Magnesium in PDB 1icc: Rat Outer Mitochondrial Membrane Cytochrome B5

The structure of Rat Outer Mitochondrial Membrane Cytochrome B5, PDB code: 1icc was solved by S.Terzyan, X.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.904, 51.315, 167.419, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24

The structure of Rat Outer Mitochondrial Membrane Cytochrome B5 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Rat Outer Mitochondrial Membrane Cytochrome B5 (pdb code 1icc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Rat Outer Mitochondrial Membrane Cytochrome B5, PDB code: 1icc:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Rat Outer Mitochondrial Membrane Cytochrome B5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg88 b:38.0 occ:1.00 O B:HOH203 2.2 31.2 1.0 O C:HOH203 2.2 32.6 1.0 O A:HOH202 2.3 33.3 1.0 O C:HOH202 2.3 39.8 1.0 O B:HOH202 2.3 37.6 1.0 O C:HOH204 2.4 34.0 1.0 O B:HOH236 3.2 60.4 1.0 O B:HOH216 3.9 33.4 1.0 OE2 C:GLU38 4.2 40.5 1.0 OE1 A:GLU69 4.3 31.4 1.0 OD2 B:ASP53 4.3 22.5 1.0 O B:HOH220 4.3 33.4 1.0 O C:SER37 4.4 40.2 1.0 CG B:ASP53 4.5 21.1 1.0 OE1 C:GLU38 4.5 39.2 1.0 O A:HOH266 4.6 40.6 1.0 OD1 A:ASP66 4.6 32.9 1.0 CB A:GLU69 4.7 26.6 1.0 CG A:GLU69 4.7 27.3 1.0 CD A:GLU69 4.7 31.2 1.0 CD C:GLU38 4.8 41.6 1.0 OD1 B:ASP53 4.8 20.7 1.0 CG B:GLU56 4.9 34.2 1.0 CB B:ASP53 4.9 22.6 1.0

Magnesium binding site 2 out of 3 in the Rat Outer Mitochondrial Membrane Cytochrome B5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg89 b:34.7 occ:1.00 O A:HOH205 2.1 24.6 1.0 O A:HOH210 2.1 23.9 1.0 O A:HOH208 2.1 29.7 1.0 O A:HOH207 2.3 33.4 1.0 O A:HOH209 2.3 27.0 1.0 O A:HOH206 2.3 40.3 1.0 O A:HOH299 4.0 54.1 1.0 NH2 A:ARG15 4.1 17.5 1.0 O A:HOH235 4.1 27.7 1.0 OE2 A:GLU20 4.2 23.8 1.0 OE1 A:GLU20 4.3 22.0 1.0 O A:HOH219 4.3 25.9 1.0 O A:HOH309 4.5 61.3 1.0 O A:HOH257 4.7 25.6 1.0 CD A:GLU20 4.7 23.6 1.0

Magnesium binding site 3 out of 3 in the Rat Outer Mitochondrial Membrane Cytochrome B5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg88 b:32.8 occ:1.00 O C:HOH206 2.2 31.8 1.0 O D:HOH202 2.3 28.6 1.0 O C:HOH205 2.3 23.9 1.0 O A:HOH204 2.3 35.1 1.0 O D:HOH203 2.3 25.2 1.0 O A:HOH203 2.3 28.8 1.0 OE1 C:GLU69 3.7 32.1 1.0 O D:HOH226 3.8 33.0 1.0 O D:HOH228 4.0 37.2 1.0 O D:HOH242 4.0 34.7 1.0 OD2 D:ASP53 4.1 20.6 1.0 O D:HOH214 4.1 23.4 1.0 CD C:GLU69 4.4 33.3 1.0 OE2 A:GLU38 4.4 29.4 1.0 CG D:ASP53 4.4 23.2 1.0 O C:HOH213 4.4 24.4 1.0 OE1 A:GLU38 4.4 28.8 1.0 O A:SER37 4.4 25.1 1.0 CG C:GLU69 4.5 30.2 1.0 CB C:GLU69 4.6 25.8 1.0 OD1 C:ASP66 4.7 24.3 1.0 CB D:ASP53 4.8 22.9 1.0 CD A:GLU38 4.8 29.5 1.0 OD1 D:ASP53 4.8 23.8 1.0

A.Altuve, S.Silchenko, K.H.Lee, K.Kuczera, S.Terzyan, X.Zhang, D.R.Benson, M.Rivera. Probing the Differences Between Rat Liver Outer Mitochondrial Membrane Cytochrome B5 and Microsomal Cytochromes B5. Biochemistry V. 40 9469 2001.
ISSN: ISSN 0006-2960
PubMed: 11583146
DOI: 10.1021/BI010636I