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Copper in PDB 5luf: Cryo-Em of Bovine Respirasome

Enzymatic activity of Cryo-Em of Bovine Respirasome

All present enzymatic activity of Cryo-Em of Bovine Respirasome:
1.10.2.2; 1.9.3.1;

Other elements in 5luf:

The structure of Cryo-Em of Bovine Respirasome also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Zinc (Zn) 1 atom
Iron (Fe) 38 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Cryo-Em of Bovine Respirasome (pdb code 5luf). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Cryo-Em of Bovine Respirasome, PDB code: 5luf:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 5luf

Go back to Copper Binding Sites List in 5luf
Copper binding site 1 out of 3 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
x:Cu601

b:15.3
occ:1.00
ND1 x:HIS240 1.9 26.2 1.0
NE2 x:HIS291 2.2 7.0 1.0
NE2 x:HIS290 2.2 7.0 1.0
CE1 x:HIS240 2.6 27.2 1.0
CD2 x:HIS291 3.0 18.9 1.0
CG x:HIS240 3.1 18.8 1.0
CE1 x:HIS290 3.1 7.0 1.0
CE1 x:HIS291 3.2 23.1 1.0
CD2 x:HIS290 3.2 17.6 1.0
CB x:HIS240 3.6 11.4 1.0
NE2 x:HIS240 3.9 7.0 1.0
CD2 x:HIS240 4.1 15.7 1.0
CG x:HIS291 4.1 20.1 1.0
CA x:HIS240 4.2 13.6 1.0
ND1 x:HIS291 4.2 23.8 1.0
ND1 x:HIS290 4.2 7.9 1.0
CG x:HIS290 4.3 14.5 1.0
NA x:HEA604 4.4 14.8 1.0
C1A x:HEA604 4.5 7.0 1.0
C4A x:HEA604 4.7 14.3 1.0
FE x:HEA604 4.7 8.0 1.0
C2A x:HEA604 4.9 7.0 1.0
C3A x:HEA604 4.9 7.0 1.0
CHA x:HEA604 4.9 8.6 1.0

Copper binding site 2 out of 3 in 5luf

Go back to Copper Binding Sites List in 5luf
Copper binding site 2 out of 3 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
y:Cu301

b:25.9
occ:1.00
ND1 y:HIS161 1.9 7.0 1.0
SG y:CYS196 2.3 10.8 1.0
SG y:CYS200 2.3 10.4 1.0
CU y:CU302 2.4 13.4 1.0
SD y:MET207 2.5 14.2 1.0
CE1 y:HIS161 2.6 7.0 1.0
CG y:HIS161 3.1 7.0 1.0
CE y:MET207 3.2 10.6 1.0
CB y:CYS200 3.3 11.0 1.0
CB y:CYS196 3.5 17.1 1.0
CB y:HIS161 3.7 7.0 1.0
CG y:MET207 3.7 10.4 1.0
O y:GLU198 3.8 20.2 1.0
NE2 y:HIS161 3.9 7.0 1.0
CD2 y:HIS161 4.1 7.0 1.0
CA y:HIS161 4.1 7.0 1.0
ND1 y:HIS204 4.2 16.2 1.0
O y:LEU160 4.6 7.0 1.0
CA y:CYS200 4.7 10.1 1.0
O y:HIS204 4.8 17.7 1.0
CA y:CYS196 4.8 8.4 1.0
N y:CYS200 4.9 16.8 1.0
CA y:HIS204 5.0 9.2 1.0
CD1 y:TRP104 5.0 16.1 1.0

Copper binding site 3 out of 3 in 5luf

Go back to Copper Binding Sites List in 5luf
Copper binding site 3 out of 3 in the Cryo-Em of Bovine Respirasome


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Cryo-Em of Bovine Respirasome within 5.0Å range:
probe atom residue distance (Å) B Occ
y:Cu302

b:13.4
occ:1.00
ND1 y:HIS204 1.9 16.2 1.0
O y:GLU198 2.2 20.2 1.0
SG y:CYS200 2.2 10.4 1.0
SG y:CYS196 2.3 10.8 1.0
CU y:CU301 2.4 25.9 1.0
CE1 y:HIS204 2.8 19.0 1.0
CG y:HIS204 3.0 9.0 1.0
CB y:CYS200 3.3 11.0 1.0
C y:GLU198 3.4 11.5 1.0
CB y:CYS196 3.4 17.1 1.0
CB y:HIS204 3.5 12.8 1.0
N y:CYS200 3.6 16.8 1.0
CA y:HIS204 3.6 9.2 1.0
O y:HIS204 3.6 17.7 1.0
NE2 y:HIS204 3.9 10.2 1.0
C y:HIS204 4.0 10.3 1.0
ND1 y:HIS161 4.1 7.0 1.0
CD2 y:HIS204 4.1 11.1 1.0
CA y:CYS200 4.1 10.1 1.0
SD y:MET207 4.1 14.2 1.0
C y:ILE199 4.1 12.8 1.0
CA y:ILE199 4.3 11.1 1.0
N y:ILE199 4.3 13.2 1.0
N y:GLU198 4.3 16.7 1.0
CA y:GLU198 4.4 8.4 1.0
O y:CYS196 4.5 15.9 1.0
CG y:MET207 4.5 10.4 1.0
C y:CYS196 4.6 14.1 1.0
CE1 y:HIS161 4.7 7.0 1.0
CA y:CYS196 4.7 8.4 1.0
N y:HIS204 4.9 15.7 1.0
C y:CYS200 4.9 7.5 1.0
O y:ILE199 4.9 8.4 1.0

Reference:

J.S.Sousa, D.J.Mills, J.Vonck, W.Kuhlbrandt. Functional Asymmetry and Electron Flow in the Bovine Respirasome. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27830641
DOI: 10.7554/ELIFE.21290
Page generated: Sun Dec 13 11:18:33 2020

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