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Copper in PDB 2vm3: Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2

Protein crystallography data

The structure of Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2, PDB code: 2vm3 was solved by M.A.Hough, S.V.Antonyuk, R.W.Strange, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.52 / 1.80
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.941, 89.941, 143.732, 90.00, 90.00, 120.00
R / Rfree (%) 18.4 / 21

Other elements in 2vm3:

The structure of Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2 (pdb code 2vm3). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2, PDB code: 2vm3:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2vm3

Go back to Copper Binding Sites List in 2vm3
Copper binding site 1 out of 2 in the Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu501

b:24.3
occ:1.00
SG A:CYS130 2.1 23.6 1.0
ND1 A:HIS139 2.1 21.0 1.0
ND1 A:HIS89 2.1 21.2 1.0
SD A:MET144 2.5 23.0 1.0
CE1 A:HIS139 3.0 21.2 1.0
CB A:CYS130 3.1 21.6 1.0
CE1 A:HIS89 3.1 24.1 1.0
CG A:HIS139 3.1 20.2 1.0
CG A:HIS89 3.1 25.0 1.0
CE A:MET144 3.4 22.2 1.0
CB A:HIS89 3.4 24.5 1.0
CB A:HIS139 3.5 18.1 1.0
CA A:HIS89 3.8 25.4 1.0
CG A:PRO132 3.9 23.9 1.0
CG A:MET144 4.1 21.2 1.0
O A:PRO88 4.1 25.8 1.0
NE2 A:HIS139 4.2 22.7 1.0
CD2 A:HIS139 4.2 20.8 1.0
NE2 A:HIS89 4.2 23.5 1.0
CD2 A:HIS89 4.3 23.9 1.0
CD A:PRO132 4.3 22.9 1.0
SD A:MET56 4.4 23.9 1.0
CA A:CYS130 4.5 20.8 1.0
CB A:MET144 4.6 18.9 1.0
CA A:HIS139 4.7 17.5 1.0
N A:ASN90 4.7 24.8 1.0
N A:HIS89 4.8 25.9 1.0
C A:HIS89 4.9 25.6 1.0
C A:PRO88 4.9 26.9 1.0

Copper binding site 2 out of 2 in 2vm3

Go back to Copper Binding Sites List in 2vm3
Copper binding site 2 out of 2 in the Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Alcaligenes Xylosoxidans in Space Group R3 - 1 of 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu502

b:18.1
occ:1.00
O A:HOH2067 1.8 22.3 1.0
NE2 A:HIS129 2.0 18.7 1.0
NE2 A:HIS94 2.0 20.4 1.0
CE1 A:HIS94 2.9 18.8 1.0
CD2 A:HIS129 3.0 16.4 1.0
CE1 A:HIS129 3.1 18.4 1.0
CD2 A:HIS94 3.1 18.8 1.0
OD2 A:ASP92 3.6 30.5 1.0
ND1 A:HIS94 4.1 18.4 1.0
CG A:HIS129 4.1 18.5 1.0
ND1 A:HIS129 4.1 17.6 1.0
CG A:HIS94 4.2 18.1 1.0
CG A:ASP92 4.2 26.1 1.0
OD1 A:ASP92 4.6 25.8 1.0
O A:HOH2066 4.9 24.6 1.0

Reference:

M.A.Hough, S.V.Antonyuk, R.W.Strange, R.R.Eady, S.S.Hasnain. Crystallography with Online Optical and X-Ray Absorption Spectroscopies Demonstrates An Ordered Mechanism in Copper Nitrite Reductase. J.Mol.Biol. V. 378 353 2008.
ISSN: ISSN 0022-2836
PubMed: 18353369
DOI: 10.1016/J.JMB.2008.01.097
Page generated: Wed Oct 28 14:21:50 2020
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