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Iron in PDB 2jim: 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: 2jim was solved by S.Najmudin, P.J.Gonzalez, J.Trincao, C.Coelho, A.Mukhopadhyay, C.C.Romao, I.Moura, J.J.G.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) 92.06 / 2.45
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.307, 106.307, 133.558, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25.2

Other elements in 2jim:

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 Binding Sites:

The binding sites of Iron 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 2jim). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron 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: 2jim:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 2jim

Go back to Iron Binding Sites List in 2jim
Iron 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 Iron with other atoms in the Fe 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:Fe800

b:38.0
occ:1.00
 FE1 A:SF4800 0.0 38.0 1.0
S2 A:SF4800 2.3 38.6 1.0
S3 A:SF4800 2.3 42.6 1.0
SG A:CYS47 2.3 44.7 1.0
S4 A:SF4800 2.4 44.7 1.0
FE4 A:SF4800 2.6 39.1 1.0
FE2 A:SF4800 2.7 42.7 1.0
FE3 A:SF4800 2.8 45.5 1.0
CB A:CYS47 3.2 46.0 1.0
N A:CYS47 3.5 46.5 1.0
CA A:CYS47 3.8 46.3 1.0
S1 A:SF4800 3.9 44.0 1.0
CG2 A:VAL183 4.3 37.1 1.0
CD A:PRO182 4.4 38.1 1.0
SG A:CYS16 4.5 47.1 1.0
C A:CYS47 4.5 46.5 1.0
N A:GLY50 4.6 47.2 1.0
CG A:PRO182 4.6 38.3 1.0
C A:LEU46 4.7 47.4 1.0
O A:CYS47 4.8 47.0 1.0
SG A:CYS20 4.8 45.3 1.0
SG A:CYS13 4.9 49.7 1.0
CB A:PRO182 5.0 37.6 1.0
CA A:GLY50 5.0 47.1 1.0
N A:VAL183 5.0 37.9 1.0

Iron binding site 2 out of 4 in 2jim

Go back to Iron Binding Sites List in 2jim
Iron 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 Iron with other atoms in the Fe 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:Fe800

b:42.7
occ:1.00
 FE2 A:SF4800 0.0 42.7 1.0
S4 A:SF4800 2.3 44.7 1.0
S1 A:SF4800 2.3 44.0 1.0
S3 A:SF4800 2.3 42.6 1.0
SG A:CYS13 2.3 49.7 1.0
FE3 A:SF4800 2.5 45.5 1.0
FE1 A:SF4800 2.7 38.0 1.0
FE4 A:SF4800 2.8 39.1 1.0
CB A:CYS13 3.2 49.1 1.0
S2 A:SF4800 3.8 38.6 1.0
CB A:TYR15 4.2 48.0 1.0
N A:CYS16 4.3 46.2 1.0
CA A:GLY50 4.4 47.1 1.0
CB A:CYS20 4.5 45.8 1.0
SG A:CYS16 4.6 47.1 1.0
N A:GLY50 4.6 47.2 1.0
SG A:CYS47 4.6 44.7 1.0
CA A:CYS13 4.6 49.1 1.0
SG A:CYS20 4.7 45.3 1.0
N A:TYR15 4.7 48.2 1.0
CD1 A:TYR15 4.8 50.0 1.0
CA A:TYR15 4.8 48.0 1.0
C A:TYR15 4.9 47.8 1.0

Iron binding site 3 out of 4 in 2jim

Go back to Iron Binding Sites List in 2jim
Iron 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 Iron with other atoms in the Fe 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:Fe800

b:45.5
occ:1.00
 FE3 A:SF4800 0.0 45.5 1.0
SG A:CYS16 2.1 47.1 1.0
S1 A:SF4800 2.3 44.0 1.0
S4 A:SF4800 2.3 44.7 1.0
S2 A:SF4800 2.3 38.6 1.0
FE2 A:SF4800 2.5 42.7 1.0
FE4 A:SF4800 2.7 39.1 1.0
FE1 A:SF4800 2.8 38.0 1.0
CB A:CYS16 3.3 45.4 1.0
N A:CYS16 3.5 46.2 1.0
CA A:CYS16 3.8 45.6 1.0
S3 A:SF4800 3.8 42.6 1.0
CB A:THR18 3.9 46.4 1.0
OG1 A:THR18 3.9 45.6 1.0
O A:CYS16 4.2 45.7 1.0
C A:CYS16 4.3 45.6 1.0
SG A:CYS13 4.6 49.7 1.0
CD A:PRO182 4.6 38.1 1.0
C A:TYR15 4.6 47.8 1.0
SG A:CYS47 4.7 44.7 1.0
N A:THR18 4.7 45.6 1.0
CB A:TYR15 4.7 48.0 1.0
SG A:CYS20 4.8 45.3 1.0
CG2 A:THR18 4.9 45.9 1.0
CA A:THR18 4.9 45.8 1.0
N A:GLY19 5.0 46.0 1.0

Iron binding site 4 out of 4 in 2jim

Go back to Iron Binding Sites List in 2jim
Iron 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 Iron with other atoms in the Fe 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:Fe800

b:39.1
occ:1.00
 FE4 A:SF4800 0.0 39.1 1.0
S3 A:SF4800 2.3 42.6 1.0
S2 A:SF4800 2.3 38.6 1.0
SG A:CYS20 2.3 45.3 1.0
S1 A:SF4800 2.3 44.0 1.0
FE1 A:SF4800 2.6 38.0 1.0
FE3 A:SF4800 2.7 45.5 1.0
FE2 A:SF4800 2.8 42.7 1.0
CB A:CYS20 3.1 45.8 1.0
CG2 A:VAL183 3.7 37.1 1.0
S4 A:SF4800 4.0 44.7 1.0
CB A:THR18 4.1 46.4 1.0
CB A:VAL183 4.2 38.2 1.0
CG2 A:THR18 4.2 45.9 1.0
N A:CYS20 4.2 46.4 1.0
CA A:CYS20 4.3 46.3 1.0
SG A:CYS16 4.5 47.1 1.0
N A:CYS47 4.5 46.5 1.0
OG1 A:THR18 4.7 45.6 1.0
CD2 A:LEU46 4.8 42.3 1.0
CB A:CYS13 4.8 49.1 1.0
SG A:CYS13 4.8 49.7 1.0
CA A:LEU46 4.9 47.5 1.0
SG A:CYS47 4.9 44.7 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: Thu Jul 17 02:41:14 2025

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