Cadmium in PDB 4qi4: Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh

The structure of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh, PDB code: 4qi4 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)	44.32 / 2.70
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	171.755, 171.755, 72.030, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 23.2

The binding sites of Cadmium atom in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh (pdb code 4qi4). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh, PDB code: 4qi4:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd907 b:0.2 occ:1.00 OD2 A:ASP339 2.1 0.3 1.0 CG A:ASP339 2.9 0.1 1.0 OD1 A:ASP339 3.3 0.6 1.0 CB A:ASP339 4.2 63.5 1.0

Cadmium binding site 2 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd908 b:0.0 occ:1.00 OE2 A:GLU456 2.1 70.0 1.0 OE1 A:GLU456 2.2 0.5 1.0 NZ A:LYS508 2.2 79.6 1.0 CD A:GLU456 2.5 97.3 1.0 NZ A:LYS441 3.3 0.5 1.0 CE A:LYS508 3.4 0.1 1.0 CE A:LYS441 3.4 0.5 1.0 CG A:GLU456 4.0 69.5 1.0 CD A:LYS441 4.6 0.3 1.0 CB A:GLU456 4.8 85.8 1.0 CD A:LYS508 4.8 94.1 1.0

Cadmium binding site 3 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd909 b:88.4 occ:1.00 SG A:CYS291 2.9 73.4 1.0 O A:CYS291 3.3 94.5 1.0 OD1 A:ASN292 3.6 0.8 1.0 O A:VAL320 3.7 0.0 1.0 C A:CYS291 3.8 91.7 1.0 N A:ALA322 3.8 59.0 1.0 NE1 A:TRP295 3.9 0.3 1.0 C A:ASN321 4.0 81.0 1.0 CA A:ALA322 4.2 59.0 1.0 CB A:CYS291 4.2 58.7 1.0 CA A:ASN321 4.3 73.2 1.0 CB A:ALA322 4.3 51.0 1.0 CD1 A:TRP295 4.4 0.7 1.0 O A:ASN321 4.4 78.8 1.0 CG2 A:ILE294 4.4 54.9 1.0 CA A:CYS291 4.5 90.3 1.0 N A:ASN292 4.5 93.0 1.0 CA A:ASN292 4.5 81.2 1.0 C7M A:FAD901 4.6 79.5 1.0 CG A:ASN292 4.7 98.3 1.0 C A:VAL320 4.8 76.2 1.0 C6 A:FAD901 4.9 90.8 1.0 CE2 A:TRP295 5.0 0.2 1.0

Cadmium binding site 4 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd910 b:0.0 occ:1.00 NE2 A:HIS405 2.9 96.0 1.0 CD2 A:HIS405 3.7 88.5 1.0 CE1 A:HIS405 3.9 85.7 1.0 CE1 A:PHE375 3.9 85.4 1.0 NH1 A:ARG369 4.4 87.5 1.0 NZ A:LYS368 4.5 0.1 1.0 CZ A:PHE375 4.5 83.8 1.0 CD1 A:PHE375 4.6 86.3 1.0 CG A:HIS405 4.9 90.1 1.0 ND1 A:HIS405 4.9 92.4 1.0

Cadmium binding site 5 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd911 b:0.4 occ:0.37 OE1 A:GLU783 2.4 97.5 1.0 OE2 A:GLU783 2.9 83.5 1.0 CD A:GLU783 3.0 0.1 1.0 NE1 A:TRP802 4.2 0.1 1.0 CG A:GLU783 4.5 0.7 1.0 CD1 A:TRP802 4.6 0.4 1.0

Cadmium binding site 6 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd912 b:0.9 occ:1.00 OE2 A:GLU304 2.1 0.4 1.0 NZ A:LYS299 2.9 0.4 1.0 CE A:LYS299 3.1 0.0 1.0 CD A:GLU304 3.3 0.5 1.0 OE1 A:GLU304 3.9 0.2 1.0 CG A:GLU304 4.5 0.5 1.0 CD A:LYS299 4.6 0.8 1.0 CA A:GLU304 4.7 81.8 1.0 CB A:GLU304 4.8 87.5 1.0 O A:CYS303 4.8 79.6 1.0

Cadmium binding site 7 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd913 b:0.3 occ:0.27 NZ A:LYS715 2.5 0.2 1.0 CE A:LYS715 4.0 0.4 1.0 CD A:LYS715 4.5 72.8 1.0

Cadmium binding site 8 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd914 b:0.8 occ:1.00 OE2 A:GLU278 2.0 0.0 1.0 CD A:GLU278 3.0 0.1 1.0 OE1 A:GLU278 3.3 0.1 1.0 CG A:GLU278 4.4 0.2 1.0 OE2 A:GLU275 4.5 0.6 1.0

Cadmium binding site 9 out of 9 in the Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Dehydrogenase Domain of Myriococcum Thermophilum Cellobiose Dehydrogenase, Mtdh within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd915 b:0.9 occ:1.00 OE2 A:GLU550 2.1 0.8 1.0 CD A:GLU550 2.6 0.9 1.0 OE1 A:GLU550 2.7 0.2 1.0 CG A:GLU550 3.9 0.4 1.0 CB A:GLU550 4.6 97.2 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