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Calcium in PDB 1m56: Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

Enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)

All present enzymatic activity of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type):
1.9.3.1;

Protein crystallography data

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56 was solved by M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brezezinski, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 340.360, 340.360, 89.668, 90.00, 90.00, 120.00
R / Rfree (%) 23.6 / 27.5

Other elements in 1m56:

The structure of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms
Copper (Cu) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) (pdb code 1m56). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type), PDB code: 1m56:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1m56

Go back to Calcium Binding Sites List in 1m56
Calcium binding site 1 out of 2 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1007

b:27.6
occ:1.00
O A:ALA57 2.3 26.7 1.0
OE1 A:GLU54 2.3 26.9 1.0
O A:GLU54 2.3 27.9 1.0
O A:GLY59 2.3 24.1 1.0
O A:HOH2061 2.4 22.3 1.0
OE1 A:GLN61 2.7 28.6 1.0
CD A:GLU54 3.5 26.1 1.0
C A:ALA57 3.5 26.0 1.0
C A:GLU54 3.5 27.9 1.0
O A:PRO58 3.6 21.7 1.0
C A:GLY59 3.6 23.0 1.0
C A:PRO58 3.8 22.6 1.0
CD A:GLN61 3.9 26.5 1.0
N A:GLN61 4.1 23.9 1.0
CA A:VAL60 4.1 23.2 1.0
CG A:GLU54 4.2 24.1 1.0
N A:GLY59 4.2 23.5 1.0
CA A:GLU54 4.3 27.8 1.0
N A:PRO58 4.3 25.0 1.0
CA A:PRO58 4.4 23.3 1.0
OE2 A:GLU54 4.4 27.8 1.0
N A:VAL60 4.4 22.5 1.0
CA A:ALA57 4.5 26.4 1.0
N A:LEU55 4.5 26.9 1.0
N A:ALA57 4.5 26.7 1.0
CA A:GLY59 4.6 22.5 1.0
NE2 A:GLN61 4.6 26.7 1.0
CA A:LEU55 4.6 26.6 1.0
C A:VAL60 4.6 24.1 1.0
O A:ILE484 4.7 23.2 1.0
CB A:ALA57 4.7 23.2 1.0
CB A:GLU54 4.8 25.1 1.0
CB A:GLN61 5.0 24.0 1.0
C A:LEU55 5.0 27.0 1.0

Calcium binding site 2 out of 2 in 1m56

Go back to Calcium Binding Sites List in 1m56
Calcium binding site 2 out of 2 in the Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Cytochrome C Oxidase From Rhodobactor Sphaeroides (Wild Type) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1007

b:27.4
occ:1.00
O G:HOH3062 2.3 21.6 1.0
O G:ALA57 2.3 27.3 1.0
OE1 G:GLU54 2.3 26.3 1.0
O G:GLU54 2.3 29.1 1.0
O G:GLY59 2.4 23.6 1.0
OE1 G:GLN61 2.8 28.7 1.0
O G:PRO58 3.4 22.2 1.0
C G:ALA57 3.5 25.9 1.0
C G:GLY59 3.5 23.2 1.0
CD G:GLU54 3.5 26.3 1.0
C G:GLU54 3.6 27.9 1.0
C G:PRO58 3.7 22.9 1.0
CD G:GLN61 4.0 27.0 1.0
N G:GLY59 4.2 24.0 1.0
CA G:VAL60 4.2 23.3 1.0
N G:GLN61 4.2 23.0 1.0
CG G:GLU54 4.3 25.1 1.0
CA G:PRO58 4.3 23.7 1.0
N G:PRO58 4.3 24.8 1.0
CA G:GLU54 4.3 27.7 1.0
N G:VAL60 4.4 22.8 1.0
OE2 G:GLU54 4.4 27.3 1.0
CA G:GLY59 4.5 22.9 1.0
CA G:ALA57 4.5 26.1 1.0
N G:LEU55 4.5 26.5 1.0
CA G:LEU55 4.6 25.9 1.0
O G:ILE484 4.6 23.3 1.0
NE2 G:GLN61 4.6 27.2 1.0
N G:ALA57 4.6 27.0 1.0
CB G:ALA57 4.7 22.8 1.0
C G:VAL60 4.7 24.2 1.0
CB G:GLU54 4.8 25.6 1.0
C G:LEU55 5.0 26.9 1.0

Reference:

M.Svensson-Ek, J.Abramson, G.Larsson, S.Tornroth, P.Brzezinski, S.Iwata. The X-Ray Crystal Structures of Wild-Type and Eq(I-286) Mutant Cytochrome C Oxidases From Rhodobacter Sphaeroides. J.Mol.Biol. V. 321 329 2002.
ISSN: ISSN 0022-2836
PubMed: 12144789
DOI: 10.1016/S0022-2836(02)00619-8
Page generated: Sat Dec 12 03:06:28 2020

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