Cadmium in PDB 8iib: Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib was solved by X.Fang, G.Lu, C.Hou, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.41 / 2.69
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.51, 150.51, 104.626, 90, 90, 120
R / Rfree (%)	21.3 / 25.4

The structure of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) also contains other interesting chemical elements:

Chlorine	(Cl)	7 atoms
Magnesium	(Mg)	8 atoms

The binding sites of Cadmium atom in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) (pdb code 8iib). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546), PDB code: 8iib:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd601 b:29.9 occ:1.00 CL A:CL606 2.6 30.4 1.0 SG A:CYS469 2.6 18.8 1.0 CL A:CL607 2.7 30.1 1.0 SG B:CYS480 2.7 29.0 1.0 CB B:CYS480 3.1 28.6 1.0 CB A:CYS469 3.3 17.2 1.0 CA B:CYS480 3.6 25.0 1.0 CA A:CYS469 3.6 22.6 1.0 N A:MET470 4.1 21.5 1.0 N B:ARG481 4.1 33.0 1.0 C B:CYS480 4.3 29.9 1.0 C A:CYS469 4.3 22.8 1.0 OE1 A:GLN449 4.3 33.5 1.0 N A:CYS469 4.8 23.9 1.0 N B:CYS480 4.8 30.4 1.0 O A:HOH720 4.8 26.6 1.0

Cadmium binding site 2 out of 4 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd602 b:24.4 occ:1.00 CL B:CL608 2.5 30.1 1.0 CL A:CL608 2.6 24.8 1.0 SG B:CYS469 2.6 24.9 1.0 SG A:CYS480 2.8 20.0 1.0 CB B:CYS469 3.2 26.4 1.0 CB A:CYS480 3.2 17.4 1.0 CA A:CYS480 3.5 16.7 1.0 CA B:CYS469 3.6 20.8 1.0 N B:MET470 4.0 17.9 1.0 NE2 B:GLN449 4.1 23.6 1.0 N A:ARG481 4.1 26.3 1.0 C A:CYS480 4.2 23.0 1.0 C B:CYS469 4.3 20.7 1.0 O B:HOH745 4.5 18.9 1.0 O B:HOH730 4.6 31.4 1.0 N A:GLY482 4.7 27.0 1.0 N A:CYS480 4.8 18.2 1.0 N B:CYS469 4.8 24.2 1.0 CD1 A:LEU484 4.9 30.2 1.0

Cadmium binding site 3 out of 4 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd603 b:76.8 occ:1.00 SG A:CYS300 2.3 78.3 1.0 CL A:CL609 3.1 75.9 1.0 CB A:CYS300 3.3 59.0 1.0 N A:CYS300 3.7 42.9 1.0 CA A:CYS300 3.9 44.3 1.0 C A:VAL299 4.5 51.4 1.0 N A:VAL299 4.9 57.7 1.0

Cadmium binding site 4 out of 4 in the Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Israeli Acute Paralysis Virus Rna-Dependent Rna Polymerase DELTA85 Mutant (Residues 86-546) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd601 b:77.5 occ:1.00 SG B:CYS300 2.5 53.7 1.0 CL B:CL609 2.7 59.5 1.0 CB B:CYS300 3.1 72.0 1.0 CL B:CL610 3.1 75.1 1.0 N B:CYS300 3.6 51.3 1.0 CA B:CYS300 3.8 57.4 1.0 C B:VAL299 4.4 51.2 1.0 N B:VAL299 4.6 62.1 1.0 CA B:VAL299 4.8 55.4 1.0 CB B:VAL299 4.9 46.1 1.0

X.Fang, G.Lu, Y.Deng, S.Yang, C.Hou, P.Gong. Unusual Substructure Conformations Observed in Crystal Structures of A Dicistrovirus Rna-Dependent Rna Polymerase Suggest Contribution of the N-Terminal Extension in Proper Folding. Virol Sin 2023.
ISSN: ISSN 1995-820X
PubMed: 37156298
DOI: 10.1016/J.VIRS.2023.05.002