Zinc in PDB 5wwp: Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)

The structure of Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13), PDB code: 5wwp was solved by W.Hao, J.A.Wojdyla, R.Zhao, R.Han, R.Das, I.Zlatev, M.Manoharan, M.Wang, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.95 / 3.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	185.675, 185.675, 185.087, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.7

The binding sites of Zinc atom in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) (pdb code 5wwp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13), PDB code: 5wwp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


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 Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn601 b:45.1 occ:1.00 SG B:CYS8 2.0 66.3 1.0 SG B:CYS26 2.0 46.0 1.0 SG B:CYS5 2.0 42.1 1.0 SG B:CYS29 2.0 46.8 1.0 CB B:CYS26 3.2 49.0 1.0 CB B:CYS5 3.3 55.5 1.0 CB B:CYS29 3.3 46.8 1.0 CB B:CYS8 3.6 50.5 1.0 N B:CYS8 3.7 53.4 1.0 N B:CYS26 3.8 42.6 1.0 CA B:CYS26 4.1 44.7 1.0 N B:CYS29 4.2 50.8 1.0 CA B:CYS8 4.2 47.1 1.0 CA B:GLY99 4.2 59.8 1.0 CA B:CYS29 4.3 48.8 1.0 CB B:VAL7 4.4 46.4 1.0 N B:GLY99 4.5 68.3 1.0 CA B:CYS5 4.7 55.6 1.0 C B:CYS8 4.7 58.1 1.0 C B:CYS26 4.8 45.4 1.0 C B:VAL7 4.8 52.3 1.0 O B:CYS8 4.8 66.1 1.0 CB B:SER10 4.9 66.5 1.0 OG B:SER10 4.9 64.6 1.0 N B:VAL7 4.9 46.4 1.0 CA B:VAL7 4.9 46.8 1.0 C B:LEU25 5.0 43.8 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


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 Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn602 b:42.8 occ:1.00 SG B:CYS19 1.7 37.9 1.0 NE2 B:HIS33 1.8 36.7 1.0 ND1 B:HIS39 1.9 43.8 1.0 SG B:CYS16 2.0 35.4 1.0 CE1 B:HIS33 2.7 39.6 1.0 CD2 B:HIS33 2.8 36.6 1.0 CE1 B:HIS39 2.9 42.8 1.0 CG B:HIS39 2.9 44.2 1.0 CB B:CYS19 3.1 45.4 1.0 CB B:CYS16 3.2 41.6 1.0 CB B:HIS39 3.3 43.5 1.0 N B:CYS19 3.6 39.9 1.0 CA B:CYS19 3.7 42.4 1.0 ND1 B:HIS33 3.8 37.9 1.0 CG B:HIS33 3.9 39.0 1.0 NE2 B:HIS39 4.0 41.1 1.0 CD2 B:HIS39 4.0 42.7 1.0 CA B:CYS16 4.6 42.8 1.0 C B:THR18 4.6 41.1 1.0 OG1 B:THR18 4.6 48.8 1.0 CB B:ALA110 4.7 38.4 1.0 CA B:HIS39 4.8 44.6 1.0 C B:CYS16 5.0 46.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


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 Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn603 b:52.2 occ:1.00 ND1 B:HIS75 1.7 73.5 1.0 SG B:CYS55 1.9 68.5 1.0 CB B:CYS72 2.2 68.9 1.0 SG B:CYS50 2.2 83.0 1.0 SG B:CYS72 2.6 85.7 1.0 CE1 B:HIS75 2.6 85.4 1.0 CG B:HIS75 2.9 70.9 1.0 CB B:CYS55 2.9 81.6 1.0 CB B:CYS50 3.3 74.3 1.0 CB B:HIS75 3.4 69.2 1.0 CA B:CYS72 3.5 74.8 1.0 N B:CYS72 3.7 82.9 1.0 NE2 B:HIS75 3.8 77.9 1.0 CD2 B:HIS75 3.9 74.3 1.0 CA B:CYS55 4.3 85.8 1.0 N B:HIS75 4.5 73.4 1.0 CB B:ALA52 4.6 76.0 1.0 CG1 B:VAL57 4.6 61.8 1.0 CA B:HIS75 4.6 73.0 1.0 C B:CYS72 4.6 74.0 1.0 CA B:CYS50 4.7 62.2 1.0 C B:CYS55 5.0 82.4 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


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 Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn601 b:52.5 occ:1.00 SG A:CYS8 1.8 57.1 1.0 SG A:CYS5 1.9 43.6 1.0 SG A:CYS29 2.1 57.9 1.0 SG A:CYS26 2.2 51.7 1.0 CB A:CYS29 3.0 53.7 1.0 CB A:CYS8 3.0 46.5 1.0 CB A:CYS5 3.1 45.5 1.0 CB A:CYS26 3.5 51.0 1.0 N A:CYS8 3.6 47.6 1.0 CA A:CYS8 3.9 44.0 1.0 N A:CYS26 3.9 46.4 1.0 N A:CYS29 4.1 61.0 1.0 CA A:CYS29 4.1 58.0 1.0 CB A:VAL7 4.2 38.3 1.0 CA A:CYS26 4.3 47.5 1.0 CA A:GLY99 4.3 55.3 1.0 C A:VAL7 4.4 41.0 1.0 N A:GLY99 4.5 55.4 1.0 CA A:CYS5 4.5 42.0 1.0 CB A:SER10 4.6 46.8 1.0 CA A:VAL7 4.7 36.9 1.0 CG1 A:VAL7 4.8 41.9 1.0 C A:GLY99 4.9 58.0 1.0 N A:VAL7 4.9 37.8 1.0 C A:CYS26 4.9 50.6 1.0 O A:CYS26 5.0 51.2 1.0 C A:CYS8 5.0 45.0 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


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 Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn602 b:50.8 occ:1.00 NE2 A:HIS33 1.6 54.6 1.0 SG A:CYS19 1.8 69.7 1.0 SG A:CYS16 2.0 49.8 1.0 CD2 A:HIS33 2.5 61.2 1.0 CE1 A:HIS33 2.7 56.5 1.0 CB A:CYS19 3.0 54.5 1.0 CB A:CYS16 3.4 46.9 1.0 N A:CYS19 3.6 60.7 1.0 CG A:HIS33 3.6 53.8 1.0 ND1 A:HIS33 3.7 55.2 1.0 CA A:CYS19 3.7 54.9 1.0 C A:THR18 4.2 66.7 1.0 O A:THR18 4.4 64.3 1.0 CB A:HIS39 4.6 81.4 1.0 CA A:CYS16 4.7 49.9 1.0 O A:CYS16 4.8 61.3 1.0 CB A:ALA110 4.9 61.8 1.0 C A:CYS16 4.9 55.2 1.0 OG1 A:THR37 5.0 71.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase (Mers-Cov NSP13) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn603 b:0.5 occ:1.00 CB A:CYS72 2.1 84.5 1.0 SG A:CYS50 2.2 98.2 1.0 SG A:CYS55 2.2 0.2 1.0 SG A:CYS72 2.5 64.4 1.0 ND1 A:HIS75 2.5 0.2 1.0 CE1 A:HIS75 2.7 0.4 1.0 CB A:CYS50 2.9 89.6 1.0 CB A:CYS55 3.3 0.9 1.0 CA A:CYS72 3.5 81.4 1.0 CG A:HIS75 3.7 0.1 1.0 NE2 A:HIS75 3.9 0.1 1.0 N A:CYS72 3.9 85.4 1.0 CA A:CYS50 4.4 90.5 1.0 CD2 A:HIS75 4.4 0.3 1.0 CB A:HIS75 4.5 97.8 1.0 C A:CYS72 4.6 78.2 1.0 O A:CYS72 4.7 79.4 1.0 CA A:CYS55 4.8 0.6 1.0 N A:HIS75 4.8 90.5 1.0 C A:PHE71 4.8 75.9 1.0 CB A:ALA52 4.8 0.1 1.0 O A:CYS50 4.8 0.8 1.0 C A:CYS50 4.9 99.5 1.0

W.Hao, J.A.Wojdyla, R.Zhao, R.Han, R.Das, I.Zlatev, M.Manoharan, M.Wang, S.Cui. Crystal Structure of Middle East Respiratory Syndrome Coronavirus Helicase Plos Pathog. V. 13 06474 2017.
ISSN: ESSN 1553-7374
PubMed: 28651017
DOI: 10.1371/JOURNAL.PPAT.1006474