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Copper in PDB 2fjs: Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis

Enzymatic activity of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis

All present enzymatic activity of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis:
1.7.2.1;

Protein crystallography data

The structure of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis, PDB code: 2fjs was solved by E.I.Tocheva, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.552, 102.428, 145.744, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 18

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis (pdb code 2fjs). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis, PDB code: 2fjs:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 2fjs

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Copper binding site 1 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:17.4
occ:1.00
 ND1 A:HIS95 2.1 9.8 1.0
ND1 A:HIS145 2.2 13.7 1.0
SG A:CYS136 2.2 9.5 1.0
SD A:MET150 2.4 13.2 1.0
CE1 A:HIS95 3.0 10.6 1.0
CE1 A:HIS145 3.0 14.4 1.0
CG A:HIS95 3.1 11.1 1.0
CB A:CYS136 3.1 9.6 1.0
CE A:MET150 3.2 10.7 1.0
CG A:HIS145 3.3 12.4 1.0
CB A:HIS95 3.5 10.0 1.0
CB A:HIS145 3.7 9.9 1.0
CG A:MET150 3.8 12.1 1.0
CA A:HIS95 3.9 11.2 1.0
NE2 A:HIS95 4.1 10.8 1.0
CD2 A:HIS95 4.2 10.0 1.0
NE2 A:HIS145 4.2 14.3 1.0
CB A:MET150 4.2 10.0 1.0
O A:MET94 4.3 11.5 1.0
CD2 A:HIS145 4.4 14.2 1.0
SD A:MET62 4.4 13.6 1.0
CG A:PRO138 4.4 13.0 1.0
CA A:CYS136 4.6 9.2 1.0
N A:ASN96 4.7 10.2 1.0
CB A:MET62 4.7 11.7 1.0
CD A:PRO138 4.8 12.0 1.0
C A:HIS95 4.9 10.6 1.0
CA A:HIS145 4.9 9.7 1.0
N A:HIS95 4.9 10.8 1.0

Copper binding site 2 out of 6 in 2fjs

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Copper binding site 2 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:13.2
occ:1.00
 NE2 A:HIS100 2.0 8.1 1.0
NE2 A:HIS135 2.0 9.7 1.0
NE2 B:HIS306 2.1 10.9 1.0
CE1 A:HIS100 2.9 9.5 1.0
CD2 A:HIS135 2.9 7.8 1.0
CE1 B:HIS306 2.9 9.6 1.0
CD2 A:HIS100 3.1 8.0 1.0
CE1 A:HIS135 3.1 9.3 1.0
CD2 B:HIS306 3.2 10.9 1.0
CD1 B:ILE257 3.5 14.7 1.0
OD1 A:ASP98 3.6 15.3 1.0
ND1 A:HIS100 4.1 8.3 1.0
ND1 B:HIS306 4.1 9.1 1.0
CG A:HIS135 4.1 9.4 1.0
ND1 A:HIS135 4.2 7.7 1.0
CG A:HIS100 4.2 8.1 1.0
CG B:HIS306 4.2 9.8 1.0
NE2 B:HIS255 4.3 10.9 1.0
CG A:ASP98 4.3 11.4 1.0
CE1 B:HIS255 4.4 10.7 1.0
O A:HOH2412 4.4 19.0 1.0
CD2 B:HIS255 4.7 9.7 1.0
ND1 B:HIS255 4.7 10.6 1.0
OD2 A:ASP98 4.8 11.6 1.0
CD2 B:LEU308 4.9 8.8 1.0
O B:HOH2720 4.9 9.9 1.0
CG B:HIS255 5.0 9.3 1.0

Copper binding site 3 out of 6 in 2fjs

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Copper binding site 3 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2501

b:16.9
occ:1.00
 ND1 B:HIS95 2.1 11.8 1.0
ND1 B:HIS145 2.2 13.4 1.0
SG B:CYS136 2.2 11.0 1.0
SD B:MET150 2.4 12.3 1.0
CE1 B:HIS95 3.0 11.6 1.0
CE1 B:HIS145 3.1 14.0 1.0
CG B:HIS95 3.1 12.5 1.0
CB B:CYS136 3.1 11.6 1.0
CE B:MET150 3.3 10.3 1.0
CG B:HIS145 3.3 12.3 1.0
CB B:HIS95 3.5 12.9 1.0
CB B:HIS145 3.7 10.7 1.0
CG B:MET150 3.8 10.9 1.0
CA B:HIS95 3.9 13.4 1.0
NE2 B:HIS95 4.2 11.2 1.0
CD2 B:HIS95 4.2 11.2 1.0
NE2 B:HIS145 4.2 13.5 1.0
CG B:PRO138 4.3 13.1 1.0
O B:MET94 4.3 14.2 1.0
CB B:MET150 4.4 9.2 1.0
CD2 B:HIS145 4.4 14.3 1.0
SD B:MET62 4.4 13.1 1.0
CA B:CYS136 4.6 10.8 1.0
N B:ASN96 4.7 13.0 1.0
CD B:PRO138 4.7 12.5 1.0
CB B:MET62 4.8 11.5 1.0
C B:HIS95 4.9 13.4 1.0
N B:HIS95 4.9 13.7 1.0
CA B:HIS145 4.9 11.0 1.0

Copper binding site 4 out of 6 in 2fjs

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Copper binding site 4 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2502

b:14.6
occ:1.00
 NE2 B:HIS135 2.0 10.4 1.0
NE2 B:HIS100 2.0 8.7 1.0
NE2 C:HIS306 2.1 12.4 1.0
CD2 B:HIS135 2.9 10.6 1.0
CE1 B:HIS100 2.9 9.2 1.0
CE1 C:HIS306 3.0 11.1 1.0
CE1 B:HIS135 3.0 10.0 1.0
CD2 B:HIS100 3.1 8.8 1.0
CD2 C:HIS306 3.2 12.2 1.0
CD1 C:ILE257 3.5 13.7 1.0
OD1 B:ASP98 3.7 14.3 1.0
ND1 B:HIS100 4.0 8.1 1.0
CG B:HIS135 4.0 9.9 1.0
ND1 B:HIS135 4.1 10.3 1.0
ND1 C:HIS306 4.1 11.5 1.0
CG B:HIS100 4.2 9.4 1.0
O B:ACT2011 4.2 22.8 1.0
CG C:HIS306 4.3 11.2 1.0
CG B:ASP98 4.3 13.1 1.0
NE2 C:HIS255 4.3 12.8 1.0
CE1 C:HIS255 4.4 13.0 1.0
CD2 C:HIS255 4.7 12.2 1.0
OD2 B:ASP98 4.8 12.0 1.0
ND1 C:HIS255 4.8 12.4 1.0
O C:HOH3696 5.0 11.9 1.0
CD1 C:LEU308 5.0 12.3 1.0
CD2 C:LEU308 5.0 12.8 1.0
CG C:HIS255 5.0 11.2 1.0

Copper binding site 5 out of 6 in 2fjs

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Copper binding site 5 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3501

b:20.3
occ:1.00
 ND1 C:HIS95 2.2 15.0 1.0
SG C:CYS136 2.2 14.3 1.0
ND1 C:HIS145 2.2 18.1 1.0
SD C:MET150 2.4 15.2 1.0
CE1 C:HIS145 3.1 18.7 1.0
CB C:CYS136 3.1 13.5 1.0
CE1 C:HIS95 3.1 15.4 1.0
CG C:HIS95 3.2 15.7 1.0
CE C:MET150 3.3 13.0 1.0
CG C:HIS145 3.3 16.0 1.0
CB C:HIS95 3.5 16.0 1.0
CB C:HIS145 3.7 13.9 1.0
CG C:MET150 3.8 13.0 1.0
CA C:HIS95 3.8 16.2 1.0
NE2 C:HIS95 4.3 15.2 1.0
NE2 C:HIS145 4.3 17.4 1.0
CB C:MET150 4.3 12.2 1.0
CD2 C:HIS95 4.3 15.8 1.0
O C:MET94 4.3 17.3 1.0
SD C:MET62 4.4 16.4 1.0
CD2 C:HIS145 4.4 17.8 1.0
CG C:PRO138 4.4 15.9 1.0
CA C:CYS136 4.6 13.5 1.0
CB C:MET62 4.7 16.2 1.0
N C:ASN96 4.7 15.7 1.0
CD C:PRO138 4.8 15.3 1.0
C C:HIS95 4.8 15.8 1.0
N C:HIS95 4.8 16.8 1.0
CA C:HIS145 4.9 13.7 1.0
C C:MET94 5.0 17.8 1.0

Copper binding site 6 out of 6 in 2fjs

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Copper binding site 6 out of 6 in the Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Anaerobically Reduced Wild Type Nitrite Reductase From A. Faecalis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3502

b:15.5
occ:1.00
 NE2 C:HIS100 2.0 13.1 1.0
NE2 C:HIS135 2.0 11.3 1.0
NE2 A:HIS306 2.1 9.9 1.0
CD2 C:HIS135 2.8 9.6 1.0
CE1 C:HIS100 2.8 13.0 1.0
CE1 A:HIS306 3.0 10.6 1.0
CD2 C:HIS100 3.1 12.1 1.0
CD2 A:HIS306 3.1 10.4 1.0
CE1 C:HIS135 3.2 10.4 1.0
CD1 A:ILE257 3.6 14.6 1.0
OD1 C:ASP98 3.7 16.0 1.0
ND1 C:HIS100 4.0 11.8 1.0
CG C:HIS135 4.0 12.1 1.0
ND1 A:HIS306 4.1 9.9 1.0
CG C:HIS100 4.2 10.8 1.0
ND1 C:HIS135 4.2 10.1 1.0
O C:ACT2012 4.2 22.4 1.0
CG A:HIS306 4.2 9.2 1.0
NE2 A:HIS255 4.3 12.2 1.0
CG C:ASP98 4.4 14.8 1.0
CE1 A:HIS255 4.4 12.8 1.0
CD2 A:HIS255 4.7 12.2 1.0
ND1 A:HIS255 4.8 13.2 1.0
OD2 C:ASP98 4.8 15.5 1.0
CG A:HIS255 5.0 11.5 1.0
CD1 A:LEU308 5.0 10.9 1.0
O A:HOH2249 5.0 13.0 1.0

Reference:

H.J.Wijma, I.Macpherson, O.Farver, E.I.Tocheva, I.Pecht, M.P.Verbeet, M.E.P.Murphy, G.W.Canters. Effect of the Methionine Ligand on the Reorganization Energy of the Type-1 Copper Site of Nitrite Reductase. J.Am.Chem.Soc. V. 129 519 2007.
ISSN: ISSN 0002-7863
PubMed: 17227014
DOI: 10.1021/JA064763J
Page generated: Tue Jul 30 23:29:21 2024

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