Cadmium in PDB 8qvc: Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol

The structure of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol, PDB code: 8qvc was solved by V.Furlanetto, D.C.Kalyani, A.Kostelac, D.Haltrich, B.M.Hallberg, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.15 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.3, 94.42, 61.53, 90, 90, 90
R / Rfree (%)	19.1 / 22.7

The binding sites of Cadmium atom in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol (pdb code 8qvc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 7 binding sites of Cadmium where determined in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol, PDB code: 8qvc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7;

Cadmium binding site 1 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd501 b:21.3 occ:0.87 OE2 A:GLU143 2.2 26.0 1.0 OD2 A:ASP175 2.2 23.6 1.0 OE1 A:GLU295 2.2 23.7 1.0 ND1 A:HIS259 2.2 23.9 1.0 O A:HOH1001 2.3 28.1 1.0 O A:HOH1017 2.3 24.4 1.0 CD A:GLU295 3.1 28.6 1.0 CE1 A:HIS259 3.1 23.5 1.0 CD A:GLU143 3.2 25.7 1.0 OE2 A:GLU295 3.2 27.0 1.0 CG A:HIS259 3.3 23.8 1.0 CG A:ASP175 3.3 24.3 1.0 OE1 A:GLU143 3.6 23.5 1.0 CB A:HIS259 3.6 22.2 1.0 NZ A:LYS261 3.8 21.7 1.0 CB A:ASP175 3.9 22.3 1.0 CE A:LYS261 4.1 24.0 1.0 NE2 A:HIS259 4.3 21.2 1.0 CD2 A:HIS259 4.4 23.3 1.0 CD A:LYS261 4.4 24.7 1.0 OD1 A:ASP175 4.4 24.9 1.0 CG A:GLU143 4.4 24.2 1.0 CG A:GLU295 4.6 23.8 1.0 NH1 A:ARG116 4.9 23.4 1.0 CA A:ASP175 5.0 22.4 1.0

Cadmium binding site 2 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd502 b:21.8 occ:0.82 O A:HOH1128 2.2 30.2 1.0 OD2 A:ASP57 2.2 28.0 1.0 O A:HOH1106 2.3 30.6 1.0 OD1 A:ASP61 2.3 23.7 1.0 OD1 A:ASP57 2.3 28.0 1.0 OD2 A:ASP61 2.3 29.6 1.0 CG A:ASP57 2.6 28.3 1.0 CG A:ASP61 2.6 27.6 1.0 CB A:ASP57 4.2 25.6 1.0 CB A:ASP61 4.2 25.6 1.0 O A:HOH1061 4.2 35.6 1.0 O A:ASP57 4.5 29.9 1.0 O A:HOH1124 4.5 39.3 1.0 NH1 A:ARG109 4.8 36.1 1.0 CA A:ASP57 4.9 27.6 1.0 C A:ASP57 5.0 27.5 1.0

Cadmium binding site 3 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd503 b:40.2 occ:0.65 NE2 A:HIS64 2.2 37.2 1.0 CE1 A:HIS64 3.0 37.2 1.0 CD2 A:HIS64 3.3 34.4 1.0 ND1 A:HIS64 4.2 32.4 1.0 CG A:HIS64 4.3 29.4 1.0

Cadmium binding site 4 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd504 b:43.0 occ:0.53 NE2 A:HIS199 2.1 36.8 1.0 O A:HOH1140 2.2 40.4 1.0 CE1 A:HIS199 3.0 32.4 1.0 CD2 A:HIS199 3.2 30.9 1.0 ND1 A:HIS199 4.2 31.1 1.0 CG A:HIS199 4.3 29.7 1.0 SD A:MET224 4.8 41.7 1.0

Cadmium binding site 5 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd505 b:71.0 occ:0.49 ND1 A:HIS132 2.2 38.1 1.0 CE1 A:HIS132 3.0 36.9 1.0 CG A:HIS132 3.3 32.7 1.0 NH2 A:ARG105 3.4 59.2 1.0 NE2 A:GLN135 3.7 58.6 1.0 CB A:HIS132 3.8 31.6 1.0 CD A:GLN135 4.0 55.7 1.0 O A:HOH1008 4.0 38.2 1.0 OE1 A:GLN135 4.1 57.6 1.0 CA A:HIS132 4.1 28.1 1.0 NE2 A:HIS132 4.2 36.5 1.0 CD2 A:HIS132 4.4 33.9 1.0 CG1 A:VAL101 4.7 31.1 1.0 CZ A:ARG105 4.7 55.5 1.0 CG A:GLN135 5.0 43.0 1.0

Cadmium binding site 6 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd506 b:71.0 occ:0.60 NE2 A:HIS145 2.2 35.1 1.0 O A:HOH1169 2.3 41.0 1.0 O A:HOH1175 2.3 45.0 1.0 O A:HOH1171 2.3 37.4 1.0 O A:HOH1167 2.4 20.0 1.0 CE1 A:HIS145 3.0 37.6 1.0 CD2 A:HIS145 3.4 35.1 1.0 O A:HOH1051 3.8 27.1 1.0 CB A:ASN119 4.1 25.2 1.0 ND1 A:HIS145 4.2 39.8 1.0 CD1 B:TYR108 4.2 37.0 1.0 CG A:HIS145 4.4 30.1 1.0 CG B:TYR108 4.5 32.3 1.0 CB B:TYR108 4.6 32.4 1.0 N A:ASN119 4.7 19.9 1.0 OD1 A:ASN119 4.8 32.8 1.0 CE1 B:TYR108 4.9 34.2 1.0 CG A:ASN119 4.9 30.5 1.0

Cadmium binding site 7 out of 7 in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd501 b:61.3 occ:0.61 OE2 B:GLU46 2.1 57.2 1.0 NE2 B:HIS89 2.1 51.1 1.0 O B:HOH643 2.2 53.9 1.0 O B:HOH647 2.3 44.8 1.0 O B:HOH641 2.7 49.2 1.0 CD B:GLU46 3.1 53.9 1.0 CD2 B:HIS89 3.1 48.6 1.0 CE1 B:HIS89 3.1 53.0 1.0 OE1 B:GLU46 3.3 58.8 1.0 ND1 B:HIS89 4.2 50.5 1.0 CG B:HIS89 4.3 49.8 1.0 CG B:GLU46 4.5 48.2 1.0

V.Furlanetto, D.C.Kalyani, A.Kostelac, J.Puc, D.Haltrich, B.M.Hallberg, C.Divne. Structural and Functional Characterization of A Gene Cluster Responsible For Deglycosylation of C-Glucosyl Flavonoids and Xanthonoids By Deinococcus Aerius. J.Mol.Biol. V. 436 68547 2024.
ISSN: ESSN 1089-8638
PubMed: 38508304
DOI: 10.1016/J.JMB.2024.168547