Zinc in PDB 4c11: Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region

The structure of Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region, PDB code: 4c11 was solved by S.P.Lim, J.Lescar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	122.990, 136.050, 103.240, 90.00, 90.00, 90.00
R / Rfree (%)	19.21 / 24.51

The binding sites of Zinc atom in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region (pdb code 4c11). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region, PDB code: 4c11:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1889 b:53.0 occ:1.00 NE2 A:HIS712 2.0 46.1 1.0 NE2 A:HIS714 2.0 49.5 1.0 SG A:CYS847 2.2 53.6 1.0 SG A:CYS728 2.2 46.9 1.0 CE1 A:HIS714 3.0 49.0 1.0 CE1 A:HIS712 3.0 45.8 1.0 CD2 A:HIS712 3.1 46.5 1.0 CD2 A:HIS714 3.1 50.3 1.0 CB A:CYS728 3.1 42.8 1.0 CB A:CYS847 3.3 49.9 1.0 ND1 A:HIS712 4.1 46.6 1.0 ND1 A:HIS714 4.2 49.9 1.0 CG A:HIS712 4.2 45.2 1.0 CD1 A:LEU839 4.2 50.3 1.0 CG A:HIS714 4.2 48.6 1.0 CA A:CYS728 4.4 42.7 1.0 C A:CYS728 4.5 47.4 1.0 N A:ARG729 4.6 44.2 1.0 O A:HOH2179 4.6 42.0 1.0 CA A:CYS847 4.6 49.7 1.0 NH1 A:ARG769 4.8 43.3 1.0 O A:GLU843 4.9 53.7 1.0 O A:ARG729 5.0 52.8 1.0 O A:CYS728 5.0 48.5 1.0

Zinc binding site 2 out of 4 in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1890 b:50.0 occ:1.00 OE2 A:GLU437 2.1 51.3 1.0 SG A:CYS446 2.1 46.6 1.0 SG A:CYS449 2.3 46.0 1.0 NE2 A:HIS441 2.3 49.8 1.0 CD A:GLU437 3.1 51.8 1.0 CB A:CYS449 3.1 43.0 1.0 CE1 A:HIS441 3.3 49.7 1.0 CD2 A:HIS441 3.4 49.7 1.0 CG A:GLU437 3.5 47.9 1.0 CB A:CYS446 3.5 43.2 1.0 N A:CYS449 3.6 46.5 1.0 CA A:CYS446 3.8 42.5 1.0 CA A:CYS449 3.9 44.4 1.0 N A:GLY447 4.1 44.2 1.0 OE1 A:GLU437 4.1 65.7 1.0 C A:CYS446 4.3 45.4 1.0 N A:SER448 4.3 51.3 1.0 CG2 A:THR571 4.3 52.2 1.0 ND1 A:HIS441 4.5 50.6 1.0 CG A:HIS441 4.5 49.1 1.0 C A:SER448 4.6 52.5 1.0 O A:LYS445 4.9 38.7 1.0 CB A:GLU437 5.0 46.8 1.0 CA A:SER448 5.0 51.1 1.0

Zinc binding site 3 out of 4 in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1890 b:50.8 occ:1.00 NE2 B:HIS712 1.9 52.5 1.0 NE2 B:HIS714 2.0 53.5 1.0 SG B:CYS847 2.3 49.0 1.0 SG B:CYS728 2.3 44.1 1.0 CE1 B:HIS714 2.9 53.2 1.0 CE1 B:HIS712 2.9 52.0 1.0 CD2 B:HIS712 2.9 52.0 1.0 CD2 B:HIS714 3.0 53.5 1.0 CB B:CYS728 3.1 40.0 1.0 CB B:CYS847 3.3 46.1 1.0 CG B:HIS712 4.0 49.9 1.0 ND1 B:HIS712 4.1 52.0 1.0 ND1 B:HIS714 4.1 53.6 1.0 CG B:HIS714 4.1 50.8 1.0 O B:HOH2150 4.3 47.0 1.0 CD1 B:LEU839 4.3 43.5 1.0 CA B:CYS728 4.4 39.9 1.0 C B:CYS728 4.5 45.2 1.0 N B:ARG729 4.5 42.1 1.0 CA B:CYS847 4.7 47.5 1.0 NH1 B:ARG769 4.8 35.8 1.0 O B:CYS728 4.9 46.4 1.0 O B:ARG729 5.0 44.9 1.0

Zinc binding site 4 out of 4 in the Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dengue Virus Rna Dependent Rna Polymerase with Residues From the NS5 Linker Region within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1891 b:73.4 occ:1.00 SG B:CYS446 2.2 87.5 1.0 OE2 B:GLU437 2.2 72.7 1.0 NE2 B:HIS441 2.2 87.8 1.0 SG B:CYS449 2.4 86.2 1.0 CB B:CYS449 3.1 82.4 1.0 CD B:GLU437 3.1 94.9 1.0 CE1 B:HIS441 3.2 87.3 1.0 CD2 B:HIS441 3.3 88.1 1.0 CB B:CYS446 3.5 83.8 1.0 CG B:GLU437 3.5 82.2 1.0 N B:CYS449 3.7 83.1 1.0 CA B:CYS446 3.9 83.4 1.0 CA B:CYS449 4.0 82.5 1.0 N B:GLY447 4.2 83.7 1.0 OE1 B:GLU437 4.2 93.7 1.0 CG2 B:THR571 4.3 69.8 1.0 ND1 B:HIS441 4.3 88.0 1.0 CG B:HIS441 4.4 86.6 1.0 C B:CYS446 4.4 86.9 1.0 N B:SER448 4.4 85.1 1.0 C B:SER448 4.7 86.9 1.0 O B:LYS445 4.8 87.5 1.0

S.P.Lim, J.H.K.Koh, C.C.Seh, C.W.Liew, A.D.Davidson, L.S.Chua, R.Chandrasekaran, T.C.Cornvik, P.Shi, J.Lescar. A Crystal Structure of the Dengue Virus NS5 Polymerase Delineates Inter-Domain Amino Acids Residues That Enhance Its Thermostability and De Novo Initiation Activities. J.Biol.Chem. V. 288 31105 2013.
ISSN: ISSN 0021-9258
PubMed: 24025331
DOI: 10.1074/JBC.M113.508606