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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:

Potassium (K) 1 atom

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

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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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