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Copper in PDB 5b7e: Structure of Perdeuterated Cueo

Protein crystallography data

The structure of Structure of Perdeuterated Cueo, PDB code: 5b7e was solved by M.Akter, Y.Higuchi, N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.20 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.321, 70.416, 134.027, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.3

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Perdeuterated Cueo (pdb code 5b7e). 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 Perdeuterated Cueo, PDB code: 5b7e:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5b7e

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Copper binding site 1 out of 4 in the Structure of Perdeuterated Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Perdeuterated Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu701

b:15.2
occ:1.00
ND1 A:HIS443 2.0 16.6 1.0
ND1 A:HIS505 2.0 15.1 1.0
SG A:CYS500 2.2 14.3 1.0
CE1 A:HIS443 3.0 15.3 1.0
CG A:HIS505 3.0 14.0 1.0
CE1 A:HIS505 3.0 14.8 1.0
CG A:HIS443 3.1 17.1 1.0
CB A:CYS500 3.2 14.2 1.0
SD A:MET510 3.3 16.7 1.0
CB A:HIS505 3.3 14.2 1.0
CB A:HIS443 3.4 16.2 1.0
CA A:HIS443 3.7 13.7 1.0
O A:LEU442 3.7 19.1 1.0
CB A:LEU502 4.0 13.2 1.0
NE2 A:HIS443 4.1 17.2 1.0
CE A:MET510 4.1 19.9 1.0
NE2 A:HIS505 4.1 14.1 1.0
CD2 A:HIS505 4.2 15.4 1.0
CD2 A:HIS443 4.2 17.6 1.0
C A:LEU442 4.4 16.5 1.0
N A:HIS443 4.4 14.5 1.0
CA A:CYS500 4.6 13.6 1.0
CD1 A:LEU502 4.6 13.8 1.0
CG A:MET510 4.7 16.9 1.0
CG A:LEU502 4.8 13.0 1.0
CA A:HIS505 4.9 15.5 1.0
C A:HIS443 4.9 14.8 1.0
O A:LEU502 4.9 13.7 1.0
N A:LEU502 5.0 12.2 1.0

Copper binding site 2 out of 4 in 5b7e

Go back to Copper Binding Sites List in 5b7e
Copper binding site 2 out of 4 in the Structure of Perdeuterated Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Perdeuterated Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu702

b:17.7
occ:0.32
NE2 A:HIS446 2.0 16.8 1.0
NE2 A:HIS101 2.0 18.9 1.0
O A:HOH969 2.7 18.9 1.0
CE1 A:HIS101 2.8 18.8 1.0
CD2 A:HIS446 2.9 17.1 1.0
CE1 A:HIS446 3.0 15.4 1.0
CD2 A:HIS101 3.1 19.1 1.0
CD2 A:HIS448 3.1 15.9 1.0
NE2 A:HIS448 3.2 15.6 1.0
CU2 A:C2O703 3.5 20.1 0.7
CA A:HIS103 3.5 12.3 1.0
CG A:HIS103 3.5 11.6 1.0
ND1 A:HIS103 3.6 12.1 1.0
O1 A:C2O703 3.7 27.7 1.0
CB A:HIS103 3.7 11.5 1.0
CG A:HIS448 3.8 15.1 1.0
CE1 A:HIS448 3.9 16.8 1.0
ND1 A:HIS101 4.0 21.1 1.0
CU3 A:C2O703 4.1 18.4 0.8
ND1 A:HIS446 4.1 15.7 1.0
CG A:HIS446 4.1 15.4 1.0
CD2 A:HIS103 4.1 11.8 1.0
CG A:HIS101 4.1 20.1 1.0
CE1 A:HIS103 4.2 13.4 1.0
ND1 A:HIS448 4.2 18.5 1.0
N A:GLY104 4.2 13.3 1.0
C A:HIS103 4.4 13.4 1.0
NE2 A:HIS103 4.4 13.6 1.0
N A:HIS103 4.4 11.7 1.0
CA A:HIS448 4.6 14.3 1.0
CB A:HIS448 4.7 16.1 1.0
O A:TRP102 4.7 14.8 1.0
O A:HOH989 4.7 18.4 1.0
O A:HOH885 4.8 17.9 1.0
C A:TRP102 4.9 13.0 1.0
NE2 A:HIS499 4.9 15.1 1.0

Copper binding site 3 out of 4 in 5b7e

Go back to Copper Binding Sites List in 5b7e
Copper binding site 3 out of 4 in the Structure of Perdeuterated Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Perdeuterated Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:20.1
occ:0.68
CU2 A:C2O703 0.0 20.1 0.7
NE2 A:HIS448 2.0 15.6 1.0
NE2 A:HIS143 2.0 23.5 1.0
NE2 A:HIS499 2.1 15.1 1.0
O1 A:C2O703 2.2 27.7 1.0
CE1 A:HIS448 2.9 16.8 1.0
CD2 A:HIS143 3.0 22.1 1.0
CE1 A:HIS499 3.0 17.4 1.0
CE1 A:HIS143 3.1 22.5 1.0
CD2 A:HIS448 3.1 15.9 1.0
CD2 A:HIS499 3.2 15.2 1.0
CU A:CU702 3.5 17.7 0.3
CD2 A:HIS446 3.6 17.1 1.0
O A:HOH832 3.6 26.5 1.0
NE2 A:HIS101 3.8 18.9 1.0
CD2 A:HIS101 3.9 19.1 1.0
NE2 A:HIS446 4.0 16.8 1.0
ND1 A:HIS448 4.1 18.5 1.0
ND1 A:HIS499 4.1 15.8 1.0
CG A:HIS143 4.1 19.1 1.0
ND1 A:HIS143 4.1 22.4 1.0
CG A:HIS448 4.2 15.1 1.0
CG A:HIS499 4.2 15.3 1.0
CU3 A:C2O703 4.4 18.4 0.8
CE1 A:HIS101 4.5 18.8 1.0
CG A:HIS101 4.7 20.1 1.0
CE1 A:HIS141 4.7 18.1 1.0
CD2 A:HIS501 4.8 15.1 1.0
CB A:MET497 4.8 16.9 1.0
CG A:HIS446 4.8 15.4 1.0
NE2 A:HIS501 4.8 12.6 1.0
OE2 A:GLU506 4.9 35.5 1.0
ND1 A:HIS101 5.0 21.1 1.0
NE2 A:HIS141 5.0 13.2 1.0

Copper binding site 4 out of 4 in 5b7e

Go back to Copper Binding Sites List in 5b7e
Copper binding site 4 out of 4 in the Structure of Perdeuterated Cueo


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Perdeuterated Cueo within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu703

b:18.4
occ:0.82
CU3 A:C2O703 0.0 18.4 0.8
ND1 A:HIS103 1.9 12.1 1.0
NE2 A:HIS141 2.0 13.2 1.0
NE2 A:HIS501 2.1 12.6 1.0
O1 A:C2O703 2.3 27.7 1.0
CE1 A:HIS103 2.8 13.4 1.0
CE1 A:HIS141 2.9 18.1 1.0
CE1 A:HIS501 3.0 13.3 1.0
CG A:HIS103 3.0 11.6 1.0
CD2 A:HIS141 3.0 13.6 1.0
CD2 A:HIS501 3.1 15.1 1.0
CB A:HIS103 3.4 11.5 1.0
CZ2 A:TRP139 3.7 12.0 1.0
NE2 A:HIS103 4.0 13.6 1.0
CE2 A:TRP139 4.0 11.5 1.0
ND1 A:HIS141 4.1 16.2 1.0
O A:HOH832 4.1 26.5 1.0
CU A:CU702 4.1 17.7 0.3
CD2 A:HIS103 4.1 11.8 1.0
CG A:HIS141 4.1 13.7 1.0
ND1 A:HIS501 4.1 16.5 1.0
NE1 A:TRP139 4.2 11.8 1.0
CD2 A:HIS101 4.2 19.1 1.0
CG A:HIS501 4.2 14.3 1.0
CU2 A:C2O703 4.4 20.1 0.7
CD2 A:HIS446 4.4 17.1 1.0
NE2 A:HIS446 4.4 16.8 1.0
CH2 A:TRP139 4.4 12.1 1.0
NE2 A:HIS101 4.5 18.9 1.0
CA A:HIS103 4.7 12.3 1.0

Reference:

M.Akter, C.Inoue, H.Komori, N.Matsuda, T.Sakurai, K.Kataoka, Y.Higuchi, N.Shibata. Biochemical, Spectroscopic and X-Ray Structural Analysis of Deuterated Multicopper Oxidase Cueo Prepared From A New Expression Construct For Neutron Crystallography Acta Crystallogr.,Sect.F V. 72 788 2016.
ISSN: ESSN 2053-230X
PubMed: 27710945
DOI: 10.1107/S2053230X1601400X
Page generated: Sun Dec 13 11:17:08 2020

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