Cadmium in PDB 8qvd: 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: 8qvd 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)	49.51 / 3.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	70.03, 93.78, 93.46, 90, 94.94, 90
R / Rfree (%)	23.9 / 29.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol (pdb code 8qvd). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Deinococcus Aerius TR0125 C-Glucosyl Deglycosidase (Cgd), Wild Type Crystal Cryoprotected with Glycerol, PDB code: 8qvd:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 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:102.3 occ:1.00 OE1 A:GLU295 2.1 111.3 1.0 OD2 A:ASP175 2.1 108.9 1.0 ND1 A:HIS259 2.2 101.1 1.0 OE2 A:GLU143 2.2 108.0 1.0 CE1 A:HIS259 2.5 101.3 1.0 CD A:GLU295 2.9 112.8 1.0 OE2 A:GLU295 3.0 111.5 1.0 NZ A:LYS261 3.3 121.0 1.0 CG A:ASP175 3.4 106.1 1.0 CG A:HIS259 3.4 101.3 1.0 CD A:GLU143 3.5 106.7 1.0 NE2 A:HIS259 3.7 101.6 1.0 CE A:LYS261 4.0 111.4 1.0 CB A:HIS259 4.1 101.2 1.0 OE1 A:GLU143 4.1 105.6 1.0 CD2 A:HIS259 4.1 101.6 1.0 CB A:ASP175 4.2 105.1 1.0 OD1 A:ASP175 4.3 105.2 1.0 CG A:GLU295 4.3 109.6 1.0 CD A:LYS261 4.3 106.2 1.0 CG A:GLU143 4.5 104.7 1.0

Cadmium binding site 2 out of 15 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:121.8 occ:1.00 OD2 A:ASP57 2.0 114.9 1.0 OD1 A:ASP61 2.1 113.7 1.0 OD2 A:ASP61 2.2 115.0 1.0 OD1 A:ASP57 2.2 113.5 1.0 CG A:ASP57 2.4 114.1 1.0 CG A:ASP61 2.5 114.1 1.0 CB A:ASP57 3.9 113.9 1.0 CB A:ASP61 4.1 113.7 1.0 O A:ASP57 4.3 113.1 1.0 NH1 A:ARG109 4.7 123.7 1.0 CA A:ASP57 4.8 113.1 1.0 C A:ASP57 4.9 113.1 1.0 CA A:ASP61 4.9 112.7 1.0

Cadmium binding site 3 out of 15 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:143.8 occ:0.75 NE2 A:HIS64 2.0 120.5 1.0 CE1 A:HIS64 2.9 120.3 1.0 CD2 A:HIS64 3.0 117.7 1.0 ND1 A:HIS64 4.1 118.5 1.0 CG A:HIS64 4.1 117.0 1.0

Cadmium binding site 4 out of 15 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:186.3 occ:0.83 NE2 A:HIS199 2.1 143.6 1.0 CE1 A:HIS199 3.0 142.1 1.0 CD2 A:HIS199 3.1 147.6 1.0 ND1 A:HIS199 4.1 140.7 1.0 CG A:HIS199 4.2 144.8 1.0

Cadmium binding site 5 out of 15 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:146.9 occ:0.33 ND1 A:HIS132 2.1 135.5 1.0 CE1 A:HIS132 2.5 134.2 1.0 CG A:HIS132 3.4 127.7 1.0 NE2 A:HIS132 3.8 135.7 1.0 NH2 A:ARG105 3.8 131.8 1.0 OE1 A:GLN135 3.9 134.9 1.0 NE2 A:GLN135 4.1 133.0 1.0 CB A:HIS132 4.2 124.6 1.0 CD2 A:HIS132 4.2 129.3 1.0 CD A:GLN135 4.3 133.2 1.0 CA A:HIS132 4.7 126.5 1.0 CG1 A:VAL101 4.9 113.5 1.0 CZ A:ARG105 5.0 132.5 1.0

Cadmium binding site 6 out of 15 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:119.9 occ:0.48 NE2 A:HIS145 2.3 124.8 1.0 CD2 A:HIS145 2.4 120.9 1.0 CE1 A:HIS145 3.6 124.9 1.0 OE1 A:GLU143 3.6 105.6 1.0 CB A:ASN119 3.8 113.1 1.0 CG A:HIS145 3.8 118.0 1.0 N A:ASN119 3.9 110.7 1.0 CD A:GLU143 4.1 106.7 1.0 CD2 A:LEU118 4.2 105.2 1.0 ND1 A:HIS145 4.3 118.9 1.0 CA A:ASN119 4.5 109.5 1.0 OE2 A:GLU143 4.6 108.0 1.0 CG A:GLU143 4.9 104.7 1.0 C A:LEU118 4.9 109.3 1.0 CG A:ASN119 4.9 110.4 1.0 CB A:HIS145 5.0 113.4 1.0 CA A:LEU118 5.0 105.4 1.0

Cadmium binding site 7 out of 15 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 A:Cd507 b:175.0 occ:0.64 CE1 A:HIS239 2.2 129.2 1.0 NE2 A:HIS239 2.2 132.0 1.0 ND1 A:HIS239 3.4 130.6 1.0 CD2 A:HIS239 3.5 131.8 1.0 CG A:HIS239 4.1 132.2 1.0 CG C:GLU215 4.4 141.7 1.0 CB C:GLU215 4.8 139.1 1.0 CG B:PRO110 4.8 125.1 1.0

Cadmium binding site 8 out of 15 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 8 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:201.6 occ:0.75 NE2 B:HIS89 2.1 187.9 1.0 OE2 B:GLU46 2.2 192.8 1.0 CD2 B:HIS89 3.0 188.8 1.0 CE1 B:HIS89 3.1 189.2 1.0 CD B:GLU46 3.2 188.5 1.0 OE1 B:GLU46 3.5 192.3 1.0 ND1 B:HIS89 4.2 187.9 1.0 CG B:HIS89 4.2 191.4 1.0 CG B:GLU46 4.5 179.9 1.0

Cadmium binding site 9 out of 15 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 9 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 C:Cd501 b:113.8 occ:1.00 OE1 C:GLU295 2.2 116.8 1.0 OD2 C:ASP175 2.2 119.4 1.0 ND1 C:HIS259 2.2 112.3 1.0 OE2 C:GLU143 2.2 113.0 1.0 OE2 C:GLU295 2.3 121.4 1.0 CD C:GLU295 2.6 122.0 1.0 CE1 C:HIS259 2.8 115.3 1.0 CG C:HIS259 3.4 111.0 1.0 CG C:ASP175 3.4 116.9 1.0 CD C:GLU143 3.4 114.1 1.0 NZ C:LYS261 3.5 123.8 1.0 NE2 C:HIS259 3.9 114.7 1.0 CB C:HIS259 4.0 111.1 1.0 OE1 C:GLU143 4.0 115.8 1.0 CE C:LYS261 4.1 120.0 1.0 CG C:GLU295 4.1 119.3 1.0 CB C:ASP175 4.2 112.0 1.0 OD1 C:ASP175 4.2 116.6 1.0 CD2 C:HIS259 4.3 113.1 1.0 CD C:LYS261 4.4 117.8 1.0 CG C:GLU143 4.6 110.2 1.0 NH1 C:ARG116 4.9 114.4 1.0

Cadmium binding site 10 out of 15 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 10 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 C:Cd502 b:130.5 occ:1.00 OD2 C:ASP57 2.1 128.3 1.0 OD1 C:ASP57 2.2 126.2 1.0 OD2 C:ASP61 2.2 129.1 1.0 OD1 C:ASP61 2.3 131.4 1.0 CG C:ASP57 2.4 127.1 1.0 CG C:ASP61 2.6 128.2 1.0 CB C:ASP57 3.9 126.8 1.0 CB C:ASP61 4.2 128.4 1.0 O C:ASP57 4.3 126.9 1.0 NH1 C:ARG109 4.7 135.5 1.0 CA C:ASP57 4.8 126.0 1.0 C C:ASP57 4.9 126.8 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