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Copper in PDB 7p2f: Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011

Enzymatic activity of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011

All present enzymatic activity of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011:
1.7.2.1;

Protein crystallography data

The structure of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011, PDB code: 7p2f was solved by C.Tolmie, D.J.Opperman, F.M.Ferroni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 78.58 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 124.43, 215.39, 114.48, 90, 90, 90
R / Rfree (%) 18.2 / 22.4

Copper Binding Sites:

The binding sites of Copper atom in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 (pdb code 7p2f). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 6 binding sites of Copper where determined in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011, PDB code: 7p2f:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6;

Copper binding site 1 out of 6 in 7p2f

Go back to Copper Binding Sites List in 7p2f
Copper binding site 1 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:37.4
occ:1.00
 ND1 A:HIS131 2.0 36.1 1.0
ND1 A:HIS181 2.0 33.8 1.0
SG A:CYS172 2.3 35.5 1.0
SD A:MET186 2.4 34.0 1.0
CE1 A:HIS131 2.9 34.7 1.0
CE1 A:HIS181 2.9 32.9 1.0
CG A:HIS131 3.1 34.9 1.0
CG A:HIS181 3.1 34.1 1.0
CB A:CYS172 3.3 35.3 1.0
CE A:MET186 3.3 34.5 1.0
CB A:HIS131 3.5 36.8 1.0
CB A:HIS181 3.5 34.4 1.0
CG A:MET186 3.8 34.4 1.0
CA A:HIS131 3.9 35.8 1.0
NE2 A:HIS131 4.0 33.1 1.0
NE2 A:HIS181 4.1 33.0 1.0
CD2 A:HIS131 4.1 35.9 1.0
CD2 A:HIS181 4.2 33.4 1.0
O A:GLN130 4.2 40.8 1.0
CG A:PRO174 4.4 42.1 1.0
CB A:MET186 4.4 34.3 1.0
CD A:PRO174 4.5 41.3 1.0
SD A:MET98 4.6 38.6 1.0
CA A:CYS172 4.7 33.8 1.0
CA A:HIS181 4.7 35.5 1.0
N A:ASN132 4.8 33.3 1.0
CB A:MET98 4.9 36.1 1.0
N A:HIS131 4.9 37.2 1.0
C A:HIS131 4.9 34.0 1.0
C A:GLN130 5.0 37.7 1.0

Copper binding site 2 out of 6 in 7p2f

Go back to Copper Binding Sites List in 7p2f
Copper binding site 2 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:34.2
occ:1.00
 O A:HOH651 2.0 24.4 1.0
NE2 A:HIS136 2.0 34.1 1.0
NE2 C:HIS342 2.0 32.8 1.0
NE2 A:HIS171 2.1 34.4 1.0
CE1 A:HIS136 2.9 33.3 1.0
CE1 C:HIS342 3.0 31.5 1.0
CD2 A:HIS171 3.0 31.8 1.0
CD2 C:HIS342 3.1 32.0 1.0
CE1 A:HIS171 3.1 32.4 1.0
CD2 A:HIS136 3.2 34.9 1.0
OD2 A:ASP134 3.9 52.0 1.0
NE2 C:HIS291 4.0 36.0 1.0
ND1 A:HIS136 4.0 31.6 1.0
ND1 C:HIS342 4.1 30.0 1.0
CG A:HIS171 4.2 29.6 1.0
ND1 A:HIS171 4.2 30.4 1.0
CG C:HIS342 4.2 30.1 1.0
CG A:HIS136 4.2 34.6 1.0
CD2 C:HIS291 4.3 36.8 1.0
CE1 C:HIS291 4.4 37.8 1.0
CG A:ASP134 4.5 49.3 1.0
OD1 A:ASP134 4.7 45.8 1.0
CG C:HIS291 4.8 37.0 1.0
ND1 C:HIS291 4.9 38.2 1.0

Copper binding site 3 out of 6 in 7p2f

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Copper binding site 3 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:36.4
occ:1.00
 ND1 B:HIS131 2.0 38.7 1.0
ND1 B:HIS181 2.1 33.1 1.0
SG B:CYS172 2.3 35.1 1.0
SD B:MET186 2.4 33.5 1.0
CE1 B:HIS131 2.8 38.4 1.0
CE1 B:HIS181 2.9 31.9 1.0
CG B:HIS181 3.2 30.4 1.0
CE B:MET186 3.2 35.5 1.0
CG B:HIS131 3.2 37.9 1.0
CB B:CYS172 3.2 32.8 1.0
CB B:HIS181 3.6 30.4 1.0
CB B:HIS131 3.6 36.7 1.0
CG B:MET186 3.9 31.8 1.0
NE2 B:HIS131 4.0 37.9 1.0
CA B:HIS131 4.0 35.4 1.0
NE2 B:HIS181 4.1 29.3 1.0
CD2 B:HIS131 4.2 40.3 1.0
CD2 B:HIS181 4.2 29.9 1.0
O B:GLN130 4.2 41.2 1.0
CG B:PRO174 4.3 37.3 1.0
CB B:MET186 4.4 29.8 1.0
SD B:MET98 4.6 35.0 1.0
CA B:CYS172 4.7 32.0 1.0
CA B:HIS181 4.7 31.9 1.0
CD B:PRO174 4.8 36.3 1.0
N B:ASN132 4.9 34.8 1.0
CB B:MET98 4.9 33.7 1.0

Copper binding site 4 out of 6 in 7p2f

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Copper binding site 4 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:35.2
occ:1.00
 O B:HOH649 2.0 22.9 1.0
NE2 B:HIS171 2.0 32.5 1.0
NE2 A:HIS342 2.0 31.3 1.0
NE2 B:HIS136 2.1 29.9 1.0
CE1 B:HIS136 2.9 29.9 1.0
CE1 B:HIS171 3.0 33.5 1.0
CD2 A:HIS342 3.0 32.0 1.0
CD2 B:HIS171 3.1 31.1 1.0
CE1 A:HIS342 3.1 30.3 1.0
CD2 B:HIS136 3.2 30.1 1.0
OD2 B:ASP134 3.7 51.5 1.0
ND1 B:HIS171 4.1 33.2 1.0
ND1 B:HIS136 4.1 27.4 1.0
CG A:HIS342 4.1 30.1 1.0
NE2 A:HIS291 4.2 37.3 1.0
ND1 A:HIS342 4.2 29.1 1.0
CG B:HIS171 4.2 33.1 1.0
CG B:HIS136 4.3 28.8 1.0
CG B:ASP134 4.4 42.7 1.0
CE1 A:HIS291 4.5 38.2 1.0
CD2 A:HIS291 4.5 37.0 1.0
OD1 B:ASP134 4.7 39.8 1.0
ND1 A:HIS291 4.9 38.1 1.0
CG A:HIS291 5.0 36.1 1.0

Copper binding site 5 out of 6 in 7p2f

Go back to Copper Binding Sites List in 7p2f
Copper binding site 5 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu501

b:38.8
occ:1.00
 ND1 C:HIS131 2.0 40.1 1.0
ND1 C:HIS181 2.0 38.2 1.0
SG C:CYS172 2.3 34.9 1.0
SD C:MET186 2.4 36.5 1.0
CE1 C:HIS181 2.9 35.6 1.0
CE1 C:HIS131 2.9 38.2 1.0
CE C:MET186 3.1 36.9 1.0
CG C:HIS131 3.1 39.7 1.0
CG C:HIS181 3.1 35.6 1.0
CB C:CYS172 3.2 37.1 1.0
CB C:HIS131 3.6 39.8 1.0
CB C:HIS181 3.6 35.6 1.0
CA C:HIS131 3.9 37.7 1.0
CG C:MET186 4.0 35.3 1.0
NE2 C:HIS181 4.1 34.1 1.0
NE2 C:HIS131 4.1 38.0 1.0
CG C:PRO174 4.1 39.4 1.0
CD2 C:HIS131 4.2 39.7 1.0
CD2 C:HIS181 4.2 34.6 1.0
O C:GLN130 4.3 36.8 1.0
CB C:MET186 4.5 33.8 1.0
SD C:MET98 4.6 36.2 1.0
CA C:CYS172 4.7 37.6 1.0
CD C:PRO174 4.7 39.4 1.0
N C:ASN132 4.8 38.7 1.0
CA C:HIS181 4.8 35.5 1.0
N C:HIS131 4.9 37.8 1.0
C C:HIS131 5.0 39.0 1.0
CB C:MET98 5.0 36.7 1.0

Copper binding site 6 out of 6 in 7p2f

Go back to Copper Binding Sites List in 7p2f
Copper binding site 6 out of 6 in the Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Green-Type Copper-Nitrite Reductase From Sinorhizobium Meliloti 2011 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu502

b:36.5
occ:1.00
 O B:HOH650 2.0 26.5 1.0
NE2 C:HIS171 2.0 33.8 1.0
NE2 B:HIS342 2.1 35.5 1.0
NE2 C:HIS136 2.1 33.4 1.0
CE1 C:HIS136 2.9 32.9 1.0
CD2 C:HIS171 3.0 31.9 1.0
CE1 B:HIS342 3.0 35.2 1.0
CE1 C:HIS171 3.1 32.7 1.0
CD2 B:HIS342 3.1 34.9 1.0
CD2 C:HIS136 3.2 33.0 1.0
OD2 C:ASP134 3.9 57.8 1.0
ND1 C:HIS136 4.1 29.9 1.0
ND1 B:HIS342 4.1 33.5 1.0
CG C:HIS171 4.2 30.9 1.0
ND1 C:HIS171 4.2 30.6 1.0
CG B:HIS342 4.2 32.2 1.0
CG C:HIS136 4.3 32.1 1.0
NE2 B:HIS291 4.3 44.5 1.0
CG C:ASP134 4.4 51.4 1.0
CE1 B:HIS291 4.5 45.0 1.0
OD1 C:ASP134 4.6 54.4 1.0
CD2 B:HIS291 4.6 44.1 1.0
O B:HOH628 4.8 41.4 1.0
ND1 B:HIS291 4.9 44.6 1.0

Reference:

C.S.Ramirez, C.Tolmie, D.J.Opperman, P.J.Gonzalez, M.G.Rivas, C.D.Brondino, F.M.Ferroni. Copper Nitrite Reductase From Sinorhizobium Meliloti 2011: Crystal Structure and Interaction with the Physiological Versus A Nonmetabolically Related Cupredoxin-Like Mediator. Protein Sci. 2021.
ISSN: ESSN 1469-896X
PubMed: 34562300
DOI: 10.1002/PRO.4195
Page generated: Wed Jul 31 08:42:57 2024

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