41.1
|
1.0
|
HB3
|
F:ARG90
|
4.2
|
44.8
|
1.0
|
HD1
|
F:TYR86
|
4.2
|
47.8
|
1.0
|
HE2
|
F:PHE22
|
4.3
|
48.4
|
1.0
|
CG1
|
F:ILE87
|
4.4
|
29.5
|
1.0
|
C
|
F:SER15
|
4.4
|
30.0
|
1.0
|
CE1
|
F:TYR60
|
4.4
|
30.9
|
1.0
|
CB
|
F:ARG90
|
4.4
|
37.3
|
1.0
|
CE1
|
F:TYR86
|
4.5
|
40.1
|
1.0
|
CD1
|
F:TYR60
|
4.5
|
28.3
|
1.0
|
HB3
|
F:SER15
|
4.5
|
36.0
|
1.0
|
CG
|
F:ARG90
|
4.6
|
37.3
|
1.0
|
CA
|
F:ILE87
|
4.6
|
33.7
|
1.0
|
HB2
|
F:GLN18
|
4.7
|
43.7
|
1.0
|
OE1
|
F:GLN19
|
4.7
|
40.3
|
1.0
|
CG
|
F:GLN19
|
4.7
|
29.1
|
1.0
|
H
|
F:GLN19
|
4.7
|
34.2
|
1.0
|
HG13
|
F:ILE87
|
4.7
|
35.4
|
1.0
|
CD1
|
F:TYR86
|
4.8
|
39.8
|
1.0
|
CG2
|
F:ILE87
|
4.8
|
30.9
|
1.0
|
CB
|
F:ILE87
|
4.8
|
33.5
|
1.0
|
CE2
|
F:PHE22
|
5.0
|
40.3
|
1.0
|
HE2
|
F:PHE63
|
5.0
|
42.8
|
1.0
|
N
|
F:GLN19
|
5.0
|
28.5
|
1.0
|
|
Reference:
M.Thulasingam,
E.Nji,
J.Z.Haeggstrom.
Crystal Structure of Human Microsomal Glutathione S-Transferase 2 To Be Published.
Page generated: Tue Oct 8 13:31:30 2024
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