Zinc in PDB 6jdu: Crystal Structure of Prrsv NSP10 (Helicase)

The structure of Crystal Structure of Prrsv NSP10 (Helicase), PDB code: 6jdu was solved by C.Tang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.81
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	92.914, 92.914, 147.696, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 23.8

The structure of Crystal Structure of Prrsv NSP10 (Helicase) also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Prrsv NSP10 (Helicase) (pdb code 6jdu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Prrsv NSP10 (Helicase), PDB code: 6jdu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Prrsv NSP10 (Helicase)


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 Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:6.2 occ:1.00 NE2 A:HIS32 2.0 25.9 1.0 ND1 A:HIS34 2.0 25.9 1.0 SG A:CYS35 2.1 23.7 1.0 SG A:CYS20 2.2 28.4 1.0 CE1 A:HIS32 2.9 26.3 1.0 CE1 A:HIS34 2.9 25.8 1.0 CD2 A:HIS32 3.0 26.7 1.0 CB A:CYS20 3.1 28.1 1.0 CG A:HIS34 3.1 26.0 1.0 CB A:CYS35 3.3 25.2 1.0 CB A:HIS34 3.5 26.4 1.0 N A:CYS35 3.7 26.4 1.0 OG1 A:THR18 4.0 28.5 1.0 CB A:THR18 4.0 28.8 1.0 ND1 A:HIS32 4.0 26.8 1.0 NE2 A:HIS34 4.1 26.0 1.0 CA A:CYS35 4.1 25.9 1.0 N A:CYS20 4.1 28.3 1.0 CG A:HIS32 4.1 27.5 1.0 CD2 A:HIS34 4.2 25.9 1.0 C A:HIS34 4.2 26.6 1.0 CA A:CYS20 4.2 28.2 1.0 CD2 A:LEU68 4.4 27.3 1.0 CA A:HIS34 4.5 26.8 1.0 CG2 A:THR18 4.5 28.9 1.0 C A:CYS35 4.8 26.0 1.0 O A:CYS35 4.9 26.2 1.0 O A:HIS34 5.0 26.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Prrsv NSP10 (Helicase)


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 Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:12.5 occ:1.00 ND1 A:HIS28 1.9 37.1 1.0 SG A:CYS10 2.1 37.8 1.0 SG A:CYS7 2.2 32.7 1.0 SG A:CYS25 2.3 29.8 1.0 CE1 A:HIS28 2.7 37.7 1.0 CG A:HIS28 3.1 37.5 1.0 CB A:CYS7 3.3 35.2 1.0 CB A:CYS25 3.5 32.0 1.0 CB A:CYS10 3.5 38.7 1.0 CB A:HIS28 3.6 36.8 1.0 N A:CYS10 3.8 38.1 1.0 NE2 A:HIS28 3.9 38.4 1.0 N A:CYS25 3.9 31.8 1.0 CD2 A:HIS28 4.1 38.0 1.0 CA A:CYS10 4.2 38.4 1.0 CA A:CYS25 4.3 32.8 1.0 CB A:TYR9 4.3 35.1 1.0 N A:HIS28 4.6 36.9 1.0 C A:CYS10 4.7 40.8 1.0 O A:CYS10 4.7 42.4 1.0 CA A:CYS7 4.7 36.8 1.0 CA A:HIS28 4.7 37.3 1.0 CD2 A:TYR9 4.8 34.3 1.0 C A:TYR9 4.8 36.6 1.0 N A:TYR9 4.8 35.6 1.0 CB A:ALA12 4.9 45.8 1.0 CA A:TYR9 4.9 35.8 1.0 C A:CYS25 5.0 34.4 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Prrsv NSP10 (Helicase)


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 Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:14.0 occ:1.00 ND1 A:HIS43 2.0 34.8 1.0 SG A:CYS50 2.0 38.5 1.0 SG A:CYS41 2.2 32.6 1.0 SG A:CYS53 2.2 36.3 1.0 CG A:HIS43 3.0 34.9 1.0 CE1 A:HIS43 3.0 34.9 1.0 CB A:CYS53 3.2 38.0 1.0 CB A:CYS50 3.3 39.6 1.0 CB A:HIS43 3.3 34.7 1.0 N A:CYS50 3.4 39.5 1.0 CB A:CYS41 3.4 33.7 1.0 N A:CYS53 3.8 40.3 1.0 CA A:CYS50 3.8 39.8 1.0 NE2 A:HIS43 4.1 35.1 1.0 CD2 A:HIS43 4.1 34.8 1.0 CA A:CYS53 4.1 38.9 1.0 O A:CYS50 4.2 41.3 1.0 C A:CYS50 4.2 40.7 1.0 C A:SER49 4.3 38.8 1.0 CB A:SER49 4.3 39.1 1.0 N A:HIS43 4.3 34.0 1.0 CA A:HIS43 4.4 34.0 1.0 O A:CYS41 4.4 33.9 1.0 C A:CYS41 4.5 33.6 1.0 CA A:CYS41 4.6 34.0 1.0 CA A:SER49 4.7 38.4 1.0 CB A:GLU52 4.7 44.9 1.0 C A:GLU52 4.7 41.8 1.0 N A:SER49 4.7 37.4 1.0 N A:GLU52 4.9 42.6 1.0 OG A:SER47 4.9 31.9 1.0 O A:HOH715 5.0 25.9 1.0 C A:HIS43 5.0 33.5 1.0

C.Tang, Z.Chen. Crystal Structure of Prrsv NSP10 (Helicase) at 2.81 Angstroms Resolution To Be Published.