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Copper in PDB 2qdw: Structure of Cu(I) Form of the M51A Mutant of Amicyanin

Protein crystallography data

The structure of Structure of Cu(I) Form of the M51A Mutant of Amicyanin, PDB code: 2qdw was solved by J.K.Ma, Y.Wang, C.J.Carrell, F.S.Mathews, V.L.Davidson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 0.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 28.210, 55.360, 27.270, 90.00, 95.75, 90.00
R / Rfree (%) 12.1 / 14.7

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Cu(I) Form of the M51A Mutant of Amicyanin (pdb code 2qdw). 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 Cu(I) Form of the M51A Mutant of Amicyanin, PDB code: 2qdw:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 2qdw

Go back to Copper Binding Sites List in 2qdw
Copper binding site 1 out of 2 in the Structure of Cu(I) Form of the M51A Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Cu(I) Form of the M51A Mutant of Amicyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1107

b:13.4
occ:0.43
CU A:CU11107 0.0 13.4 0.4
CU A:CU11107 1.1 9.4 0.6
ND1 A:HIS53 2.0 10.3 1.0
SG A:CYS92 2.1 7.9 1.0
ND1 A:HIS95 2.1 11.9 0.4
CD2 A:HIS95 2.5 14.5 0.6
CE1 A:HIS53 2.9 12.3 1.0
CG A:HIS95 3.0 12.6 0.4
CG A:HIS53 3.1 6.9 1.0
CG A:HIS95 3.1 11.2 0.6
CB A:HIS95 3.1 8.9 0.6
SD A:MET98 3.1 11.3 1.0
CB A:HIS95 3.2 11.6 0.4
CE1 A:HIS95 3.2 9.6 0.4
CB A:CYS92 3.3 5.9 1.0
CB A:HIS53 3.5 6.6 1.0
CA A:HIS53 3.7 6.5 1.0
NE2 A:HIS95 3.7 17.3 0.6
O A:PRO52 3.9 10.7 1.0
NE2 A:HIS53 4.0 10.8 1.0
CG A:PRO94 4.0 9.4 1.0
N A:HIS95 4.0 7.9 1.0
CD2 A:HIS53 4.1 9.2 1.0
CA A:HIS95 4.1 8.8 1.0
CD2 A:HIS95 4.2 12.4 0.4
CE A:MET98 4.2 15.1 1.0
NE2 A:HIS95 4.3 11.4 0.4
ND1 A:HIS95 4.4 14.5 0.6
CG A:MET98 4.5 8.5 1.0
O A:HIS95 4.5 7.7 1.0
C A:PRO52 4.6 8.5 1.0
N A:HIS53 4.6 7.5 1.0
CE1 A:HIS95 4.6 16.0 0.6
CA A:CYS92 4.6 4.7 1.0
N A:ASN54 4.6 6.1 1.0
CE A:MET28 4.6 20.7 0.2
CD A:PRO94 4.7 7.5 1.0
C A:HIS95 4.8 7.8 1.0
C A:HIS53 4.8 6.5 1.0
CB A:PRO94 4.9 11.1 1.0
C A:PRO94 4.9 9.8 1.0

Copper binding site 2 out of 2 in 2qdw

Go back to Copper Binding Sites List in 2qdw
Copper binding site 2 out of 2 in the Structure of Cu(I) Form of the M51A Mutant of Amicyanin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Cu(I) Form of the M51A Mutant of Amicyanin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu1107

b:9.4
occ:0.57
CU A:CU11107 0.0 9.4 0.6
CU A:CU11107 1.1 13.4 0.4
ND1 A:HIS53 2.0 10.3 1.0
SG A:CYS92 2.2 7.9 1.0
SD A:MET98 2.4 11.3 1.0
CE1 A:HIS53 3.0 12.3 1.0
CB A:CYS92 3.0 5.9 1.0
CG A:HIS53 3.0 6.9 1.0
CE A:MET98 3.1 15.1 1.0
ND1 A:HIS95 3.2 11.9 0.4
CB A:HIS53 3.4 6.6 1.0
CD2 A:HIS95 3.6 14.5 0.6
CB A:HIS95 3.7 8.9 0.6
CB A:HIS95 3.7 11.6 0.4
CG A:MET98 3.8 8.5 1.0
CG A:HIS95 3.8 12.6 0.4
CG A:HIS95 3.9 11.2 0.6
CA A:HIS53 4.0 6.5 1.0
NE2 A:HIS53 4.1 10.8 1.0
CD2 A:HIS53 4.1 9.2 1.0
CB A:MET98 4.2 7.2 1.0
CE1 A:HIS95 4.3 9.6 0.4
CA A:CYS92 4.4 4.7 1.0
O A:HIS95 4.5 7.7 1.0
N A:ASN54 4.6 6.1 1.0
O A:PRO52 4.7 10.7 1.0
CA A:HIS95 4.7 8.8 1.0
N A:HIS95 4.7 7.9 1.0
NE2 A:HIS95 4.8 17.3 0.6
CE A:MET28 4.8 20.7 0.2
O A:ASN54 4.8 5.5 1.0
C A:HIS53 4.9 6.5 1.0
OH A:TYR30 4.9 6.2 1.0
CG2 A:ILE25 4.9 12.0 1.0
CG A:PRO94 4.9 9.4 1.0

Reference:

J.K.Ma, Y.Wang, C.J.Carrell, F.S.Mathews, V.L.Davidson. A Single Methionine Residue Dictates the Kinetic Mechanism of Interprotein Electron Transfer From Methylamine Dehydrogenase to Amicyanin. Biochemistry V. 46 11137 2007.
ISSN: ISSN 0006-2960
PubMed: 17824674
DOI: 10.1021/BI7012307
Page generated: Thu Sep 3 16:49:31 2020
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