Zinc in PDB 5gq1: Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)

The structure of Crystal Structure of 2C Helicase From Enterovirus 71 (EV71), PDB code: 5gq1 was solved by H.X.Guan, J.Tian, B.Qin, J.Wojdyla, M.T.Wang, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.64 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.109, 159.654, 75.606, 90.00, 90.16, 90.00
R / Rfree (%)	22.9 / 28.6

The binding sites of Zinc atom in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71) (pdb code 5gq1). 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 2C Helicase From Enterovirus 71 (EV71), PDB code: 5gq1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:68.0 occ:1.00 O A:HOH511 2.2 68.7 1.0 SG A:CYS270 2.2 62.8 1.0 SG A:CYS286 2.2 58.0 1.0 SG A:CYS281 2.3 71.1 1.0 HB3 A:CYS286 2.7 69.2 1.0 HB2 A:CYS270 3.0 63.4 1.0 CB A:CYS286 3.1 57.7 1.0 CB A:CYS270 3.1 52.8 1.0 HB3 A:CYS270 3.2 63.4 1.0 O A:SER282 3.3 56.6 1.0 HZ2 A:LYS288 3.4 82.0 1.0 HD2 A:LYS288 3.5 70.3 1.0 HB3 A:CYS281 3.6 62.2 1.0 CB A:CYS281 3.6 51.9 1.0 HB2 A:CYS286 3.6 69.2 1.0 H A:CYS286 3.6 67.1 1.0 C A:SER282 3.7 56.9 1.0 N A:SER282 3.8 57.4 1.0 HE3 A:LYS288 3.9 72.7 1.0 HA A:PRO283 3.9 70.5 1.0 H A:SER282 4.0 68.9 1.0 OE2 A:GLU272 4.0 69.2 1.0 C A:CYS281 4.0 57.8 1.0 HA A:SER282 4.1 64.3 1.0 NZ A:LYS288 4.1 68.3 1.0 CA A:SER282 4.1 53.6 1.0 N A:CYS286 4.2 55.9 1.0 CD A:LYS288 4.3 58.6 1.0 CA A:CYS286 4.3 50.3 1.0 CE A:LYS288 4.3 60.6 1.0 N A:PRO283 4.3 56.7 1.0 HB2 A:CYS281 4.4 62.2 1.0 CA A:CYS281 4.4 52.5 1.0 HG3 A:LYS288 4.4 68.0 1.0 HG2 A:GLU272 4.4 82.8 1.0 HD3 A:PRO283 4.5 69.0 1.0 HZ1 A:LYS288 4.5 82.0 1.0 O A:GLU272 4.5 59.0 1.0 O A:HOH509 4.5 62.5 1.0 O A:CYS281 4.5 58.4 1.0 H A:CYS270 4.5 74.5 1.0 CA A:CYS270 4.5 62.1 1.0 HB A:VAL285 4.6 65.0 1.0 CA A:PRO283 4.6 58.8 1.0 HA A:CYS281 4.7 63.1 1.0 HZ3 A:LYS288 4.8 82.0 1.0 CD A:GLU272 4.8 67.7 1.0 HA A:CYS270 4.9 74.5 1.0 HA A:CYS286 4.9 60.4 1.0 CG A:LYS288 4.9 56.7 1.0 CD A:PRO283 5.0 57.5 1.0 HD3 A:LYS288 5.0 70.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:79.4 occ:1.00 SG B:CYS281 1.8 53.3 1.0 SG B:CYS270 2.1 65.2 1.0 SG B:CYS286 2.2 70.1 1.0 HB3 B:CYS286 3.2 73.4 1.0 HE3 B:LYS288 3.2 61.9 1.0 H B:SER282 3.3 63.4 1.0 HB2 B:CYS270 3.3 88.9 1.0 CB B:CYS270 3.4 74.1 1.0 CB B:CYS286 3.4 61.2 1.0 O B:SER282 3.4 52.5 1.0 HZ2 B:LYS288 3.5 66.5 1.0 N B:SER282 3.6 52.8 1.0 C B:SER282 3.6 52.4 1.0 HB3 B:CYS270 3.6 88.9 1.0 CB B:CYS281 3.6 62.7 1.0 HB3 B:CYS281 3.9 75.3 1.0 HB2 B:CYS286 3.9 73.4 1.0 CE B:LYS288 3.9 51.6 1.0 NZ B:LYS288 4.0 55.4 1.0 HA B:PRO283 4.0 70.6 1.0 HZ1 B:LYS288 4.0 66.5 1.0 CA B:SER282 4.0 53.5 1.0 HA B:SER282 4.0 64.1 1.0 H B:CYS286 4.1 66.9 1.0 HD2 B:LYS288 4.1 72.4 1.0 N B:PRO283 4.1 50.5 1.0 HB2 B:CYS281 4.2 75.3 1.0 C B:CYS281 4.2 56.6 1.0 HD3 B:PRO283 4.3 71.0 1.0 O B:GLU272 4.5 75.2 1.0 HG3 B:LYS288 4.5 69.6 1.0 CD B:LYS288 4.5 60.3 1.0 CA B:CYS281 4.5 53.0 1.0 CA B:PRO283 4.6 58.9 1.0 CA B:CYS286 4.6 55.3 1.0 N B:CYS286 4.6 55.8 1.0 H B:CYS270 4.7 88.7 1.0 HE2 B:LYS288 4.7 61.9 1.0 CA B:CYS270 4.7 74.9 1.0 CD B:PRO283 4.8 59.1 1.0 HZ3 B:LYS288 4.8 66.5 1.0 HB B:VAL285 4.9 66.2 1.0 HA B:CYS281 4.9 63.6 1.0 O B:CYS281 4.9 62.8 1.0 HB2 B:LYS288 5.0 61.9 1.0 HG2 B:GLU272 5.0 82.5 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:75.2 occ:1.00 HG C:CYS286 1.9 69.2 1.0 SG C:CYS281 2.1 67.6 1.0 SG C:CYS270 2.2 61.1 1.0 HB2 C:CYS286 2.3 92.1 1.0 SG C:CYS286 2.4 57.7 1.0 CB C:CYS286 2.8 76.7 1.0 HB2 C:CYS270 2.9 73.1 1.0 HB3 C:CYS281 3.1 67.2 1.0 CB C:CYS270 3.1 60.9 1.0 CB C:CYS281 3.2 56.0 1.0 HB3 C:CYS270 3.3 73.1 1.0 HB3 C:CYS286 3.3 92.1 1.0 H C:SER282 3.5 68.9 1.0 O C:SER282 3.6 48.4 1.0 N C:SER282 3.6 57.4 1.0 C C:CYS281 3.8 59.3 1.0 C C:SER282 3.8 54.6 1.0 HB2 C:CYS281 3.9 67.2 1.0 HA C:CYS286 4.1 70.5 1.0 CA C:CYS281 4.1 49.6 1.0 CA C:CYS286 4.1 58.8 1.0 CA C:SER282 4.2 59.5 1.0 HA C:PRO283 4.2 59.0 1.0 HA C:SER282 4.2 71.5 1.0 O C:CYS281 4.4 64.2 1.0 N C:PRO283 4.4 49.1 1.0 HA C:CYS281 4.4 59.5 1.0 H C:CYS270 4.4 79.8 1.0 O C:GLU272 4.4 58.6 1.0 HD3 C:PRO283 4.5 75.2 1.0 CA C:CYS270 4.6 63.0 1.0 HB C:VAL285 4.6 53.7 1.0 HG2 C:LYS288 4.7 85.4 1.0 H C:CYS286 4.7 71.8 1.0 N C:CYS286 4.7 59.8 1.0 OE1 C:GLU272 4.7 80.0 1.0 CA C:PRO283 4.8 49.2 1.0 HG2 C:GLU272 4.8 76.9 1.0 HG3 C:LYS288 4.8 85.4 1.0 N C:CYS270 4.9 66.5 1.0 CD C:PRO283 5.0 62.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:76.7 occ:1.00 HG D:CYS270 1.4 76.7 1.0 SG D:CYS286 2.3 47.4 1.0 SG D:CYS281 2.4 65.0 1.0 SG D:CYS270 2.5 63.9 1.0 HE2 D:LYS288 2.8 80.6 1.0 HB3 D:CYS286 2.9 51.5 1.0 HZ1 D:LYS288 3.1 78.7 1.0 H D:SER282 3.1 62.5 1.0 CB D:CYS286 3.2 43.0 1.0 HB2 D:CYS270 3.2 78.4 1.0 O D:SER282 3.3 50.8 1.0 CB D:CYS270 3.4 65.3 1.0 N D:SER282 3.5 52.1 1.0 C D:SER282 3.5 47.9 1.0 HZ3 D:LYS288 3.5 78.7 1.0 CE D:LYS288 3.5 67.1 1.0 HB3 D:CYS270 3.6 78.4 1.0 NZ D:LYS288 3.6 65.6 1.0 HB2 D:CYS286 3.8 51.5 1.0 H D:CYS286 3.8 61.8 1.0 HA D:SER282 3.8 59.4 1.0 CB D:CYS281 3.8 67.8 1.0 HB3 D:CYS281 3.8 81.3 1.0 HA D:PRO283 3.8 61.3 1.0 CA D:SER282 3.8 49.5 1.0 HE3 D:LYS288 3.9 80.6 1.0 HG3 D:LYS288 4.1 87.3 1.0 N D:PRO283 4.1 50.2 1.0 C D:CYS281 4.1 51.7 1.0 HD3 D:PRO283 4.3 68.1 1.0 N D:CYS286 4.3 51.5 1.0 CA D:CYS286 4.3 46.5 1.0 HZ2 D:LYS288 4.4 78.7 1.0 CA D:PRO283 4.5 51.1 1.0 HB2 D:CYS281 4.5 81.3 1.0 CA D:CYS281 4.6 47.5 1.0 O D:GLU272 4.6 76.3 1.0 CD D:PRO283 4.7 56.8 1.0 CD D:LYS288 4.8 63.9 1.0 CA D:CYS270 4.8 71.5 1.0 OE1 D:GLU272 4.8 80.5 1.0 HG3 D:PRO283 4.8 64.0 1.0 CG D:LYS288 4.9 72.8 1.0 HA D:CYS281 4.9 57.0 1.0 O D:CYS281 4.9 53.7 1.0 HA D:CYS286 4.9 55.8 1.0 H D:CYS270 4.9 83.6 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn401 b:0.6 occ:1.00 HB2 E:CYS286 1.9 95.2 1.0 SG E:CYS281 2.1 91.6 1.0 CB E:CYS286 2.5 79.3 1.0 HB3 E:CYS286 2.5 95.2 1.0 SG E:CYS286 2.9 0.4 1.0 HB2 E:CYS270 3.2 0.5 1.0 HE3 E:LYS288 3.4 0.4 1.0 O E:SER282 3.5 81.0 1.0 CB E:CYS281 3.6 95.8 1.0 HB2 E:CYS281 3.6 1.0 1.0 HD2 E:LYS288 3.6 98.6 1.0 HZ2 E:LYS288 3.7 0.1 1.0 CB E:CYS270 3.9 0.8 1.0 SG E:CYS270 3.9 0.1 1.0 CA E:CYS286 3.9 78.3 1.0 C E:SER282 4.0 79.7 1.0 HA E:PRO283 4.0 94.6 1.0 HB3 E:CYS270 4.0 0.5 1.0 CE E:LYS288 4.1 0.0 1.0 H E:CYS286 4.1 92.3 1.0 HA E:CYS286 4.2 94.0 1.0 HB3 E:CYS281 4.2 1.0 1.0 HG3 E:LYS288 4.2 95.2 1.0 N E:CYS286 4.3 77.0 1.0 CD E:LYS288 4.3 82.2 1.0 NZ E:LYS288 4.3 0.4 1.0 N E:SER282 4.3 92.0 1.0 C E:CYS281 4.3 95.2 1.0 HG3 E:GLU272 4.4 0.5 1.0 HA E:SER282 4.4 0.1 1.0 H E:SER282 4.5 0.5 1.0 N E:PRO283 4.5 80.8 1.0 HZ1 E:LYS288 4.5 0.1 1.0 CA E:SER282 4.5 85.0 1.0 CA E:CYS281 4.6 98.7 1.0 O E:GLU272 4.6 0.6 1.0 O E:CYS281 4.7 95.6 1.0 CA E:PRO283 4.7 78.8 1.0 HB E:VAL285 4.7 95.2 1.0 CG E:LYS288 4.8 79.3 1.0 HD3 E:PRO283 4.9 0.8 1.0 H E:CYS270 4.9 1.0 1.0 C E:CYS286 4.9 71.3 1.0 HE2 E:LYS288 5.0 0.4 1.0 HG2 E:GLU272 5.0 0.5 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of 2C Helicase From Enterovirus 71 (EV71)


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 2C Helicase From Enterovirus 71 (EV71) within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn401 b:0.4 occ:1.00 HB2 F:CYS286 1.8 0.4 1.0 HG F:CYS270 1.9 0.7 1.0 SG F:CYS281 2.2 99.6 1.0 CB F:CYS286 2.5 91.2 1.0 HB3 F:CYS286 2.7 0.4 1.0 SG F:CYS270 2.7 0.6 1.0 HB2 F:CYS270 2.8 0.4 1.0 SG F:CYS286 3.0 0.6 1.0 CB F:CYS270 3.2 0.4 1.0 O F:SER282 3.2 99.5 1.0 HE3 F:LYS288 3.4 0.2 1.0 HB3 F:CYS270 3.4 0.4 1.0 HZ2 F:LYS288 3.5 1.0 1.0 H F:SER282 3.8 0.8 1.0 C F:SER282 3.8 0.5 1.0 HD2 F:LYS288 3.8 0.2 1.0 CA F:CYS286 3.9 93.1 1.0 H F:CYS286 3.9 0.3 1.0 CB F:CYS281 3.9 0.8 1.0 OE2 F:GLU272 3.9 0.2 1.0 N F:SER282 4.0 97.3 1.0 CE F:LYS288 4.1 0.3 1.0 HA F:PRO283 4.1 0.2 1.0 HG3 F:LYS288 4.1 0.9 1.0 NZ F:LYS288 4.1 0.8 1.0 HA F:CYS286 4.1 0.7 1.0 HB3 F:CYS281 4.1 0.6 1.0 HG2 F:GLU272 4.2 0.6 1.0 N F:CYS286 4.2 95.2 1.0 HZ1 F:LYS288 4.3 1.0 1.0 H F:CYS270 4.3 0.1 1.0 CA F:SER282 4.3 99.5 1.0 CD F:LYS288 4.3 0.7 1.0 O F:GLU272 4.3 0.3 1.0 HA F:SER282 4.4 0.3 1.0 HB2 F:CYS281 4.4 0.6 1.0 N F:PRO283 4.4 99.3 1.0 C F:CYS281 4.5 98.7 1.0 CA F:CYS270 4.6 1.0 1.0 CG F:LYS288 4.7 0.2 1.0 CA F:PRO283 4.7 95.2 1.0 CD F:GLU272 4.8 0.7 1.0 HG23 F:VAL285 4.8 0.5 1.0 CA F:CYS281 4.8 0.0 1.0 N F:CYS270 4.9 0.6 1.0 HZ3 F:LYS288 4.9 1.0 1.0 CG F:GLU272 4.9 0.0 1.0 HE2 F:LYS288 4.9 0.2 1.0 HB2 F:LYS288 5.0 0.4 1.0 C F:CYS286 5.0 94.4 1.0

H.X.Guan, J.Tian, B.Qin, J.Wojdyla, B.Wang, Z.D.Zhao, M.T.Wang, S.Cui. Crystal Structure of 2C Helicase From Enterovirus 71 Sci Adv V. 3 02573 2017.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.1602573