Magnesium in PDB 6ci0: Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

Enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation

All present enzymatic activity of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation:
1.9.3.1;

Protein crystallography data

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation, PDB code: 6ci0 was solved by J.Liu, C.Hiser, S.Ferguson-Miller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.09 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.916, 130.969, 177.788, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 23.4

Other elements in 6ci0:

The structure of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation also contains other interesting chemical elements:

Potassium (K) 1 atom
Cadmium (Cd) 2 atoms
Iron (Fe) 4 atoms
Calcium (Ca) 2 atoms
Copper (Cu) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation (pdb code 6ci0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation, PDB code: 6ci0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6ci0

Go back to Magnesium Binding Sites List in 6ci0
Magnesium binding site 1 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg615

b:37.6
occ:1.00
 O B:HOH413 1.9 50.1 1.0
OD2 A:ASP412 1.9 62.5 1.0
OE1 B:GLU254 2.0 60.8 1.0
O A:HOH788 2.1 50.1 1.0
O A:HOH707 2.2 43.0 1.0
NE2 A:HIS411 2.3 41.7 1.0
CG A:ASP412 3.0 55.1 1.0
CD B:GLU254 3.1 52.8 1.0
CE1 A:HIS411 3.1 37.7 1.0
CD2 A:HIS411 3.4 40.3 1.0
OD1 A:ASP412 3.5 47.4 1.0
OE2 B:GLU254 3.6 46.8 1.0
O A:HOH752 4.0 47.3 1.0
O B:SER253 4.0 44.1 1.0
OD2 B:ASP229 4.1 59.6 1.0
O A:HOH745 4.2 55.8 1.0
ND1 A:HIS411 4.2 37.3 1.0
CG B:GLU254 4.3 38.4 1.0
CB A:ASP412 4.3 46.7 1.0
CG A:HIS411 4.4 43.2 1.0
O A:HOH710 4.4 48.7 1.0
O A:HOH764 4.5 46.2 1.0
OD1 B:ASP229 4.5 48.5 1.0
O B:HOH435 4.5 50.4 1.0
CB B:GLU254 4.5 42.9 1.0
OG1 A:THR337 4.6 47.1 1.0
O A:HOH772 4.6 40.0 1.0
CG B:ASP229 4.7 52.5 1.0
CA B:GLU254 4.8 39.8 1.0
CE2 A:TYR175 4.8 43.7 1.0

Magnesium binding site 2 out of 2 in 6ci0

Go back to Magnesium Binding Sites List in 6ci0
Magnesium binding site 2 out of 2 in the Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Core Subunits (I and II) of Cytochrome C Oxidase From Rhodobacter Sphaeroides with E101A (II) Mutation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg602

b:46.2
occ:1.00
 O C:HOH701 1.8 52.0 1.0
OD1 C:ASP412 1.9 65.9 1.0
OE2 D:GLU254 2.0 72.9 1.0
O D:HOH438 2.1 62.6 1.0
NE2 C:HIS411 2.4 51.2 1.0
O D:HOH412 2.5 52.2 1.0
CG C:ASP412 2.7 61.6 1.0
CD D:GLU254 3.0 70.4 1.0
OD2 C:ASP412 3.0 56.3 1.0
CE1 C:HIS411 3.2 52.9 1.0
CD2 C:HIS411 3.3 51.3 1.0
OE1 D:GLU254 3.4 58.8 1.0
O C:HOH723 3.6 56.1 1.0
O D:SER253 3.8 52.0 1.0
CB C:ASP412 4.0 47.0 1.0
ND1 C:HIS411 4.2 49.0 1.0
CG D:GLU254 4.2 54.7 1.0
CG C:HIS411 4.3 52.7 1.0
OD2 D:ASP229 4.4 67.8 1.0
O C:HOH703 4.4 55.5 1.0
O C:HOH728 4.4 59.9 1.0
CB D:GLU254 4.5 50.0 1.0
OD1 D:ASP229 4.5 59.9 1.0
O C:HOH702 4.5 63.0 1.0
CA D:GLU254 4.7 50.5 1.0
O D:HOH435 4.7 63.5 1.0
OG1 C:THR337 4.9 58.1 1.0
CG D:ASP229 4.9 60.4 1.0
O C:HOH732 4.9 50.9 1.0
C D:SER253 4.9 62.1 1.0
CA C:ASP412 5.0 49.1 1.0
O C:HOH721 5.0 49.5 1.0
CE2 C:TYR175 5.0 69.3 1.0

Reference:

C.Hiser, J.Liu, S.Ferguson-Miller. The K-Path Entrance in Cytochrome C Oxidase Is Defined By Mutation of E101 and Controlled By An Adjacent Ligand Binding Domain. Biochim. Biophys. Acta V.1859 725 2018.
ISSN: ISSN 0006-3002
PubMed: 29626419
DOI: 10.1016/J.BBABIO.2018.03.017
Page generated: Mon Dec 14 22:30:10 2020

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