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Copper in PDB 5ndc: Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography

Enzymatic activity of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography

All present enzymatic activity of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography:
1.9.3.1;

Protein crystallography data

The structure of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography, PDB code: 5ndc was solved by R.Andersson, C.Safari, R.Dods, E.Nango, R.Tanaka, T.Nakane, K.Tono, Y.Joti, P.Bath, E.Dunevall, E.Bosman, O.Nureki, S.Iwata, R.Neutze, G.Branden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.40 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 145.850, 100.320, 96.620, 90.00, 126.76, 90.00
R / Rfree (%) 16.2 / 19.7

Other elements in 5ndc:

The structure of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography (pdb code 5ndc). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography, PDB code: 5ndc:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5ndc

Go back to Copper Binding Sites List in 5ndc
Copper binding site 1 out of 3 in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu601

b:35.5
occ:1.00
 NE2 A:HIS283 2.0 38.3 1.0
ND1 A:HIS233 2.0 37.9 1.0
NE2 A:HIS282 2.0 39.8 1.0
O A:HOH752 2.3 18.6 1.0
CG A:HIS233 2.9 38.4 1.0
CE1 A:HIS283 2.9 37.8 1.0
CE1 A:HIS282 3.0 39.8 1.0
CD2 A:HIS283 3.0 37.6 1.0
CD2 A:HIS282 3.0 39.1 1.0
CE1 A:HIS233 3.0 38.6 1.0
CB A:HIS233 3.2 37.5 1.0
CA A:HIS233 3.7 37.9 1.0
ND1 A:HIS283 4.0 36.2 1.0
CD2 A:HIS233 4.1 38.8 1.0
CG A:HIS283 4.1 37.7 1.0
ND1 A:HIS282 4.1 38.5 1.0
NE2 A:HIS233 4.1 40.9 1.0
CG A:HIS282 4.1 38.0 1.0
C1D A:HAS603 4.3 36.0 1.0
ND A:HAS603 4.4 35.9 1.0
C4D A:HAS603 4.5 33.9 1.0
N A:HIS233 4.6 39.3 1.0
C2D A:HAS603 4.6 35.1 1.0
C A:HIS233 4.7 38.0 1.0
C3D A:HAS603 4.7 34.5 1.0
O A:HIS233 4.8 37.2 1.0
CHB A:HAS603 4.8 35.8 1.0
O A:GLY232 4.8 37.1 1.0
FE A:HAS603 4.8 36.1 1.0

Copper binding site 2 out of 3 in 5ndc

Go back to Copper Binding Sites List in 5ndc
Copper binding site 2 out of 3 in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:33.0
occ:1.00
 CU1 B:CUA201 0.0 33.0 1.0
ND1 B:HIS157 1.9 35.1 1.0
SG B:CYS153 2.3 36.5 1.0
SG B:CYS149 2.3 36.6 1.0
O B:GLN151 2.5 38.2 1.0
CU2 B:CUA201 2.6 32.4 1.0
CE1 B:HIS157 2.8 33.4 1.0
CG B:HIS157 3.0 34.8 1.0
CB B:CYS153 3.4 37.6 1.0
CB B:CYS149 3.4 37.3 1.0
CB B:HIS157 3.5 35.4 1.0
C B:GLN151 3.6 36.4 1.0
N B:CYS153 3.6 38.3 1.0
CA B:HIS157 3.8 35.3 1.0
NE2 B:HIS157 3.9 35.6 1.0
CD2 B:HIS157 4.1 35.4 1.0
O B:CYS149 4.1 36.8 1.0
CA B:CYS153 4.1 37.4 1.0
O B:HIS157 4.1 34.9 1.0
C B:TYR152 4.2 38.2 1.0
CA B:TYR152 4.2 37.3 1.0
N B:TYR152 4.3 36.1 1.0
C B:CYS149 4.3 37.2 1.0
C B:HIS157 4.4 34.8 1.0
N B:GLN151 4.4 36.5 1.0
ND1 B:HIS114 4.4 37.8 1.0
SD B:MET160 4.5 36.6 1.0
CA B:CYS149 4.5 37.1 1.0
CA B:GLN151 4.6 36.7 1.0
CB B:MET160 5.0 37.4 1.0

Copper binding site 3 out of 3 in 5ndc

Go back to Copper Binding Sites List in 5ndc
Copper binding site 3 out of 3 in the Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of BA3-Type Cytochrome C Oxidase From Thermus Thermophilus By Serial Femtosecond Crystallography within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu201

b:32.4
occ:1.00
 CU2 B:CUA201 0.0 32.4 1.0
ND1 B:HIS114 2.1 37.8 1.0
SG B:CYS153 2.3 36.5 1.0
SG B:CYS149 2.3 36.6 1.0
SD B:MET160 2.4 36.6 1.0
CU1 B:CUA201 2.6 33.0 1.0
CE1 B:HIS114 3.0 38.4 1.0
CG B:HIS114 3.1 38.2 1.0
CE B:MET160 3.2 37.2 1.0
CB B:CYS153 3.3 37.6 1.0
CB B:CYS149 3.4 37.3 1.0
CB B:HIS114 3.4 38.6 1.0
CG B:MET160 3.8 37.7 1.0
CA B:HIS114 4.0 36.8 1.0
O B:GLN151 4.2 38.2 1.0
NE2 B:HIS114 4.2 39.9 1.0
CD2 B:HIS114 4.2 37.6 1.0
CB B:MET160 4.3 37.4 1.0
ND1 B:HIS157 4.5 35.1 1.0
CA B:CYS153 4.7 37.4 1.0
CA B:CYS149 4.7 37.1 1.0
O B:ILE113 4.7 40.3 1.0
N B:GLY115 4.7 38.2 1.0
CD1 B:PHE88 4.8 37.4 1.0
C B:HIS114 5.0 37.2 1.0
N B:CYS153 5.0 38.3 1.0

Reference:

R.Andersson, C.Safari, R.Dods, E.Nango, R.Tanaka, A.Yamashita, T.Nakane, K.Tono, Y.Joti, P.Bath, E.Dunevall, R.Bosman, O.Nureki, S.Iwata, R.Neutze, G.Branden. Serial Femtosecond Crystallography Structure of Cytochrome C Oxidase at Room Temperature. Sci Rep V. 7 4518 2017.
ISSN: ESSN 2045-2322
PubMed: 28674417
DOI: 10.1038/S41598-017-04817-Z
Page generated: Mon Jul 14 05:04:53 2025

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