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Copper in PDB 2vw4: Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3

Enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3

All present enzymatic activity of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3:
1.7.2.1;

Protein crystallography data

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3, PDB code: 2vw4 was solved by M.J.Ellis, S.G.Buffey, M.A.Hough, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 96.23 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.080, 89.080, 288.303, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 19.7

Other elements in 2vw4:

The structure of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 (pdb code 2vw4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3, PDB code: 2vw4:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2vw4

Go back to Copper Binding Sites List in 2vw4
Copper binding site 1 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:21.9
occ:1.00
SG A:CYS130 2.1 17.7 1.0
ND1 A:HIS139 2.2 15.2 1.0
ND1 A:HIS89 2.2 15.5 1.0
SD A:MET144 2.5 13.5 0.8
CB A:CYS130 3.1 15.5 1.0
CE1 A:HIS139 3.1 15.3 1.0
CE1 A:HIS89 3.2 16.3 1.0
CG A:HIS89 3.2 17.3 1.0
CE A:MET144 3.2 16.1 0.1
CG A:HIS139 3.2 14.2 1.0
CE A:MET144 3.5 14.9 0.8
CB A:HIS89 3.5 17.7 1.0
CB A:HIS139 3.5 12.8 1.0
CA A:HIS89 3.8 18.5 1.0
CG A:PRO132 3.9 17.8 1.0
CG A:MET144 4.0 15.2 1.0
SD A:MET144 4.0 15.9 0.1
O A:PRO88 4.1 18.1 1.0
NE2 A:HIS139 4.3 15.9 1.0
NE2 A:HIS89 4.3 15.7 1.0
CD2 A:HIS139 4.3 15.1 1.0
CD2 A:HIS89 4.3 15.7 1.0
CD A:PRO132 4.4 16.5 1.0
SD A:MET56 4.4 17.0 0.7
CA A:CYS130 4.5 15.5 1.0
CB A:MET144 4.6 13.5 1.0
SD A:MET56 4.6 16.5 0.3
N A:ASN90 4.7 17.5 1.0
CA A:HIS139 4.7 12.8 1.0
N A:HIS89 4.8 18.6 1.0
C A:HIS89 4.8 18.6 1.0
C A:PRO88 4.9 19.2 1.0

Copper binding site 2 out of 4 in 2vw4

Go back to Copper Binding Sites List in 2vw4
Copper binding site 2 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:16.4
occ:1.00
O A:HOH2135 1.9 16.9 1.0
NE2 A:HIS129 2.0 12.8 1.0
NE2 A:HIS94 2.0 14.0 1.0
CD2 A:HIS129 2.9 12.4 1.0
CE1 A:HIS94 3.0 13.9 1.0
CE1 A:HIS129 3.0 13.8 1.0
CD2 A:HIS94 3.1 12.8 1.0
OD2 A:ASP92 3.6 24.9 1.0
CG A:HIS129 4.1 13.7 1.0
ND1 A:HIS94 4.1 13.7 1.0
ND1 A:HIS129 4.1 12.0 1.0
CG A:HIS94 4.2 12.6 1.0
CG A:ASP92 4.3 20.8 1.0
OD1 A:ASP92 4.5 19.3 1.0
O A:HOH2134 4.9 17.9 1.0

Copper binding site 3 out of 4 in 2vw4

Go back to Copper Binding Sites List in 2vw4
Copper binding site 3 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu501

b:22.1
occ:1.00
SG B:CYS130 2.1 17.5 1.0
ND1 B:HIS139 2.2 16.4 1.0
ND1 B:HIS89 2.2 16.0 1.0
SD B:MET144 2.5 14.1 0.8
CE B:MET144 3.1 16.9 0.1
CB B:CYS130 3.1 16.3 1.0
CE1 B:HIS139 3.1 17.3 1.0
CG B:HIS89 3.2 18.2 1.0
CE1 B:HIS89 3.2 17.4 1.0
CG B:HIS139 3.2 15.7 1.0
CE B:MET144 3.3 15.4 0.8
CB B:HIS89 3.4 18.7 1.0
CB B:HIS139 3.6 14.0 1.0
CA B:HIS89 3.8 18.9 1.0
CG B:MET144 4.0 15.2 1.0
CG B:PRO132 4.0 19.0 1.0
SD B:MET144 4.1 17.4 0.1
O B:PRO88 4.2 19.4 1.0
NE2 B:HIS139 4.2 18.0 1.0
NE2 B:HIS89 4.3 18.5 1.0
CD2 B:HIS89 4.3 17.5 1.0
CD2 B:HIS139 4.3 17.6 1.0
SD B:MET56 4.4 16.5 0.7
CD B:PRO132 4.4 17.9 1.0
CB B:MET144 4.5 13.6 1.0
CA B:CYS130 4.5 16.4 1.0
SD B:MET56 4.6 16.5 0.3
N B:ASN90 4.7 18.3 1.0
CA B:HIS139 4.8 13.6 1.0
C B:HIS89 4.8 19.1 1.0
N B:HIS89 4.8 19.4 1.0
C B:PRO88 4.9 19.8 1.0

Copper binding site 4 out of 4 in 2vw4

Go back to Copper Binding Sites List in 2vw4
Copper binding site 4 out of 4 in the Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Nitrite Reductase From Alcaligenes Xylosoxidans - 2 of 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu502

b:17.6
occ:1.00
O B:HOH2111 1.9 18.3 1.0
NE2 B:HIS129 2.0 14.6 1.0
NE2 B:HIS94 2.0 14.7 1.0
CE1 B:HIS94 2.9 15.3 1.0
CD2 B:HIS129 2.9 15.7 1.0
CE1 B:HIS129 3.0 15.2 1.0
CD2 B:HIS94 3.1 14.9 1.0
OD2 B:ASP92 3.7 27.1 1.0
ND1 B:HIS94 4.1 15.7 1.0
CG B:HIS129 4.1 15.4 1.0
ND1 B:HIS129 4.1 14.1 1.0
CG B:HIS94 4.2 14.8 1.0
CG B:ASP92 4.3 21.1 1.0
OD1 B:ASP92 4.6 21.4 1.0
O B:HOH2112 4.9 19.6 1.0

Reference:

M.J.Ellis, S.G.Buffey, M.A.Hough, S.S.Hasnain. On-Line Optical and X-Ray Spectroscopies with Crystallography: An Integrated Approach For Determining Metalloprotein Structures in Functionally Well Defined States. J.Synchrotron Radiat. V. 15 433 2008.
ISSN: ISSN 0909-0495
PubMed: 18728313
DOI: 10.1107/S0909049508014945
Page generated: Sun Dec 13 11:07:17 2020

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