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Copper in PDB 1sjm: Nitrite Bound Copper Containing Nitrite Reductase

Enzymatic activity of Nitrite Bound Copper Containing Nitrite Reductase

All present enzymatic activity of Nitrite Bound Copper Containing Nitrite Reductase:
1.7.2.1;

Protein crystallography data

The structure of Nitrite Bound Copper Containing Nitrite Reductase, PDB code: 1sjm was solved by E.I.Tocheva, F.I.Rosell, A.G.Mauk, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.600, 102.450, 145.980, 90.00, 90.00, 90.00
R / Rfree (%) 11.3 / 13.8

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite Bound Copper Containing Nitrite Reductase (pdb code 1sjm). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Nitrite Bound Copper Containing Nitrite Reductase, PDB code: 1sjm:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 1sjm

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Copper binding site 1 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1501

b:9.4
occ:1.00
 ND1 A:HIS145 2.1 9.4 1.0
ND1 A:HIS95 2.1 8.6 1.0
SG A:CYS136 2.2 9.4 1.0
SD A:MET150 2.4 8.8 1.0
CE1 A:HIS145 2.9 9.4 1.0
CE1 A:HIS95 3.0 9.4 1.0
CG A:HIS95 3.1 8.8 1.0
CG A:HIS145 3.1 7.9 1.0
CB A:CYS136 3.2 7.6 1.0
CE A:MET150 3.3 9.5 1.0
CB A:HIS95 3.5 8.8 1.0
CB A:HIS145 3.5 7.7 1.0
CG A:MET150 3.8 7.4 1.0
CA A:HIS95 3.9 8.7 1.0
NE2 A:HIS145 4.1 9.2 1.0
NE2 A:HIS95 4.2 9.6 1.0
CD2 A:HIS145 4.2 9.7 1.0
CD2 A:HIS95 4.2 9.2 1.0
CB A:MET150 4.3 7.6 1.0
CG A:PRO138 4.3 9.7 1.0
O A:MET94 4.3 9.3 1.0
SD A:MET62 4.4 11.1 1.0
CA A:CYS136 4.6 7.9 1.0
N A:ASN96 4.7 8.8 1.0
CD A:PRO138 4.7 8.8 1.0
CB A:MET62 4.8 9.6 1.0
CA A:HIS145 4.8 7.7 1.0
C A:HIS95 4.9 8.9 1.0
N A:HIS95 4.9 8.7 1.0

Copper binding site 2 out of 6 in 1sjm

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Copper binding site 2 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1502

b:9.2
occ:1.00
 NE2 A:HIS100 2.0 8.3 1.0
O2 A:NO21503 2.0 24.2 1.0
NE2 B:HIS306 2.0 8.1 1.0
NE2 A:HIS135 2.1 8.8 1.0
O1 A:NO21503 2.3 24.8 1.0
N A:NO21503 2.4 26.0 1.0
CE1 A:HIS100 2.9 8.0 1.0
CE1 B:HIS306 3.0 7.9 1.0
CD2 A:HIS135 3.1 8.3 1.0
CE1 A:HIS135 3.1 7.0 1.0
CD2 B:HIS306 3.1 7.7 1.0
CD2 A:HIS100 3.1 7.6 1.0
OD1 A:ASP98 3.7 19.0 1.0
CE1 B:HIS255 4.0 13.6 1.0
ND1 A:HIS100 4.1 7.8 1.0
ND1 B:HIS306 4.1 7.5 1.0
NE2 B:HIS255 4.2 12.8 1.0
ND1 A:HIS135 4.2 7.9 1.0
CG B:HIS306 4.2 7.5 1.0
CG A:HIS100 4.2 7.2 1.0
CG A:HIS135 4.2 8.1 1.0
O A:HOH5728 4.4 33.6 1.0
CG A:ASP98 4.4 13.7 1.0
ND1 B:HIS255 4.6 11.9 1.0
OD2 A:ASP98 4.7 17.4 1.0
CD2 B:HIS255 4.8 12.7 1.0
CD2 B:LEU308 4.9 10.4 1.0
O B:HOH5598 4.9 15.5 1.0

Copper binding site 3 out of 6 in 1sjm

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Copper binding site 3 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2501

b:11.1
occ:1.00
 ND1 B:HIS145 2.1 10.6 1.0
ND1 B:HIS95 2.1 9.7 1.0
SG B:CYS136 2.2 11.0 1.0
SD B:MET150 2.5 10.2 1.0
CE1 B:HIS145 3.0 11.9 1.0
CE1 B:HIS95 3.0 10.2 1.0
CG B:HIS95 3.1 10.3 1.0
CG B:HIS145 3.1 10.0 1.0
CB B:CYS136 3.2 10.2 1.0
CE B:MET150 3.2 11.3 1.0
CB B:HIS95 3.5 10.4 1.0
CB B:HIS145 3.5 9.8 1.0
CA B:HIS95 3.8 10.5 1.0
CG B:MET150 3.9 9.7 1.0
NE2 B:HIS145 4.1 11.8 1.0
NE2 B:HIS95 4.1 10.8 1.0
CD2 B:HIS95 4.2 10.7 1.0
CD2 B:HIS145 4.2 11.3 1.0
CG B:PRO138 4.2 12.3 1.0
O B:MET94 4.3 11.9 1.0
SD B:MET62 4.4 12.4 1.0
CB B:MET150 4.4 9.3 1.0
CD B:PRO138 4.6 10.2 1.0
CA B:CYS136 4.6 9.8 1.0
N B:ASN96 4.7 10.6 1.0
CA B:HIS145 4.8 9.5 1.0
CB B:MET62 4.8 10.6 1.0
C B:HIS95 4.8 10.8 1.0
N B:HIS95 4.9 10.7 1.0
C B:MET94 5.0 10.9 1.0

Copper binding site 4 out of 6 in 1sjm

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Copper binding site 4 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu2502

b:10.6
occ:1.00
 NE2 B:HIS135 2.1 9.8 1.0
NE2 B:HIS100 2.1 9.0 1.0
NE2 C:HIS306 2.1 9.8 1.0
O2 B:NO22503 2.1 28.2 1.0
O1 B:NO22503 2.3 29.7 1.0
N B:NO22503 2.3 29.8 1.0
CE1 B:HIS100 3.0 9.7 1.0
CE1 C:HIS306 3.0 9.9 1.0
CD2 B:HIS135 3.0 9.5 1.0
CE1 B:HIS135 3.1 9.6 1.0
CD2 C:HIS306 3.1 9.3 1.0
CD2 B:HIS100 3.1 8.2 1.0
OD1 B:ASP98 3.7 20.7 1.0
NE2 C:HIS255 4.1 14.3 1.0
ND1 B:HIS100 4.1 9.0 1.0
ND1 C:HIS306 4.1 8.7 1.0
ND1 B:HIS135 4.2 9.1 1.0
CG B:HIS135 4.2 9.2 1.0
CG B:HIS100 4.2 8.9 1.0
CG C:HIS306 4.2 9.7 1.0
CE1 C:HIS255 4.3 13.2 1.0
O B:HOH5716 4.3 34.3 1.0
CG B:ASP98 4.4 15.6 1.0
CD2 C:HIS255 4.5 14.3 1.0
OD2 B:ASP98 4.7 17.8 1.0
ND1 C:HIS255 4.8 12.4 1.0
CD2 C:LEU308 4.9 11.7 1.0
CG C:HIS255 4.9 11.0 1.0
O C:HOH3555 4.9 17.1 1.0

Copper binding site 5 out of 6 in 1sjm

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Copper binding site 5 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3501

b:14.3
occ:1.00
 ND1 C:HIS145 2.1 13.7 1.0
ND1 C:HIS95 2.1 14.6 1.0
SG C:CYS136 2.2 13.7 1.0
SD C:MET150 2.5 13.1 1.0
CE1 C:HIS145 3.0 14.8 1.0
CE1 C:HIS95 3.0 13.5 1.0
CG C:HIS95 3.1 13.8 1.0
CG C:HIS145 3.1 11.6 1.0
CB C:CYS136 3.2 12.5 1.0
CE C:MET150 3.3 12.8 1.0
CB C:HIS95 3.5 14.1 1.0
CB C:HIS145 3.5 11.2 1.0
CA C:HIS95 3.8 13.7 1.0
CG C:MET150 3.9 12.7 1.0
NE2 C:HIS145 4.1 13.7 1.0
NE2 C:HIS95 4.1 14.2 1.0
CD2 C:HIS95 4.2 14.3 1.0
CD2 C:HIS145 4.2 13.2 1.0
CG C:PRO138 4.2 14.1 1.0
O C:MET94 4.3 15.1 1.0
CB C:MET150 4.4 11.3 1.0
SD C:MET62 4.4 14.5 1.0
CD C:PRO138 4.6 13.3 1.0
CA C:CYS136 4.6 12.1 1.0
N C:ASN96 4.6 13.5 1.0
CB C:MET62 4.8 13.4 1.0
CA C:HIS145 4.8 11.3 1.0
C C:HIS95 4.8 13.5 1.0
N C:HIS95 4.8 13.9 1.0
C C:MET94 5.0 14.1 1.0

Copper binding site 6 out of 6 in 1sjm

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Copper binding site 6 out of 6 in the Nitrite Bound Copper Containing Nitrite Reductase


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Nitrite Bound Copper Containing Nitrite Reductase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu3502

b:11.8
occ:1.00
 NE2 C:HIS100 2.0 10.3 1.0
NE2 A:HIS306 2.0 10.8 1.0
NE2 C:HIS135 2.1 11.3 1.0
O2 C:NO23503 2.1 28.7 1.0
N C:NO23503 2.3 29.0 1.0
O1 C:NO23503 2.4 28.6 1.0
CE1 C:HIS100 2.9 10.4 1.0
CE1 A:HIS306 3.0 9.9 1.0
CD2 C:HIS135 3.0 10.5 1.0
CE1 C:HIS135 3.1 10.3 1.0
CD2 A:HIS306 3.1 9.9 1.0
CD2 C:HIS100 3.1 10.3 1.0
OD1 C:ASP98 3.7 24.2 1.0
ND1 C:HIS100 4.1 9.8 1.0
NE2 A:HIS255 4.1 14.8 1.0
ND1 A:HIS306 4.1 9.2 1.0
ND1 C:HIS135 4.2 11.1 1.0
CG C:HIS135 4.2 10.7 1.0
CG C:HIS100 4.2 9.9 1.0
CG A:HIS306 4.2 10.2 1.0
CE1 A:HIS255 4.3 15.3 1.0
O C:HOH3675 4.3 35.4 1.0
CG C:ASP98 4.4 18.4 1.0
CD2 A:HIS255 4.5 14.0 1.0
OD2 C:ASP98 4.8 21.5 1.0
ND1 A:HIS255 4.8 13.7 1.0
CG A:HIS255 4.9 11.0 1.0
CD2 A:LEU308 4.9 11.7 1.0
O A:HOH5594 5.0 18.1 1.0

Reference:

E.I.Tocheva, F.I.Rosell, A.G.Mauk, M.E.Murphy. Side-on Copper-Nitrosyl Coordination By Nitrite Reductase. Science V. 304 867 2004.
ISSN: ISSN 0036-8075
PubMed: 15131305
DOI: 10.1126/SCIENCE.1095109
Page generated: Tue Jul 30 22:46:44 2024

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