Magnesium in PDB 2i89: Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5

The structure of Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5, PDB code: 2i89 was solved by S.Terzyan, X.C.Zhang, D.R.Benson, L.Wang, N.Sun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.965, 51.409, 167.435, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 27.8

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

Iron

(Fe)

8 atoms

The binding sites of Magnesium atom in the Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 (pdb code 2i89). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5, PDB code: 2i89:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of Septuple Mutant of 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 Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:52.1 occ:1.00 O C:HOH802 2.2 44.5 1.0 O C:HOH803 2.3 38.2 1.0 O B:HOH703 2.4 52.0 1.0 O B:HOH702 2.5 42.3 1.0 O A:HOH454 2.7 38.4 1.0 O B:HOH737 3.8 31.5 1.0 OE2 C:GLU38 3.8 31.5 1.0 O B:HOH730 4.0 31.5 1.0 CG A:GLU69 4.0 20.9 1.0 OE1 C:GLU38 4.0 31.3 1.0 O C:SER37 4.1 25.4 1.0 CB A:GLU69 4.3 20.0 1.0 CD A:GLU69 4.3 21.7 1.0 CD C:GLU38 4.3 30.1 1.0 OE1 A:GLU69 4.3 21.1 1.0 CG B:GLU56 4.4 29.4 1.0 O A:HOH406 4.7 14.9 1.0 OD2 B:ASP53 5.0 17.8 1.0 O B:HOH749 5.0 40.4 1.0 OE2 A:GLU69 5.0 22.8 1.0 OD1 A:ASP66 5.0 25.4 1.0

Magnesium binding site 2 out of 3 in the Structure of Septuple Mutant of 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 Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:74.7 occ:1.00 O B:HOH707 2.3 32.0 1.0 O B:HOH704 2.5 43.8 1.0 O B:HOH706 2.5 46.5 1.0 O B:HOH745 2.6 37.7 1.0 O B:HOH705 2.6 44.9 1.0 O B:GLY62 3.3 33.2 1.0 O B:VAL61 3.6 32.5 1.0 C B:GLY62 4.0 32.9 1.0 O1A B:HEM701 4.0 24.0 0.5 O1D B:HEM701 4.1 18.3 0.5 O1D B:HEM701 4.1 31.6 0.5 CBA B:HEM701 4.3 27.2 0.5 CBD B:HEM701 4.3 28.3 0.5 O1A B:HEM701 4.3 30.5 0.5 CBA B:HEM701 4.6 25.4 0.5 CGA B:HEM701 4.6 25.3 0.5 C B:VAL61 4.6 32.4 1.0 CGD B:HEM701 4.6 29.5 0.5 CA B:GLY62 4.6 32.1 1.0 CG1 B:VAL61 4.7 32.9 1.0 N B:HIS63 4.7 31.3 1.0 CGA B:HEM701 4.7 28.7 0.5 CBD B:HEM701 4.8 21.1 0.5 CGD B:HEM701 4.8 20.4 0.5 O B:HOH748 4.8 36.5 1.0 CA B:HIS63 4.9 30.1 1.0

Magnesium binding site 3 out of 3 in the Structure of Septuple Mutant of 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 Structure of Septuple Mutant of Rat Outer Mitochondrial Membrane Cytochrome B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:50.6 occ:1.00 O A:HOH403 2.3 18.6 1.0 O D:HOH902 2.3 27.1 1.0 O C:HOH804 2.4 52.8 1.0 O A:HOH402 2.4 33.2 1.0 O D:HOH903 2.5 47.0 1.0 O C:HOH805 2.6 46.5 1.0 O D:HOH908 3.6 29.6 1.0 OD2 D:ASP53 4.0 18.6 1.0 OE1 C:GLU69 4.0 29.3 1.0 CG D:ASP53 4.2 19.6 1.0 O D:HOH912 4.4 20.7 1.0 OE2 A:GLU38 4.4 30.6 1.0 CG C:GLU69 4.5 26.7 1.0 OD1 C:ASP66 4.6 23.3 1.0 CB C:GLU69 4.6 24.5 1.0 CD C:GLU69 4.6 27.7 1.0 OE1 A:GLU38 4.6 31.2 1.0 OD1 D:ASP53 4.7 19.5 1.0 CB D:ASP53 4.7 20.9 1.0 O A:SER37 4.8 25.6 1.0 CD A:GLU38 4.9 30.9 1.0

L.Wang, N.Sun, S.Terzyan, X.Zhang, D.R.Benson. A Histidine/Tryptophan Pi-Stacking Interaction Stabilizes the Heme-Independent Folding Core of Microsomal Apocytochrome B5 Relative to That of Mitochondrial Apocytochrome B5. Biochemistry V. 45 13750 2006.
ISSN: ISSN 0006-2960
PubMed: 17105194
DOI: 10.1021/BI0615689