Magnesium in PDB 4qi3: Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt

The structure of Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt, PDB code: 4qi3 was solved by T.C.Tan, R.Gandini, C.Sygmund, R.Kittl, D.Haltrich, R.Ludwig, B.M.Hallberg, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.06 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.405, 56.357, 73.005, 90.00, 104.56, 90.00
R / Rfree (%)	17.8 / 22.8

The structure of Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Magnesium atom in the Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt (pdb code 4qi3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt, PDB code: 4qi3:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:16.9 occ:0.66 O1A B:HEM602 2.0 27.3 1.0 OE1 A:GLN186 2.0 25.6 1.0 O A:HOH1003 2.1 25.0 1.0 O B:HOH703 2.2 28.8 1.0 O B:HOH702 2.2 21.7 1.0 O A:GLY149 2.3 22.0 1.0 CD A:GLN186 3.2 23.3 1.0 C A:GLY149 3.2 20.5 1.0 CGA B:HEM602 3.2 28.2 1.0 CA A:GLY149 3.8 21.7 1.0 NE2 A:GLN186 4.0 24.4 1.0 CAA B:HEM602 4.0 23.1 1.0 O2A B:HEM602 4.0 31.0 1.0 CB A:GLN186 4.1 19.9 1.0 N A:VAL150 4.1 21.5 1.0 O2D B:HEM602 4.1 20.3 1.0 O B:HOH809 4.2 41.4 1.0 CG A:GLN186 4.2 22.2 1.0 CBA B:HEM602 4.2 26.0 1.0 O A:LEU187 4.2 24.7 1.0 O A:HOH1175 4.3 32.4 1.0 N A:LEU187 4.3 20.0 1.0 CB A:VAL150 4.3 19.9 1.0 O A:GLY148 4.4 24.4 1.0 CA A:GLN186 4.4 18.6 1.0 CA A:VAL150 4.5 20.4 1.0 C A:GLN186 4.9 19.0 1.0 N A:GLY149 5.0 22.3 1.0

Magnesium binding site 2 out of 3 in the Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:15.4 occ:0.58 OE1 B:GLN186 2.0 21.9 1.0 O1A A:HEM401 2.1 26.6 1.0 O B:HOH701 2.1 22.2 1.0 O A:HOH1002 2.2 27.3 1.0 O A:HOH1001 2.2 19.2 1.0 O B:GLY149 2.3 20.3 1.0 CD B:GLN186 3.2 19.6 1.0 C B:GLY149 3.2 19.1 1.0 CGA A:HEM401 3.3 25.9 1.0 CA B:GLY149 3.8 20.5 1.0 NE2 B:GLN186 3.9 21.8 1.0 O2A A:HEM401 4.1 27.6 1.0 CAA A:HEM401 4.1 21.5 1.0 N B:VAL150 4.1 17.8 1.0 CB B:GLN186 4.1 18.6 1.0 O2D A:HEM401 4.2 17.7 1.0 CG B:GLN186 4.2 20.0 1.0 CB B:VAL150 4.2 18.7 1.0 O B:LEU187 4.3 23.0 1.0 N B:LEU187 4.3 18.6 1.0 O B:HOH715 4.3 25.0 1.0 CBA A:HEM401 4.3 23.5 1.0 O B:GLY148 4.4 24.3 1.0 CA B:GLN186 4.4 17.2 1.0 CA B:VAL150 4.5 18.5 1.0 C B:GLN186 4.8 19.2 1.0 N B:GLY149 5.0 21.3 1.0

Magnesium binding site 3 out of 3 in the Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cytochrome Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtcyt within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg608 b:40.3 occ:1.00 O B:HOH864 2.0 43.1 1.0 O B:HOH770 2.1 38.6 1.0 O B:HOH737 2.2 29.6 1.0 O B:HOH796 2.2 46.9 1.0 O B:HOH818 2.3 41.6 1.0 OD2 B:ASP108 3.9 35.2 1.0 OD1 B:ASP108 4.2 30.4 1.0 O B:HOH758 4.2 26.5 1.0 OD1 B:ASN131 4.2 28.2 1.0 O B:HOH744 4.3 26.1 1.0 CG B:ASN131 4.3 27.6 1.0 CG B:ASP108 4.5 32.0 1.0 CB B:ASN131 4.7 25.1 1.0 ND2 B:ASN131 4.7 30.5 1.0

T.C.Tan, D.Kracher, R.Gandini, C.Sygmund, R.Kittl, D.Haltrich, B.M.Hallberg, R.Ludwig, C.Divne. Structural Basis For Cellobiose Dehydrogenase Action During Oxidative Cellulose Degradation. Nat Commun V. 6 7542 2015.
ISSN: ESSN 2041-1723
PubMed: 26151670
DOI: 10.1038/NCOMMS8542