Zinc in PDB 6kr3: Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)

The structure of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2), PDB code: 6kr3 was solved by J.Wu, G.Lu, H.Q.Ye, P.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.81 / 2.93
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	178.845, 209.975, 157.873, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.8

The structure of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) also contains other interesting chemical elements:

Iodine

(I)

15 atoms

The binding sites of Zinc atom in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) (pdb code 6kr3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2), PDB code: 6kr3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1015 b:0.5 occ:1.00 OE1 A:GLU438 1.6 77.8 1.0 SG A:CYS450 1.9 74.7 1.0 SG A:CYS447 2.1 77.4 1.0 NE2 A:HIS442 2.1 75.1 1.0 CB A:CYS447 2.1 79.9 1.0 CD A:GLU438 2.5 84.6 1.0 CB A:CYS450 2.8 76.4 1.0 CE1 A:HIS442 2.9 76.3 1.0 OE2 A:GLU438 2.9 87.8 1.0 CD2 A:HIS442 3.2 78.0 1.0 CA A:CYS447 3.4 80.5 1.0 CG A:GLU438 3.6 85.4 1.0 CA A:CYS450 4.0 74.2 1.0 ND1 A:HIS442 4.1 72.6 1.0 N A:GLU448 4.1 71.6 1.0 N A:CYS450 4.2 73.0 1.0 CG A:HIS442 4.2 74.7 1.0 C A:CYS447 4.3 77.1 1.0 NH2 A:ARG280 4.3 80.4 1.0 CG2 A:THR572 4.3 62.4 1.0 N A:CYS447 4.4 77.8 1.0 C A:THR449 4.4 75.7 1.0 O A:THR449 4.5 86.7 1.0 O A:LYS446 4.6 80.2 1.0 N A:THR449 4.7 75.0 1.0 CB A:GLU438 4.9 81.0 1.0 C A:LYS446 5.0 79.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1016 b:55.6 occ:0.89 NE2 A:HIS712 1.8 34.1 1.0 SG A:CYS847 1.9 38.0 1.0 NE2 A:HIS714 2.1 61.3 1.0 CE1 A:HIS714 2.1 47.5 1.0 SG A:CYS728 2.1 35.3 1.0 CD2 A:HIS712 2.6 46.9 1.0 CE1 A:HIS712 2.9 42.6 1.0 ND1 A:HIS714 3.1 49.6 1.0 CB A:CYS728 3.1 38.2 1.0 CD2 A:HIS714 3.1 47.4 1.0 CB A:CYS847 3.5 51.5 1.0 CG A:HIS714 3.6 41.2 1.0 CG A:HIS712 3.8 40.8 1.0 ND1 A:HIS712 3.9 35.2 1.0 CA A:CYS728 4.4 29.5 1.0 CD1 A:LEU839 4.4 44.1 1.0 C A:CYS728 4.4 36.0 1.0 O A:CYS728 4.7 33.9 1.0 N A:ARG729 4.8 41.7 1.0 CA A:CYS847 4.8 44.0 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1006 b:0.5 occ:1.00 OE2 B:GLU438 1.6 0.4 1.0 SG B:CYS447 1.9 86.4 1.0 SG B:CYS450 2.0 81.0 1.0 NE2 B:HIS442 2.0 70.6 1.0 CB B:CYS450 2.4 81.7 1.0 CB B:CYS447 2.8 82.3 1.0 CE1 B:HIS442 2.9 69.5 1.0 CD B:GLU438 3.0 0.9 1.0 CD2 B:HIS442 3.2 76.2 1.0 CA B:CYS447 3.7 74.3 1.0 CA B:CYS450 3.7 78.2 1.0 CG2 B:THR572 3.8 69.3 1.0 OE1 B:GLU438 3.9 97.3 1.0 CG B:GLU438 3.9 87.8 1.0 N B:CYS450 3.9 80.8 1.0 ND1 B:HIS442 4.1 69.7 1.0 C B:THR449 4.2 82.1 1.0 O B:THR449 4.2 89.1 1.0 CG B:HIS442 4.2 76.8 1.0 N B:GLU448 4.5 79.7 1.0 N B:THR449 4.6 73.7 1.0 NE B:ARG280 4.6 80.4 1.0 C B:CYS447 4.6 79.8 1.0 N B:CYS447 4.7 76.5 1.0 C B:CYS450 4.8 75.5 1.0 O B:LYS446 4.9 77.7 1.0 O B:CYS450 5.0 75.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Dengue Virus Nonstructural Protein NS5 (Form 2) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:62.9 occ:0.87 NE2 B:HIS712 1.7 49.1 1.0 NE2 B:HIS714 1.8 50.7 1.0 SG B:CYS847 2.0 31.9 1.0 CE1 B:HIS714 2.1 63.5 1.0 SG B:CYS728 2.2 50.8 1.0 CD2 B:HIS712 2.6 46.5 1.0 CB B:CYS728 2.7 55.6 1.0 CD2 B:HIS714 2.8 54.2 1.0 CE1 B:HIS712 2.9 50.6 1.0 ND1 B:HIS714 3.1 62.9 1.0 CG B:HIS714 3.5 45.4 1.0 CB B:CYS847 3.5 51.1 1.0 CG B:HIS712 3.8 40.2 1.0 ND1 B:HIS712 3.9 48.2 1.0 CA B:CYS728 4.0 39.9 1.0 C B:CYS728 4.3 41.8 1.0 N B:ARG729 4.3 44.3 1.0 CD1 B:LEU839 4.6 47.0 1.0 CA B:CYS847 4.7 52.5 1.0 CB B:HIS714 4.8 43.5 1.0 O B:CYS728 4.9 42.4 1.0

J.Wu, G.Lu, H.Q.Ye, P.Gong. Crystal Structure of Dengue Virus Nonstructural Protein NS5 To Be Published.