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Copper in PDB 3ef4: Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans

Protein crystallography data

The structure of Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans, PDB code: 3ef4 was solved by D.Hira, M.Nojiri, S.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.95 / 1.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 97.690, 50.623, 82.378, 90.00, 90.98, 90.00
R / Rfree (%) 13.5 / 16.9

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans (pdb code 3ef4). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans, PDB code: 3ef4:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3ef4

Go back to Copper Binding Sites List in 3ef4
Copper binding site 1 out of 3 in the Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu401

b:11.3
occ:1.00
ND1 A:HIS41 2.0 11.4 1.0
ND1 A:HIS82 2.0 10.6 1.0
SG A:CYS79 2.2 10.4 1.0
SD A:MET87 2.5 10.3 1.0
CE1 A:HIS41 3.0 11.8 1.0
CE1 A:HIS82 3.0 11.5 1.0
CG A:HIS41 3.0 11.7 1.0
CG A:HIS82 3.1 11.0 1.0
CB A:CYS79 3.2 10.0 1.0
CB A:HIS82 3.3 10.8 1.0
CE A:MET87 3.3 12.0 1.0
CB A:HIS41 3.4 11.7 1.0
CA A:HIS41 3.7 10.6 1.0
CG A:MET87 3.9 8.9 1.0
NE2 A:HIS41 4.1 12.6 1.0
NE2 A:HIS82 4.1 11.6 1.0
CD2 A:HIS41 4.2 12.7 1.0
CD2 A:HIS82 4.2 11.7 1.0
O A:SER40 4.3 19.1 1.0
CB A:MET87 4.4 9.0 1.0
N A:HIS82 4.4 10.5 1.0
CA A:HIS82 4.5 9.8 1.0
CG A:PRO81 4.5 11.9 1.0
CA A:CYS79 4.6 9.1 1.0
N A:ASN42 4.7 10.4 1.0
N A:HIS41 4.7 11.1 1.0
C A:HIS41 4.8 10.6 1.0
C A:SER40 4.9 13.6 1.0
SD A:MET17 5.0 17.7 1.0

Copper binding site 2 out of 3 in 3ef4

Go back to Copper Binding Sites List in 3ef4
Copper binding site 2 out of 3 in the Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu401

b:11.3
occ:1.00
ND1 B:HIS41 2.0 11.6 1.0
ND1 B:HIS82 2.0 10.5 1.0
SG B:CYS79 2.2 10.3 1.0
SD B:MET87 2.5 10.6 1.0
CE1 B:HIS41 3.0 11.9 1.0
CG B:HIS41 3.0 11.2 1.0
CE1 B:HIS82 3.0 11.4 1.0
CG B:HIS82 3.1 9.9 1.0
CB B:CYS79 3.2 8.8 1.0
CB B:HIS82 3.3 10.0 1.0
CE B:MET87 3.4 12.6 1.0
CB B:HIS41 3.4 11.2 1.0
CA B:HIS41 3.7 10.4 1.0
CG B:MET87 3.9 9.5 1.0
NE2 B:HIS41 4.1 12.9 1.0
NE2 B:HIS82 4.2 11.4 1.0
CD2 B:HIS41 4.2 12.3 1.0
CD2 B:HIS82 4.2 10.7 1.0
O B:SER40 4.4 19.1 1.0
CB B:MET87 4.4 9.4 1.0
N B:HIS82 4.4 9.4 1.0
CA B:HIS82 4.5 10.0 1.0
CG B:PRO81 4.5 10.2 1.0
N B:ASN42 4.6 10.5 1.0
CA B:CYS79 4.6 8.2 1.0
N B:HIS41 4.7 11.4 1.0
C B:HIS41 4.7 10.5 1.0
C B:SER40 4.9 14.0 1.0
SD B:MET17 4.9 16.4 1.0

Copper binding site 3 out of 3 in 3ef4

Go back to Copper Binding Sites List in 3ef4
Copper binding site 3 out of 3 in the Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Native Pseudoazurin From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu401

b:11.7
occ:1.00
ND1 C:HIS41 2.0 11.2 1.0
ND1 C:HIS82 2.1 11.1 1.0
SG C:CYS79 2.2 10.3 1.0
SD C:MET87 2.6 10.3 1.0
CE1 C:HIS41 3.0 12.6 1.0
CG C:HIS41 3.0 12.2 1.0
CE1 C:HIS82 3.0 11.7 1.0
CG C:HIS82 3.1 10.2 1.0
CB C:CYS79 3.2 9.0 1.0
CB C:HIS82 3.4 10.7 1.0
CB C:HIS41 3.4 11.2 1.0
CE C:MET87 3.4 11.3 1.0
CA C:HIS41 3.7 11.3 1.0
CG C:MET87 3.9 9.5 1.0
NE2 C:HIS41 4.1 13.0 1.0
NE2 C:HIS82 4.2 11.2 1.0
CD2 C:HIS82 4.2 11.3 1.0
CD2 C:HIS41 4.2 13.1 1.0
O C:SER40 4.3 16.2 1.0
CB C:MET87 4.4 9.4 1.0
N C:HIS82 4.4 10.2 1.0
CA C:HIS82 4.5 9.9 1.0
N C:ASN42 4.5 11.2 1.0
CG C:PRO81 4.6 11.9 1.0
CA C:CYS79 4.6 9.0 1.0
N C:HIS41 4.7 11.1 1.0
C C:HIS41 4.7 10.8 1.0
C C:SER40 4.9 13.4 1.0
SD C:MET17 4.9 16.1 1.0

Reference:

D.Hira, M.Nojiri, S.Suzuki. Atomic Resolution Structure of Pseudoazurin From the Methylotrophic Denitrifying Bacterium Hyphomicrobium Denitrificans: Structural Insights Into Its Spectroscopic Properties Acta Crystallogr.,Sect.D V. 65 85 2009.
ISSN: ISSN 0907-4449
PubMed: 19153470
DOI: 10.1107/S0907444908040195
Page generated: Wed Oct 28 14:23:43 2020
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