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Ruthenium in PDB 8ax1: Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate

Enzymatic activity of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate

All present enzymatic activity of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate:
2.5.1.18;

Protein crystallography data

The structure of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate, PDB code: 8ax1 was solved by M.Schwartz, C.Didierjean, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.71 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.59, 104.59, 108.17, 90, 90, 90
R / Rfree (%) 17.8 / 20

Other elements in 8ax1:

The structure of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Ruthenium Binding Sites:

The binding sites of Ruthenium atom in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate (pdb code 8ax1). This binding sites where shown within 5.0 Angstroms radius around Ruthenium atom.
In total 5 binding sites of Ruthenium where determined in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate, PDB code: 8ax1:
Jump to Ruthenium binding site number: 1; 2; 3; 4; 5;

Ruthenium binding site 1 out of 5 in 8ax1

Go back to Ruthenium Binding Sites List in 8ax1
Ruthenium binding site 1 out of 5 in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 1 of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru301

b:28.4
occ:1.00
 RU1 A:ODU301 0.0 28.4 1.0
N12 A:ODU301 1.7 43.5 1.0
O01 A:ODU301 2.0 39.8 1.0
N09 A:ODU301 2.1 36.2 1.0
N14 A:ODU301 2.1 36.5 1.0
N03 A:ODU301 2.1 37.8 1.0
N06 A:ODU301 2.1 54.1 1.0
H1 A:ODU301 2.4 47.8 1.0
O13 A:ODU301 2.7 31.9 1.0
O05 A:ODU301 2.7 42.0 1.0
O16 A:ODU301 2.7 46.4 1.0
O11 A:ODU301 2.8 30.5 1.0
O07 A:ODU301 2.8 42.5 1.0
O08 A:ODU301 2.8 69.4 1.0
O10 A:ODU301 2.8 41.4 1.0
O04 A:ODU301 2.9 40.1 1.0
O15 A:ODU301 3.0 33.3 1.0
HG2 A:ARG208 4.2 24.6 1.0
HG3 A:ARG208 4.4 24.6 1.0
HG12 A:VAL207 4.6 23.9 1.0
HG11 A:VAL207 4.6 23.9 1.0
HD2 A:ARG204 4.6 27.2 1.0
CG A:ARG208 4.8 20.5 1.0
HH11 A:ARG208 4.8 27.2 1.0
CD2 A:PHE173 4.9 24.2 1.0
HD3 A:ARG208 4.9 27.4 1.0
HG2 A:ARG204 4.9 21.3 1.0

Ruthenium binding site 2 out of 5 in 8ax1

Go back to Ruthenium Binding Sites List in 8ax1
Ruthenium binding site 2 out of 5 in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 2 of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru302

b:36.0
occ:0.50
 RU1 A:ODU302 0.0 36.0 0.5
N14 A:ODU302 1.8 35.8 0.5
O01 A:ODU302 1.9 20.6 0.5
N03 A:ODU302 2.0 35.4 0.5
N06 A:ODU302 2.1 19.1 0.5
N09 A:ODU302 2.1 23.0 0.5
H1 A:ODU302 2.3 24.8 0.5
O07 A:ODU302 2.8 31.8 0.5
O04 A:ODU302 2.8 26.8 0.5
O16 A:ODU302 2.9 41.3 0.5
O05 A:ODU302 2.9 41.2 0.5
O08 A:ODU302 2.9 38.0 0.5
O11 A:ODU302 2.9 31.8 0.5
O10 A:ODU302 3.0 30.8 0.5
HE1 A:PHE14 3.1 39.7 1.0
RU A:RU305 3.6 61.3 0.5
HD21 A:LEU40 3.8 39.3 1.0
CE1 A:PHE14 4.0 33.1 1.0
HB2 A:SER15 4.0 19.9 1.0
HB A:ILE56 4.0 20.1 1.0
HD2 A:TYR17 4.1 22.0 1.0
HZ A:PHE14 4.1 34.4 1.0
HG A:SER15 4.2 20.1 1.0
O A:ILE56 4.2 17.4 1.0
H A:ILE56 4.2 21.3 1.0
HG21 A:ILE39 4.3 28.1 1.0
OG A:SER15 4.3 16.7 1.0
CZ A:PHE14 4.5 28.6 1.0
HD11 A:LEU40 4.5 42.1 1.0
CB A:SER15 4.7 16.6 1.0
HD3 A:LYS55 4.7 52.2 1.0
CD2 A:LEU40 4.8 32.7 1.0
HG23 A:ILE39 4.8 28.1 1.0
HA A:SER15 4.8 16.5 1.0
CD2 A:TYR17 4.9 18.3 1.0
HG22 A:ILE56 4.9 28.5 1.0
CB A:ILE56 4.9 16.7 1.0
N A:ILE56 5.0 17.7 1.0
CG2 A:ILE39 5.0 23.4 1.0

Ruthenium binding site 3 out of 5 in 8ax1

Go back to Ruthenium Binding Sites List in 8ax1
Ruthenium binding site 3 out of 5 in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 3 of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ru305

b:61.3
occ:0.50
 O16 A:ODU302 2.1 41.3 0.5
O07 A:ODU302 2.3 31.8 0.5
N14 A:ODU302 2.5 35.8 0.5
N06 A:ODU302 2.9 19.1 0.5
O05 A:ODU302 3.5 41.2 0.5
RU1 A:ODU302 3.6 36.0 0.5
O08 A:ODU302 3.7 38.0 0.5
HZ A:PHE128 3.8 41.3 1.0
N03 A:ODU302 3.9 35.4 0.5
HE1 A:PHE14 4.0 39.7 1.0
HE2 A:TYR17 4.1 22.4 1.0
HH12 A:ARG124 4.3 67.5 1.0
O A:HOH535 4.4 42.9 1.0
HD2 A:PRO16 4.5 21.6 1.0
HG11 A:VAL233 4.6 25.7 1.0
CZ A:PHE128 4.6 34.4 1.0
HD2 A:TYR17 4.6 22.0 1.0
HD11 A:LEU40 4.6 42.1 1.0
HE2 A:PHE128 4.7 39.5 1.0
O01 A:ODU302 4.7 20.6 0.5
HD1 A:PHE14 4.8 33.5 1.0
CE1 A:PHE14 4.8 33.1 1.0
H1 A:ODU302 4.9 24.8 0.5
CE2 A:TYR17 4.9 18.7 1.0
NH1 A:ARG124 4.9 56.2 1.0
HG13 A:VAL233 5.0 25.7 1.0
O04 A:ODU302 5.0 26.8 0.5

Ruthenium binding site 4 out of 5 in 8ax1

Go back to Ruthenium Binding Sites List in 8ax1
Ruthenium binding site 4 out of 5 in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 4 of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru301

b:31.1
occ:1.00
 RU1 B:ODU301 0.0 31.1 1.0
N12 B:ODU301 1.7 39.8 1.0
O01 B:ODU301 2.0 76.8 1.0
N06 B:ODU301 2.1 53.9 1.0
N03 B:ODU301 2.1 33.4 1.0
N14 B:ODU301 2.1 46.1 1.0
N09 B:ODU301 2.1 48.6 1.0
H1 B:ODU301 2.4 92.2 1.0
O13 B:ODU301 2.7 29.6 1.0
O16 B:ODU301 2.7 41.0 1.0
O11 B:ODU301 2.8 34.9 1.0
O08 B:ODU301 2.8 35.8 1.0
O05 B:ODU301 2.8 38.8 1.0
O04 B:ODU301 2.8 34.6 1.0
O07 B:ODU301 2.9 58.8 1.0
O15 B:ODU301 2.9 48.3 1.0
O10 B:ODU301 2.9 49.1 1.0
HG2 B:ARG208 4.3 26.0 1.0
HG3 B:ARG208 4.4 26.0 1.0
HG12 B:VAL207 4.6 20.8 1.0
HG11 B:VAL207 4.6 20.8 1.0
HD2 B:ARG204 4.6 23.4 1.0
HH11 B:ARG208 4.7 27.7 1.0
CG B:ARG208 4.8 21.7 1.0
CD2 B:PHE173 4.8 23.2 1.0
HD3 B:ARG208 4.9 24.0 1.0
CG B:PHE173 4.9 21.8 1.0

Ruthenium binding site 5 out of 5 in 8ax1

Go back to Ruthenium Binding Sites List in 8ax1
Ruthenium binding site 5 out of 5 in the Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate


Mono view


Stereo pair view

A full contact list of Ruthenium with other atoms in the Ru binding site number 5 of Crystal Structure of Trametes Versicolor Glutathione Transferase Omega 3S in Complex with Hydroxy-Tetranitro-Nitrosyl-Ruthenate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ru302

b:30.6
occ:1.00
 RU1 B:ODU302 0.0 30.6 1.0
N12 B:ODU302 1.6 50.0 1.0
O01 B:ODU302 1.9 21.4 1.0
N09 B:ODU302 2.1 45.3 1.0
N06 B:ODU302 2.1 52.8 1.0
N03 B:ODU302 2.1 30.1 1.0
N14 B:ODU302 2.1 53.3 1.0
H1 B:ODU302 2.4 25.7 1.0
O04 B:ODU302 2.7 37.8 1.0
O13 B:ODU302 2.7 46.1 1.0
O11 B:ODU302 2.7 38.5 1.0
O07 B:ODU302 2.8 42.1 1.0
O16 B:ODU302 2.8 34.4 1.0
O10 B:ODU302 2.9 31.9 1.0
O08 B:ODU302 2.9 52.0 1.0
O05 B:ODU302 2.9 39.5 1.0
O15 B:ODU302 3.0 48.2 1.0
HG B:SER15 3.8 20.5 1.0
HD2 B:TYR17 3.9 25.2 1.0
HD21 B:LEU40 4.0 38.8 1.0
HB2 B:SER15 4.1 22.6 1.0
HB B:ILE56 4.2 19.5 1.0
H B:ILE56 4.3 20.6 1.0
O B:ILE56 4.3 17.1 1.0
HE2 B:PHE14 4.3 47.3 1.0
OG B:SER15 4.4 17.1 1.0
HG21 B:ILE39 4.4 33.8 1.0
HA B:SER15 4.6 20.6 1.0
HD11 B:LEU40 4.6 44.4 1.0
HD2 B:PHE14 4.7 38.9 1.0
CB B:SER15 4.7 18.8 1.0
HE2 B:TYR17 4.7 27.9 1.0
CD2 B:TYR17 4.7 21.0 1.0
CD2 B:LEU40 5.0 32.3 1.0
HG23 B:ILE39 5.0 33.8 1.0
HD2 B:PRO16 5.0 17.7 1.0

Reference:

M.Schwartz, T.Perrot, J.Beurton, F.Zannini, M.Morel-Rouhier, E.Gelhaye, F.Neiers, D.Schaniel, F.Favier, J.P.Jacquot, P.Leroy, I.Clarot, A.Boudier, C.Didierjean. Structural Insights Into the Interactions of Glutathione Transferases with A Nitric Oxide Carrier and Sodium Nitroprusside. Biochem.Biophys.Res.Commun. V. 649 79 2023.
ISSN: ESSN 1090-2104
PubMed: 36758482
DOI: 10.1016/J.BBRC.2023.01.099
Page generated: Thu Oct 10 13:11:04 2024

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