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Chlorine in PDB 2v3v: A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand

Enzymatic activity of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand

All present enzymatic activity of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand:
1.7.99.4;

Protein crystallography data

The structure of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand, PDB code: 2v3v was solved by S.Najmudin, P.J.Gonzalez, J.Trincao, C.Coelho, A.Mukhopadhyay, C.C.Romao, I.Moura, J.J.Moura, C.D.Brondino, M.J.Romao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.45 / 1.99
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.566, 106.566, 135.479, 90.00, 90.00, 120.00
R / Rfree (%) 18.2 / 24.6

Other elements in 2v3v:

The structure of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand also contains other interesting chemical elements:

Molybdenum (Mo) 1 atom
Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand (pdb code 2v3v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand, PDB code: 2v3v:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2v3v

Go back to Chlorine Binding Sites List in 2v3v
Chlorine binding site 1 out of 4 in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl814

b:18.6
occ:0.75
 CL A:LCP814 0.0 18.6 0.8
O1 A:LCP814 1.8 21.1 0.8
O4 A:LCP814 1.8 25.9 0.8
O3 A:LCP814 1.8 23.0 0.8
O2 A:LCP814 1.8 22.2 0.8
CD2 A:LEU359 3.4 21.7 1.0
CG A:ARG354 3.7 15.9 1.0
CG2 A:VAL145 3.8 9.4 1.0
N A:ALA142 3.8 10.9 1.0
CA A:ALA142 3.9 11.4 1.0
CB A:PRO137 4.0 12.0 1.0
O A:PRO137 4.1 12.5 1.0
C A:MET141 4.1 12.4 1.0
C A:PRO137 4.3 12.2 1.0
CB A:ALA142 4.4 11.3 1.0
CG A:LEU359 4.4 20.2 1.0
CD A:ARG354 4.4 16.2 1.0
CB A:MET141 4.5 12.3 1.0
O A:MET141 4.5 13.4 1.0
N A:ARG138 4.6 11.5 1.0
CB A:VAL145 4.7 11.7 1.0
O1 A:LCP815 4.7 39.9 0.8
CA A:PRO137 4.8 12.2 1.0
CD1 A:LEU359 4.8 17.9 1.0
CA A:MET141 4.8 12.7 1.0
CB A:ARG354 4.9 17.5 1.0
CG1 A:VAL353 5.0 18.1 1.0

Chlorine binding site 2 out of 4 in 2v3v

Go back to Chlorine Binding Sites List in 2v3v
Chlorine binding site 2 out of 4 in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl815

b:41.6
occ:0.75
 CL A:LCP815 0.0 41.6 0.8
O4 A:LCP815 1.8 41.4 0.8
O2 A:LCP815 1.8 41.2 0.8
O3 A:LCP815 1.8 41.7 0.8
O1 A:LCP815 1.8 39.9 0.8
NE2 A:HIS361 3.6 18.2 1.0
O A:HOH2754 3.8 29.3 1.0
O A:HOH2753 3.9 19.1 1.0
O A:ALA142 4.1 13.2 1.0
CE1 A:HIS361 4.1 17.5 1.0
CA A:SER708 4.2 17.8 1.0
N A:GLY146 4.4 12.7 1.0
NH2 A:ARG138 4.4 20.3 1.0
CG1 A:VAL145 4.4 10.8 1.0
CA A:GLY146 4.5 14.1 1.0
CD2 A:HIS361 4.5 15.9 1.0
O A:VAL707 4.6 19.1 1.0
CB A:SER708 4.6 17.0 1.0
CB A:VAL145 4.8 11.7 1.0
O A:SER708 4.8 17.9 1.0
N A:SER708 4.9 18.2 1.0
O2 A:LCP814 4.9 22.2 0.8
C A:SER708 5.0 17.8 1.0
C A:VAL707 5.0 18.6 1.0

Chlorine binding site 3 out of 4 in 2v3v

Go back to Chlorine Binding Sites List in 2v3v
Chlorine binding site 3 out of 4 in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl816

b:28.1
occ:0.50
 CL A:LCP816 0.0 28.1 0.5
O4 A:LCP816 1.8 31.1 0.5
O3 A:LCP816 1.8 28.6 0.5
O1 A:LCP816 1.8 28.4 0.5
O2 A:LCP816 1.8 27.7 0.5
O A:HOH2756 3.2 33.9 1.0
O A:HOH2388 4.0 17.6 1.0
CB A:ASP155 4.0 16.4 1.0
OH A:TYR533 4.1 25.4 1.0
CD2 A:LEU362 4.1 16.4 1.0
CG1 A:VAL145 4.1 10.8 1.0
O A:HOH2553 4.2 12.1 1.0
O A:HOH2754 4.2 29.3 1.0
O A:HOH2755 4.3 28.8 1.0
CD1 A:LEU362 4.4 13.1 1.0
OD2 A:ASP155 4.4 21.9 1.0
O A:ARG354 4.5 17.6 1.0
CG A:ASP155 4.6 19.5 1.0
CG2 A:VAL149 4.6 12.7 1.0
O A:HOH2552 4.7 20.6 1.0
CA A:GLY366 4.8 16.4 1.0
CG A:LEU362 4.9 16.4 1.0

Chlorine binding site 4 out of 4 in 2v3v

Go back to Chlorine Binding Sites List in 2v3v
Chlorine binding site 4 out of 4 in the A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of A New Catalytic Mechanism of Periplasmic Nitrate Reductase From Desulfovibrio Desulfuricans Atcc 27774 From Crystallographic and Epr Data and Based on Detailed Analysis of the Sixth Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl817

b:35.9
occ:0.50
 CL A:LCP817 0.0 35.9 0.5
O1 A:LCP817 1.8 36.5 0.5
O2 A:LCP817 1.8 33.9 0.5
O4 A:LCP817 1.8 35.8 0.5
O3 A:LCP817 1.8 36.7 0.5
NH2 A:ARG91 3.1 33.0 1.0
O A:HOH2136 3.7 34.4 1.0
O A:HOH2098 3.7 27.5 1.0
O A:ARG70 3.8 15.2 1.0
O A:ARG69 3.9 13.5 1.0
CZ A:ARG91 4.2 31.3 1.0
O A:HOH2757 4.5 17.4 1.0
O A:HOH2480 4.5 17.4 1.0
C A:ARG70 4.5 15.3 1.0
CG2 A:VAL68 4.6 13.3 1.0
CA A:ARG70 4.7 15.0 1.0
O A:HOH2466 4.7 27.4 1.0
NE A:ARG91 4.7 28.5 1.0
CE1 A:PHE439 4.8 13.6 1.0
C A:ARG69 4.8 14.1 1.0
CD1 A:LEU87 4.8 25.1 1.0
CD1 A:PHE439 5.0 12.8 1.0

Reference:

S.Najmudin, P.J.Gonzalez, J.Trincao, C.Coelho, A.Mukhopadhyay, N.M.F.S.A.Cerqueira, C.C.Romao, I.Moura, J.J.G.Moura, C.D.Brondino, M.J.Romao. Periplasmic Nitrate Reductase Revisited: A Sulfur Atom Completes the Sixth Coordination of the Catalytic Molybdenum. J.Biol.Inorg.Chem. V. 13 737 2008.
ISSN: ISSN 0949-8257
PubMed: 18327621
DOI: 10.1007/S00775-008-0359-6
Page generated: Sat Jul 20 11:35:35 2024

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