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Sodium in PDB 8bbs: Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor

Enzymatic activity of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor

All present enzymatic activity of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor:
1.1.1.188; 1.1.1.210; 1.1.1.357; 1.1.1.53; 1.1.1.62;

Protein crystallography data

The structure of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor, PDB code: 8bbs was solved by E.T.Petri, J.Skerlova, M.Marinovic, J.Brynda, M.Kugler, D.Skoric, S.Bekic, A.S.Celic, P.Rezacova, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.93 / 1.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 39.462, 51.413, 77.879, 77.26, 86.74, 77.63
R / Rfree (%) 15.5 / 17.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor (pdb code 8bbs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor, PDB code: 8bbs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 8bbs

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Sodium binding site 1 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na403

b:46.2
occ:1.00
 OD1 B:ASP204 2.3 18.0 0.5
O B:HOH581 3.3 25.9 1.0
CG B:ASP204 3.5 17.0 0.5
CA B:PHE205 3.6 14.0 1.0
O B:ASP204 3.7 14.5 0.5
N B:PHE205 3.7 13.2 1.0
C B:ASP204 3.8 14.1 0.5
O B:ASP204 3.8 14.8 0.5
C B:ASP204 3.8 13.9 0.5
OG B:SER208 4.0 14.9 1.0
CB B:SER208 4.2 15.1 1.0
O B:HOH553 4.3 22.7 1.0
CB B:ASP204 4.3 15.4 0.5
CB B:PHE205 4.3 14.0 1.0
CB B:ASP204 4.4 17.0 0.5
OD2 B:ASP204 4.5 18.2 0.5
CD1 B:PHE205 4.7 16.8 1.0
NH2 B:ARG170 4.7 25.7 0.5
CA B:ASP204 4.7 15.0 0.5
CA B:ASP204 4.7 15.2 0.5
C B:PHE205 4.8 13.7 1.0
O B:HOH557 4.9 32.1 1.0
CG B:PHE205 5.0 15.9 1.0
O B:PHE205 5.0 13.5 1.0

Sodium binding site 2 out of 9 in 8bbs

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Sodium binding site 2 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na404

b:38.2
occ:1.00
 OE2 B:GLU285 2.4 22.4 1.0
O B:HOH523 2.7 27.9 1.0
O B:HOH835 2.7 27.9 1.0
CD B:GLU285 3.3 17.8 1.0
CG B:GLU285 3.5 16.7 1.0
CA B:GLN282 4.1 14.5 1.0
O B:VAL281 4.2 15.2 1.0
CG B:GLN282 4.3 18.3 1.0
O B:HOH623 4.4 39.5 1.0
OE1 B:GLU285 4.5 20.2 1.0
C B:VAL281 4.5 14.2 1.0
N B:GLN282 4.6 13.4 1.0
O B:HOH822 4.6 53.6 1.0
CB B:GLN282 4.7 15.5 1.0
CG2 B:VAL281 4.8 14.9 1.0
O B:HOH524 4.9 29.2 1.0
O B:HOH793 5.0 27.8 1.0
CB B:GLU285 5.0 15.2 1.0

Sodium binding site 3 out of 9 in 8bbs

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Sodium binding site 3 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:40.1
occ:1.00
 OE2 B:GLU127 2.4 31.5 1.0
N B:SER129 2.9 17.1 1.0
CD B:GLU127 3.2 30.4 1.0
O B:HOH745 3.2 32.6 1.0
CG B:GLU127 3.2 29.6 1.0
CB B:SER129 3.3 17.3 1.0
N B:LEU128 3.4 19.0 1.0
CA B:SER129 3.5 16.6 1.0
O B:SER129 3.7 17.0 1.0
C B:SER129 3.8 17.6 1.0
C B:GLU127 3.9 21.0 1.0
C B:LEU128 3.9 17.6 1.0
CA B:LEU128 4.2 19.5 1.0
CA B:GLU127 4.2 23.3 1.0
CB B:GLU127 4.2 26.3 1.0
OE1 B:GLU127 4.3 33.9 1.0
OG B:SER129 4.6 21.0 1.0
CB B:LEU128 4.6 22.2 1.0
N B:PRO130 4.7 16.6 1.0
O B:GLU127 4.8 19.7 1.0

Sodium binding site 4 out of 9 in 8bbs

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Sodium binding site 4 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na406

b:51.1
occ:1.00
 OE1 B:GLU174 2.6 30.2 1.0
O B:HOH599 2.7 19.6 1.0
O B:HOH790 2.8 24.2 1.0
NE B:ARG171 3.1 32.0 0.5
CD B:ARG171 3.3 28.5 0.5
O B:HOH762 3.5 17.1 1.0
CD B:GLU174 3.8 23.9 1.0
CB B:GLU174 3.9 15.8 1.0
CZ B:ARG171 4.3 34.4 0.5
CA B:ARG171 4.4 16.6 0.5
CB B:ARG171 4.4 19.8 0.5
CG B:ARG171 4.4 19.4 0.5
CG B:ARG171 4.4 23.6 0.5
O B:ARG171 4.4 15.8 0.5
CG B:GLU174 4.4 18.1 1.0
CA B:ARG171 4.4 15.3 0.5
O B:ARG171 4.4 16.0 0.5
OE2 B:GLU174 4.7 26.4 1.0
NH1 B:ARG171 4.7 35.7 0.5
CB B:ARG171 4.8 17.3 0.5
NH2 B:ARG170 4.8 23.3 0.5
C B:ARG171 4.9 14.7 0.5
C B:ARG171 4.9 15.4 0.5

Sodium binding site 5 out of 9 in 8bbs

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Sodium binding site 5 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:51.9
occ:1.00
 OD2 A:ASP210 2.4 33.3 1.0
CG A:ASP210 3.3 25.8 1.0
CB A:ASP210 3.5 23.0 1.0
CB A:ASN11 3.9 15.4 1.0
CA A:ASN11 4.2 15.2 1.0
OD1 A:ASP210 4.4 32.6 1.0
O A:HOH660 4.5 25.9 1.0
O A:ASN11 4.6 17.8 1.0
O A:HOH767 4.6 31.6 1.0
NZ A:LYS185 4.7 31.7 1.0
C A:ASN11 4.9 17.1 1.0
CA A:ASP210 5.0 20.0 1.0

Sodium binding site 6 out of 9 in 8bbs

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Sodium binding site 6 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:48.4
occ:1.00
 OE1 A:GLU126 2.2 40.2 1.0
O A:HOH553 2.5 28.2 1.0
O A:HOH758 2.5 26.7 1.0
CD A:GLU126 3.3 36.1 1.0
OD1 A:ASN101 3.4 34.1 1.0
NE2 A:HIS53 3.5 19.0 1.0
CE1 A:HIS53 3.8 21.2 1.0
OE2 A:GLU126 4.0 37.3 1.0
CZ A:PHE89 4.1 16.2 1.0
NZ A:LYS105 4.2 26.6 0.5
CG A:GLU126 4.3 30.4 1.0
CG A:ASN101 4.3 21.7 1.0
CB A:GLU126 4.3 29.6 1.0
O A:HOH564 4.4 26.8 1.0
CD2 A:HIS53 4.7 21.3 1.0
O A:HOH661 4.7 25.1 1.0
CA A:GLU126 4.7 26.3 1.0
O A:GLU126 4.8 26.2 1.0
CE1 A:PHE89 4.8 16.8 1.0
ND1 A:HIS53 4.9 20.7 1.0
CE2 A:PHE89 4.9 15.8 1.0

Sodium binding site 7 out of 9 in 8bbs

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Sodium binding site 7 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:47.1
occ:1.00
 OD2 A:ASP204 2.6 31.1 1.0
O A:HOH665 3.0 25.4 1.0
O A:HOH574 3.2 21.7 1.0
CB A:ASP204 3.2 22.3 1.0
CG A:ASP204 3.3 27.8 1.0
O A:HOH621 3.7 26.6 1.0
CA A:ASP204 4.2 18.9 1.0
O A:HOH510 4.3 33.2 1.0
O A:SER200 4.3 17.3 1.0
O A:HOH828 4.5 38.6 1.0
OD1 A:ASP204 4.5 34.0 1.0
N A:ASP204 4.8 17.3 1.0
O A:HOH592 4.8 44.2 1.0

Sodium binding site 8 out of 9 in 8bbs

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Sodium binding site 8 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:44.8
occ:1.00
 OE1 A:GLU100 2.4 25.3 1.0
O A:HOH625 2.5 23.9 1.0
CD A:GLU100 3.6 20.9 1.0
CA A:PRO97 3.8 13.6 1.0
CB A:PRO97 3.9 15.7 1.0
CB A:GLU100 4.1 14.6 1.0
O A:HOH805 4.3 26.7 1.0
O A:HOH817 4.3 36.8 1.0
CG A:PRO97 4.3 14.6 1.0
OE2 A:GLU100 4.4 19.1 1.0
O A:PRO97 4.4 13.2 1.0
CG A:GLU100 4.5 17.1 1.0
C A:PRO97 4.7 13.0 1.0
O A:HOH536 4.7 22.5 1.0
N A:PRO97 4.8 14.0 1.0

Sodium binding site 9 out of 9 in 8bbs

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Sodium binding site 9 out of 9 in the Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Structure of AKR1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:55.0
occ:1.00
 OE1 A:GLU237 2.5 30.5 1.0
O A:HOH695 2.8 35.6 1.0
O A:HOH645 3.1 36.3 1.0
CB A:GLU237 3.6 21.0 1.0
CD A:GLU237 3.7 27.1 1.0
O A:HOH827 4.0 58.3 1.0
O A:HOH598 4.2 22.7 1.0
CG A:GLU237 4.2 23.1 1.0
O A:HOH842 4.7 53.2 1.0
CB A:VAL234 4.7 20.4 1.0
OE2 A:GLU237 4.7 33.2 1.0
O A:GLU237 4.7 18.6 1.0
O A:VAL234 4.9 17.9 1.0
CA A:GLU237 4.9 19.0 1.0
N A:VAL234 5.0 19.0 1.0

Reference:

M.A.Marinovic, S.S.Bekic, M.Kugler, J.Brynda, J.Skerlova, D.D.Skoric, P.Rezacova, E.T.Petri, A.S.Celic. X-Ray Structure of Human Aldo-Keto Reductase 1C3 in Complex with A Bile Acid Fused Tetrazole Inhibitor: Experimental Validation, Molecular Docking and Structural Analysis. Rsc Med Chem V. 14 341 2023.
ISSN: ESSN 2632-8682
PubMed: 36846371
DOI: 10.1039/D2MD00387B
Page generated: Wed Oct 9 10:39:35 2024

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