Cadmium in PDB 6ixi: Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus

The structure of Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus, PDB code: 6ixi was solved by P.Kumar, N.Sharma, V.Dalal, D.K.Ghosh, P.Kumar, A.K.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.68 / 2.07
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.274, 93.274, 93.991, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.9

The binding sites of Cadmium atom in the Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus (pdb code 6ixi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus, PDB code: 6ixi:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in the Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd301 b:37.3 occ:1.00 NE2 A:HIS39 2.1 39.4 1.0 NE2 A:HIS106 2.2 27.2 1.0 OE2 A:GLU172 2.2 40.8 1.0 OD1 A:ASP247 2.3 32.4 1.0 OD2 A:ASP247 2.3 42.6 1.0 OE1 A:GLU172 2.4 36.9 1.0 CD A:GLU172 2.6 41.4 1.0 CG A:ASP247 2.6 37.5 1.0 CD2 A:HIS39 3.0 41.1 1.0 CD2 A:HIS106 3.1 27.5 1.0 CE1 A:HIS39 3.1 34.8 1.0 CE1 A:HIS106 3.2 31.3 1.0 ND2 A:ASN193 3.9 38.0 1.0 CG A:GLU172 4.1 35.5 1.0 CB A:ASP247 4.1 34.0 1.0 CG A:HIS39 4.2 43.7 1.0 ND1 A:HIS39 4.2 46.5 1.0 CG A:HIS106 4.3 32.6 1.0 ND1 A:HIS106 4.3 32.9 1.0 O A:HOH405 4.5 63.6 1.0 O A:HOH460 4.5 39.3 1.0 CG A:ASN193 4.6 42.7 1.0 N A:ASN193 4.8 42.5 1.0 CA A:ASP247 4.9 35.2 1.0 CB A:ASN193 4.9 38.0 1.0 O A:HOH465 5.0 58.5 1.0

Cadmium binding site 2 out of 3 in the Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd302 b:85.3 occ:0.50 OE2 A:GLU66 2.2 65.1 1.0 O A:HOH416 2.3 70.6 1.0 OE1 A:GLU102 2.4 69.2 1.0 OE2 A:GLU102 2.6 85.2 1.0 CD A:GLU102 2.7 78.6 1.0 CD A:GLU66 3.0 62.5 1.0 OE1 A:GLU66 3.2 66.3 1.0 O A:HOH567 4.1 63.4 1.0 CG A:GLU102 4.1 72.1 1.0 CG A:GLU66 4.5 55.1 1.0 O A:ACT318 4.7 87.1 1.0 ND1 A:HIS63 4.8 54.4 1.0 CB A:GLU102 5.0 62.0 1.0

Cadmium binding site 3 out of 3 in the Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Cd-Bound Periplasmic Metal Binding Protein From Candidatus Liberibacter Asiaticus within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd303 b:80.5 occ:0.50 ND1 A:HIS213 2.3 66.5 1.0 O A:HOH585 2.7 71.8 1.0 CE1 A:HIS213 3.1 66.8 1.0 O A:HOH604 3.1 69.0 1.0 O A:HOH571 3.1 69.6 1.0 CG A:HIS213 3.4 63.6 1.0 CB A:HIS213 3.8 61.8 1.0 CA A:HIS213 4.2 63.0 1.0 NE1 A:TRP167 4.3 53.5 1.0 NE2 A:HIS213 4.3 66.1 1.0 CD2 A:HIS213 4.4 62.5 1.0 O A:GLU164 4.5 85.8 1.0 CZ2 A:TRP167 4.6 51.8 1.0 O A:HIS213 4.8 69.9 1.0 CE2 A:TRP167 4.8 49.2 1.0

P.Kumar, V.Dalal, N.Sharma, S.Kokane, D.K.Ghosh, P.Kumar, A.K.Sharma. Characterization of the Heavy Metal Binding Properties of Periplasmic Metal Uptake Protein Clas-ZNUA2. Metallomics 2019.
ISSN: ESSN 1756-591X
PubMed: 31853532
DOI: 10.1039/C9MT00200F