Zinc in PDB 6xd1: Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640

The structure of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640, PDB code: 6xd1 was solved by R.Arora, T.E.Benson, C.W.Liew, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.75 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	161.533, 175.198, 57.748, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.4

The binding sites of Zinc atom in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640 (pdb code 6xd1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640, PDB code: 6xd1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:31.0 occ:1.00 NE2 A:HIS714 2.1 30.2 1.0 NE2 A:HIS712 2.1 29.8 1.0 SG A:CYS728 2.3 29.9 1.0 CE1 A:HIS714 3.0 31.2 1.0 CD2 A:HIS712 3.0 29.2 1.0 SG A:CYS847 3.1 37.0 1.0 CB A:CYS728 3.1 26.2 1.0 CE1 A:HIS712 3.1 29.7 1.0 CD2 A:HIS714 3.1 29.5 1.0 CB A:CYS847 3.8 32.4 1.0 CD1 A:LEU839 4.1 34.1 1.0 CG A:HIS712 4.2 28.4 1.0 ND1 A:HIS714 4.2 31.4 1.0 ND1 A:HIS712 4.2 29.8 1.0 CG A:HIS714 4.2 29.5 1.0 O A:HOH1507 4.3 50.2 1.0 CA A:CYS728 4.4 26.7 1.0 C A:CYS728 4.6 27.2 1.0 NH2 A:ARG769 4.7 26.6 1.0 N A:ARG729 4.7 27.7 1.0 O A:HOH1109 4.9 56.3 1.0 O A:HOH1513 4.9 46.6 1.0

Zinc binding site 2 out of 2 in the Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:33.0 occ:1.00 OE1 A:GLU437 2.0 38.7 1.0 NE2 A:HIS441 2.1 37.8 1.0 SG A:CYS449 2.2 34.0 1.0 SG A:CYS446 2.3 34.0 1.0 CE1 A:HIS441 3.1 38.2 1.0 CD A:GLU437 3.1 37.9 1.0 CD2 A:HIS441 3.1 36.5 1.0 CB A:CYS449 3.2 33.1 1.0 CB A:CYS446 3.5 31.9 1.0 CG A:GLU437 3.5 32.9 1.0 N A:CYS449 3.7 33.1 1.0 CA A:CYS446 3.8 33.6 1.0 CA A:CYS449 4.1 32.9 1.0 N A:GLY447 4.2 35.1 1.0 OE2 A:GLU437 4.2 38.5 1.0 CG A:HIS441 4.2 35.8 1.0 ND1 A:HIS441 4.2 37.6 1.0 N A:SER448 4.4 36.4 1.0 C A:CYS446 4.4 34.6 1.0 O A:HOH1305 4.7 33.3 1.0 C A:SER448 4.7 34.9 1.0 O A:HOH1205 4.9 37.2 1.0 O A:LYS445 4.9 34.1 1.0 CG2 A:THR571 4.9 35.4 1.0

R.Arora, T.E.Benson, C.W.Liew, J.Lescar. Dengue Serotype 3 Rna-Dependent Rna Polymerase Bound to Nitd-640 To Be Published.