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Copper in PDB 2xxg: Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans

Protein crystallography data

The structure of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xxg was solved by M.A.Hough, 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) 29.16 / 1.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 89.552, 89.552, 287.678, 90.00, 90.00, 120.00
R / Rfree (%) 16.75 / 21.074

Other elements in 2xxg:

The structure of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans (pdb code 2xxg). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans, PDB code: 2xxg:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 2xxg

Go back to Copper Binding Sites List in 2xxg
Copper binding site 1 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1337

b:21.5
occ:0.75
ND1 A:HIS89 2.1 20.9 1.0
ND1 A:HIS139 2.2 19.5 1.0
SG A:CYS130 2.2 21.5 1.0
SD A:MET144 2.6 19.1 0.7
CE1 A:HIS89 3.0 21.9 1.0
CE1 A:HIS139 3.1 18.7 1.0
CB A:CYS130 3.1 17.2 1.0
CG A:HIS89 3.1 22.2 1.0
CG A:HIS139 3.2 16.9 1.0
CB A:HIS89 3.5 23.0 1.0
CB A:HIS139 3.5 15.8 1.0
CE A:MET144 3.5 16.6 0.7
CE A:MET144 3.7 16.2 0.3
CG A:MET144 3.8 15.9 0.3
CA A:HIS89 3.9 22.6 1.0
O A:PRO88 4.1 23.7 1.0
CG A:PRO132 4.1 23.0 1.0
CG A:MET144 4.1 16.7 0.7
SD A:MET144 4.2 17.4 0.3
NE2 A:HIS89 4.2 22.3 1.0
NE2 A:HIS139 4.2 18.9 1.0
CD2 A:HIS89 4.3 23.3 1.0
CD2 A:HIS139 4.3 18.1 1.0
CD A:PRO132 4.4 21.1 1.0
SD A:MET56 4.5 21.7 1.0
CA A:CYS130 4.6 17.3 1.0
CB A:MET144 4.6 15.2 0.3
CB A:MET144 4.6 16.1 0.7
CA A:HIS139 4.7 14.8 1.0
N A:SER90 4.8 21.5 1.0
N A:HIS89 4.8 23.2 1.0
C A:PRO88 4.8 24.2 1.0
C A:HIS89 4.9 22.4 1.0

Copper binding site 2 out of 4 in 2xxg

Go back to Copper Binding Sites List in 2xxg
Copper binding site 2 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1338

b:14.8
occ:1.00
O A:HOH2122 1.9 20.2 1.0
NE2 A:HIS94 2.0 13.0 1.0
NE2 A:HIS129 2.0 14.3 1.0
CE1 A:HIS94 2.9 14.8 1.0
CD2 A:HIS129 2.9 14.2 1.0
CD2 A:HIS94 3.1 13.4 1.0
CE1 A:HIS129 3.1 14.0 1.0
OD2 A:ASP92 3.7 19.3 1.0
ND1 A:HIS94 4.1 12.4 1.0
CG A:HIS129 4.1 12.8 1.0
ND1 A:HIS129 4.2 13.9 1.0
CG A:HIS94 4.2 13.6 1.0
CG A:ASP92 4.2 19.4 1.0
OD1 A:ASP92 4.5 20.7 1.0
O A:HOH2121 5.0 19.6 1.0

Copper binding site 3 out of 4 in 2xxg

Go back to Copper Binding Sites List in 2xxg
Copper binding site 3 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1338

b:20.8
occ:0.70
ND1 C:HIS139 2.0 20.3 1.0
ND1 C:HIS89 2.0 22.1 1.0
SG C:CYS130 2.1 25.1 1.0
SD C:MET144 2.4 20.4 0.7
CE1 C:HIS139 2.9 19.2 1.0
CE1 C:HIS89 3.0 22.9 1.0
CG C:HIS139 3.1 19.8 1.0
CG C:HIS89 3.1 22.5 1.0
CB C:CYS130 3.1 20.6 1.0
CE C:MET144 3.4 18.5 0.7
CB C:HIS89 3.5 22.5 1.0
CB C:HIS139 3.5 16.7 1.0
CE C:MET144 3.5 19.0 0.3
CA C:HIS89 3.8 24.0 1.0
CG C:MET144 3.9 17.8 0.3
CG C:PRO132 3.9 24.5 1.0
SD C:MET144 4.0 20.5 0.3
CG C:MET144 4.0 17.9 0.7
NE2 C:HIS139 4.1 20.5 1.0
O C:PRO88 4.1 24.1 1.0
NE2 C:HIS89 4.1 21.9 1.0
CD2 C:HIS139 4.2 20.5 1.0
CD2 C:HIS89 4.2 22.1 1.0
SD C:MET56 4.3 24.5 1.0
CD C:PRO132 4.4 22.7 1.0
CB C:MET144 4.6 16.8 0.3
CB C:MET144 4.6 16.9 0.7
CA C:CYS130 4.6 19.3 1.0
CA C:HIS139 4.7 16.4 1.0
N C:SER90 4.7 24.0 1.0
N C:HIS89 4.8 24.3 1.0
C C:HIS89 4.9 24.1 1.0
C C:PRO88 4.9 25.8 1.0

Copper binding site 4 out of 4 in 2xxg

Go back to Copper Binding Sites List in 2xxg
Copper binding site 4 out of 4 in the Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of the N90S Mutant of Nitrite Reductase From Alcaligenes Xylosoxidans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu1339

b:15.5
occ:1.00
NE2 C:HIS129 2.0 15.6 1.0
NE2 C:HIS94 2.1 15.2 1.0
O C:HOH2111 2.2 29.7 1.0
CD2 C:HIS129 3.0 13.8 1.0
CE1 C:HIS94 3.0 15.1 1.0
CE1 C:HIS129 3.0 17.3 1.0
CD2 C:HIS94 3.1 17.4 1.0
OD2 C:ASP92 3.6 25.7 1.0
ND1 C:HIS129 4.1 16.4 1.0
ND1 C:HIS94 4.1 15.4 1.0
CG C:HIS129 4.2 15.8 1.0
CG C:HIS94 4.2 15.8 1.0
CG C:ASP92 4.2 21.1 1.0
OD1 C:ASP92 4.6 22.2 1.0
O C:HOH2109 5.0 20.4 1.0

Reference:

M.A.Hough, R.R.Eady, S.S.Hasnain. Identification of the Proton Channel to the Active Site Type 2 Cu Centre of Nitrite Reductase: Structural and Enzymatic Properties of the HIS254PHE and ASN90SER Mutants Biochemistry V. 47 13547 2008.
ISSN: ISSN 0006-2960
PubMed: 19053252
DOI: 10.1021/BI801369Y
Page generated: Sun Dec 13 11:07:50 2020

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