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

The structure of Crystal Structure of Methylated Prrsv NSP10 (Helicase), PDB code: 6jdr was solved by Z.Deng, 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 / 2.50
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	93.158, 93.158, 148.108, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.2

The binding sites of Zinc atom in the Crystal Structure of Methylated Prrsv NSP10 (Helicase) (pdb code 6jdr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Methylated Prrsv NSP10 (Helicase), PDB code: 6jdr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Methylated 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 Methylated Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:36.8 occ:1.00 NE2 A:HIS32 2.1 37.2 1.0 ND1 A:HIS34 2.2 40.5 1.0 SG A:CYS35 2.3 38.4 1.0 SG A:CYS20 2.3 36.6 1.0 CE1 A:HIS32 3.1 37.7 1.0 CG A:HIS34 3.1 40.5 1.0 CE1 A:HIS34 3.2 40.2 1.0 CD2 A:HIS32 3.2 38.2 1.0 CB A:CYS20 3.2 37.0 1.0 CB A:HIS34 3.4 41.5 1.0 CB A:CYS35 3.4 40.5 1.0 N A:CYS35 3.7 42.9 1.0 OG1 A:THR18 4.0 38.4 1.0 CB A:THR18 4.0 40.1 1.0 C A:HIS34 4.1 42.8 1.0 N A:CYS20 4.2 37.9 1.0 CA A:CYS35 4.2 41.8 1.0 ND1 A:HIS32 4.2 37.9 1.0 NE2 A:HIS34 4.3 40.6 1.0 CA A:CYS20 4.3 38.0 1.0 CD2 A:HIS34 4.3 40.3 1.0 CG A:HIS32 4.3 38.2 1.0 CA A:HIS34 4.3 42.4 1.0 CD1 A:LEU68 4.6 35.5 1.0 CG2 A:THR18 4.6 41.4 1.0 O A:HIS34 4.7 44.4 1.0 C A:CYS35 4.8 41.5 1.0 O A:CYS35 4.8 42.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Methylated 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 Methylated Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:46.0 occ:1.00 ND1 A:HIS28 2.1 42.5 1.0 SG A:CYS10 2.2 49.2 1.0 SG A:CYS7 2.3 42.7 1.0 SG A:CYS25 2.3 50.4 1.0 CE1 A:HIS28 2.8 43.9 1.0 CB A:CYS7 3.1 45.4 1.0 CG A:HIS28 3.3 44.1 1.0 CB A:CYS10 3.4 48.4 1.0 CB A:CYS25 3.5 49.5 1.0 N A:CYS10 3.8 47.8 1.0 CB A:HIS28 3.8 45.1 1.0 N A:CYS25 4.0 50.5 1.0 NE2 A:HIS28 4.0 43.5 1.0 CA A:CYS10 4.2 48.8 1.0 CD2 A:HIS28 4.2 43.7 1.0 CB A:TYR9 4.2 44.5 1.0 CA A:CYS25 4.3 49.8 1.0 CA A:CYS7 4.6 46.0 1.0 N A:HIS28 4.7 47.5 1.0 CB A:ALA12 4.7 51.2 1.0 C A:CYS10 4.8 49.2 1.0 C A:TYR9 4.8 47.0 1.0 N A:GLY11 4.9 50.0 1.0 CA A:HIS28 4.9 46.1 1.0 CD2 A:TYR9 4.9 42.9 1.0 N A:ALA12 4.9 51.4 1.0 CA A:TYR9 4.9 45.3 1.0 N A:TYR9 4.9 45.5 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Methylated 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 Methylated Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:53.1 occ:1.00 SG A:CYS41 2.2 51.1 1.0 ND1 A:HIS43 2.3 54.3 1.0 SG A:CYS50 2.4 59.2 1.0 SG A:CYS53 2.5 60.0 1.0 CB A:CYS53 3.1 59.6 1.0 CG A:HIS43 3.1 53.7 1.0 CB A:HIS43 3.2 52.0 1.0 CB A:CYS41 3.3 49.9 1.0 CE1 A:HIS43 3.4 55.0 1.0 CB A:CYS50 3.5 60.7 1.0 N A:CYS53 3.6 61.3 1.0 N A:CYS50 3.7 61.5 1.0 CA A:CYS53 4.0 61.7 1.0 CA A:CYS50 4.0 61.3 1.0 O A:CYS41 4.2 49.4 1.0 O A:CYS50 4.3 62.8 1.0 N A:HIS43 4.3 50.4 1.0 C A:CYS50 4.3 61.2 1.0 CA A:HIS43 4.4 50.5 1.0 CD2 A:HIS43 4.4 55.0 1.0 CB A:GLU52 4.4 62.0 1.0 C A:CYS41 4.4 49.1 1.0 C A:GLU52 4.4 61.2 1.0 CA A:CYS41 4.5 48.5 1.0 NE2 A:HIS43 4.5 55.3 1.0 N A:GLU52 4.6 59.1 1.0 C A:SER49 4.7 61.5 1.0 CB A:SER49 4.7 61.9 1.0 CA A:GLU52 4.7 61.2 1.0 N A:SER49 5.0 57.6 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Methylated Prrsv NSP10 (Helicase)


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 Methylated Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn504 b:60.3 occ:1.00 O A:ALA228 2.3 39.2 1.0 O A:SER260 2.4 48.8 1.0 O A:HOH656 2.5 50.7 1.0 C A:ALA228 3.5 39.5 1.0 C A:SER260 3.5 48.6 1.0 N A:SER260 4.0 55.7 1.0 O A:HOH642 4.1 39.6 1.0 CA A:SER260 4.2 51.6 1.0 CA A:TYR229 4.2 41.0 1.0 N A:TYR229 4.3 39.8 1.0 CB A:SER260 4.4 51.0 1.0 CA A:ALA228 4.5 40.4 1.0 CB A:ALA228 4.5 39.4 1.0 N A:HIS261 4.6 46.6 1.0 CA A:HIS261 4.8 45.5 1.0 OG A:SER260 4.9 50.6 1.0 CD1 A:TYR229 4.9 51.5 1.0 OD2 A:ASP259 5.0 68.2 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Methylated Prrsv NSP10 (Helicase)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Methylated Prrsv NSP10 (Helicase) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn505 b:0.0 occ:1.00 O A:HOH716 2.7 63.4 1.0 O A:HOH728 2.9 69.1 1.0 OE2 A:GLU226 2.9 50.0 1.0 O A:HOH620 3.0 53.7 1.0 OD1 A:ASP225 3.2 49.0 1.0 O A:HOH761 3.3 60.7 1.0 O A:HOH781 3.7 54.8 1.0 O A:HOH688 3.9 64.5 1.0 CD A:GLU226 3.9 49.7 1.0 OD2 A:ASP225 4.0 49.0 1.0 CG A:ASP225 4.0 48.1 1.0 CG A:GLU226 4.2 48.6 1.0

Z.Deng, C.Tang, Z.Chen. Crystal Structure of Methylated Prrsv NSP10 (Helicase) at 2.5 Angstroms Resolution To Be Published.