Atomistry » Copper » PDB 2xv2-2z7w » 2ybb
Atomistry »
  Copper »
    PDB 2xv2-2z7w »
      2ybb »

Copper in PDB 2ybb: Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

Enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)

All present enzymatic activity of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876):
1.10.2.2; 1.6.5.3; 1.6.99.5; 1.9.3.1;

Other elements in 2ybb:

The structure of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms
Calcium (Ca) 1 atom
Iron (Fe) 45 atoms
Zinc (Zn) 1 atom

Copper Binding Sites:

The binding sites of Copper atom in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) (pdb code 2ybb). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876), PDB code: 2ybb:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 2ybb

Go back to Copper Binding Sites List in 2ybb
Copper binding site 1 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cu517

b:15.3
occ:1.00
ND1 L:HIS240 1.9 26.2 1.0
NE2 L:HIS291 2.2 7.0 1.0
NE2 L:HIS290 2.2 7.0 1.0
CE1 L:HIS240 2.6 27.2 1.0
CD2 L:HIS291 3.0 18.9 1.0
CG L:HIS240 3.1 18.8 1.0
CE1 L:HIS290 3.1 7.0 1.0
CE1 L:HIS291 3.2 23.1 1.0
CD2 L:HIS290 3.2 17.6 1.0
CB L:HIS240 3.6 11.4 1.0
NE2 L:HIS240 3.9 7.0 1.0
CD2 L:HIS240 4.1 15.7 1.0
CG L:HIS291 4.2 20.1 1.0
CA L:HIS240 4.2 13.6 1.0
ND1 L:HIS291 4.2 23.8 1.0
ND1 L:HIS290 4.2 7.9 1.0
CG L:HIS290 4.3 14.5 1.0
NA L:HEA516 4.4 14.8 1.0
C1A L:HEA516 4.5 7.0 1.0
C4A L:HEA516 4.7 14.3 1.0
FE L:HEA516 4.7 8.0 1.0
C2A L:HEA516 4.9 7.0 1.0
C3A L:HEA516 4.9 7.0 1.0
CHA L:HEA516 4.9 8.6 1.0

Copper binding site 2 out of 3 in 2ybb

Go back to Copper Binding Sites List in 2ybb
Copper binding site 2 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cu228

b:25.9
occ:1.00
ND1 M:HIS161 1.9 7.0 1.0
SG M:CYS196 2.3 10.8 1.0
SG M:CYS200 2.3 10.4 1.0
CU M:CU229 2.4 13.4 1.0
SD M:MET207 2.5 14.2 1.0
CE1 M:HIS161 2.6 7.0 1.0
CG M:HIS161 3.1 7.0 1.0
CE M:MET207 3.2 10.6 1.0
CB M:CYS200 3.3 11.0 1.0
CB M:CYS196 3.5 17.1 1.0
CB M:HIS161 3.7 7.0 1.0
CG M:MET207 3.7 10.4 1.0
O M:GLU198 3.8 20.2 1.0
NE2 M:HIS161 3.9 7.0 1.0
CD2 M:HIS161 4.1 7.0 1.0
CA M:HIS161 4.1 7.0 1.0
ND1 M:HIS204 4.2 16.2 1.0
O M:LEU160 4.6 7.0 1.0
CA M:CYS200 4.7 10.1 1.0
O M:HIS204 4.8 17.7 1.0
CA M:CYS196 4.8 8.4 1.0
N M:CYS200 4.9 16.8 1.0
CA M:HIS204 5.0 9.2 1.0
CD1 M:TRP104 5.0 16.1 1.0

Copper binding site 3 out of 3 in 2ybb

Go back to Copper Binding Sites List in 2ybb
Copper binding site 3 out of 3 in the Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876)


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Fitted Model For Bovine Mitochondrial Supercomplex I1III2IV1 By Single Particle Cryo-Em (Emd-1876) within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Cu229

b:13.4
occ:1.00
ND1 M:HIS204 1.9 16.2 1.0
O M:GLU198 2.2 20.2 1.0
SG M:CYS200 2.2 10.4 1.0
SG M:CYS196 2.3 10.8 1.0
CU M:CU228 2.4 25.9 1.0
CE1 M:HIS204 2.8 19.0 1.0
CG M:HIS204 3.0 9.0 1.0
CB M:CYS200 3.3 11.0 1.0
C M:GLU198 3.4 11.5 1.0
CB M:CYS196 3.4 17.1 1.0
CB M:HIS204 3.5 12.8 1.0
N M:CYS200 3.6 16.8 1.0
CA M:HIS204 3.6 9.2 1.0
O M:HIS204 3.6 17.7 1.0
NE2 M:HIS204 3.9 10.2 1.0
C M:HIS204 4.0 10.3 1.0
ND1 M:HIS161 4.1 7.0 1.0
CD2 M:HIS204 4.1 11.1 1.0
CA M:CYS200 4.1 10.1 1.0
SD M:MET207 4.1 14.2 1.0
C M:ILE199 4.1 12.8 1.0
CA M:ILE199 4.3 11.1 1.0
N M:ILE199 4.3 13.2 1.0
N M:GLU198 4.3 16.7 1.0
CA M:GLU198 4.4 8.4 1.0
O M:CYS196 4.5 15.9 1.0
CG M:MET207 4.5 10.4 1.0
C M:CYS196 4.6 14.1 1.0
CE1 M:HIS161 4.7 7.0 1.0
CA M:CYS196 4.7 8.4 1.0
N M:HIS204 4.9 15.7 1.0
C M:CYS200 4.9 7.5 1.0
O M:ILE199 4.9 8.4 1.0

Reference:

T.Althoff, D.J.Mills, J.-L.Popot, W.Kuehlbrandt. Arrangement of Electron Transport Chain Components in Bovine Mitochondrial Supercomplex I(1)III(2)IV(1). Embo J. V. 30 4652 2011.
ISSN: ISSN 0261-4189
PubMed: 21909073
DOI: 10.1038/EMBOJ.2011.324
Page generated: Sun Dec 13 11:08:10 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy