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Copper in PDB 5b7f: Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease

Protein crystallography data

The structure of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease, PDB code: 5b7f 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) 35.11 / 1.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.513, 88.786, 53.951, 90.00, 94.24, 90.00
R / Rfree (%) 15.3 / 18.1

Other elements in 5b7f:

The structure of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease (pdb code 5b7f). 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 Cueo - the Signal Peptide Was Truncated By HRV3C Protease, PDB code: 5b7f:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 5b7f

Go back to Copper Binding Sites List in 5b7f
Copper binding site 1 out of 4 in the Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:10.1
occ:1.00
ND1 A:HIS505 2.0 10.0 1.0
ND1 A:HIS443 2.1 8.7 1.0
SG A:CYS500 2.2 9.0 1.0
CE1 A:HIS443 3.0 10.9 1.0
CE1 A:HIS505 3.0 11.2 1.0
CG A:HIS505 3.0 7.7 1.0
CG A:HIS443 3.1 8.3 1.0
SD A:MET510 3.2 10.1 1.0
CB A:CYS500 3.2 9.0 1.0
CB A:HIS505 3.4 8.3 1.0
CB A:HIS443 3.5 8.3 1.0
CA A:HIS443 3.7 8.4 1.0
O A:LEU442 3.9 12.6 1.0
CE A:MET510 3.9 14.3 1.0
CB A:LEU502 4.1 7.9 1.0
NE2 A:HIS505 4.1 10.7 1.0
NE2 A:HIS443 4.1 12.1 1.0
CD2 A:HIS505 4.2 8.4 1.0
CD2 A:HIS443 4.2 10.7 1.0
N A:HIS443 4.5 8.6 1.0
C A:LEU442 4.5 11.9 1.0
CA A:CYS500 4.6 8.9 1.0
CG A:MET510 4.7 9.1 1.0
CD1 A:LEU502 4.7 9.6 1.0
CA A:HIS505 4.9 9.5 1.0
O A:LEU502 4.9 8.4 1.0
CG A:LEU502 4.9 7.5 1.0
C A:HIS443 4.9 9.7 1.0
N A:LEU502 5.0 9.1 1.0

Copper binding site 2 out of 4 in 5b7f

Go back to Copper Binding Sites List in 5b7f
Copper binding site 2 out of 4 in the Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu602

b:15.8
occ:0.29
NE2 A:HIS446 1.7 10.2 1.0
NE2 A:HIS101 1.7 11.7 1.0
CD2 A:HIS446 2.5 10.6 1.0
CD2 A:HIS101 2.7 12.2 1.0
CE1 A:HIS101 2.7 12.9 1.0
CE1 A:HIS446 2.8 10.2 1.0
O A:HOH1043 3.1 13.3 1.0
O A:HOH843 3.2 14.3 1.0
NE2 A:HIS448 3.3 9.6 1.0
CD2 A:HIS448 3.3 9.9 1.0
ND1 A:HIS103 3.5 9.9 1.0
CG A:HIS103 3.5 7.2 1.0
CU A:CU603 3.5 18.1 0.4
CA A:HIS103 3.7 7.7 1.0
CG A:HIS446 3.7 9.1 1.0
CB A:HIS103 3.8 7.7 1.0
ND1 A:HIS101 3.8 11.8 1.0
CG A:HIS101 3.8 10.5 1.0
ND1 A:HIS446 3.8 10.4 1.0
CE1 A:HIS448 3.9 11.8 1.0
CG A:HIS448 3.9 10.3 1.0
CE1 A:HIS103 4.0 11.0 1.0
CU A:CU604 4.0 13.2 0.6
CD2 A:HIS103 4.0 9.3 1.0
ND1 A:HIS448 4.2 13.8 1.0
NE2 A:HIS103 4.3 9.8 1.0
N A:GLY104 4.5 8.7 1.0
C A:HIS103 4.6 10.2 1.0
N A:HIS103 4.6 8.8 1.0
NE2 A:HIS499 4.7 11.7 1.0
CA A:HIS448 4.8 9.8 1.0
NE2 A:HIS141 4.9 9.5 1.0
CB A:HIS448 4.9 11.0 1.0
O A:TRP102 4.9 10.1 1.0
NE2 A:HIS143 5.0 23.1 1.0

Copper binding site 3 out of 4 in 5b7f

Go back to Copper Binding Sites List in 5b7f
Copper binding site 3 out of 4 in the Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu603

b:18.1
occ:0.43
NE2 A:HIS448 1.9 9.6 1.0
NE2 A:HIS499 1.9 11.7 1.0
NE2 A:HIS143 2.0 23.1 1.0
O A:HOH1043 2.3 13.3 1.0
CE1 A:HIS448 2.7 11.8 1.0
CE1 A:HIS499 2.8 11.8 1.0
CD2 A:HIS143 2.9 21.0 1.0
CD2 A:HIS499 2.9 10.5 1.0
CE1 A:HIS143 3.0 20.6 1.0
CD2 A:HIS448 3.1 9.9 1.0
CU A:CU602 3.5 15.8 0.3
CD2 A:HIS446 3.5 10.6 1.0
O A:HOH765 3.7 31.3 1.0
NE2 A:HIS101 3.9 11.7 1.0
CD2 A:HIS101 3.9 12.2 1.0
ND1 A:HIS448 3.9 13.8 1.0
ND1 A:HIS499 3.9 10.2 1.0
CG A:HIS499 4.0 9.7 1.0
CG A:HIS143 4.0 16.7 1.0
NE2 A:HIS446 4.1 10.2 1.0
ND1 A:HIS143 4.1 20.6 1.0
CG A:HIS448 4.1 10.3 1.0
CE1 A:HIS101 4.5 12.9 1.0
CB A:MET497 4.5 11.4 1.0
CG A:HIS101 4.6 10.5 1.0
CG A:HIS446 4.7 9.1 1.0
CU A:CU604 4.8 13.2 0.6
ND1 A:HIS101 4.9 11.8 1.0
CD2 A:HIS501 5.0 12.4 1.0
OE1 A:GLU506 5.0 23.1 1.0

Copper binding site 4 out of 4 in 5b7f

Go back to Copper Binding Sites List in 5b7f
Copper binding site 4 out of 4 in the Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu604

b:13.2
occ:0.58
ND1 A:HIS103 1.9 9.9 1.0
NE2 A:HIS141 1.9 9.5 1.0
NE2 A:HIS501 2.1 14.6 1.0
O A:HOH1043 2.6 13.3 1.0
CE1 A:HIS103 2.7 11.0 1.0
CE1 A:HIS141 2.8 11.6 1.0
CD2 A:HIS141 3.0 8.7 1.0
CG A:HIS103 3.0 7.2 1.0
CD2 A:HIS501 3.1 12.4 1.0
CE1 A:HIS501 3.1 15.5 1.0
CB A:HIS103 3.6 7.7 1.0
CZ2 A:TRP139 3.6 8.0 1.0
NE2 A:HIS103 3.8 9.8 1.0
ND1 A:HIS141 3.9 9.2 1.0
CE2 A:TRP139 4.0 8.0 1.0
CU A:CU602 4.0 15.8 0.3
CG A:HIS141 4.0 8.5 1.0
CD2 A:HIS103 4.0 9.3 1.0
NE1 A:TRP139 4.1 7.8 1.0
CD2 A:HIS101 4.1 12.2 1.0
ND1 A:HIS501 4.2 13.4 1.0
CG A:HIS501 4.2 10.1 1.0
O A:HOH765 4.2 31.3 1.0
CD2 A:HIS446 4.3 10.6 1.0
CH2 A:TRP139 4.3 8.2 1.0
NE2 A:HIS446 4.4 10.2 1.0
NE2 A:HIS101 4.5 11.7 1.0
CU A:CU603 4.8 18.1 0.4
CA A:HIS103 4.8 7.7 1.0
O A:HOH786 5.0 11.4 1.0
CD2 A:TRP139 5.0 6.9 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 11:17:11 2020

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