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Zinc in PDB 5grb: Crystal Structure of 2C Helicase From Enterovirus 71 (EV71) Bound with Atpgammas

Protein crystallography data

The structure of Crystal Structure of 2C Helicase From Enterovirus 71 (EV71) Bound with Atpgammas, PDB code: 5grb 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) 45.55 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.668, 54.912, 163.097, 90.00, 89.98, 90.00
R / Rfree (%) 24.5 / 29.6

Zinc Binding Sites:

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

Zinc binding site 1 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:56.4
occ:1.00
SG A:CYS286 1.9 40.4 1.0
SG A:CYS270 2.2 61.9 1.0
O A:HOH502 2.3 58.9 1.0
SG A:CYS281 2.3 60.8 1.0
CB A:CYS270 2.9 45.6 1.0
CB A:CYS281 3.6 48.7 1.0
O A:SER282 3.6 40.8 1.0
CB A:CYS286 3.6 42.8 1.0
C A:SER282 3.7 45.6 1.0
N A:SER282 3.8 30.9 1.0
C A:CYS281 3.9 46.9 1.0
CA A:SER282 4.0 42.7 1.0
N A:PRO283 4.2 44.9 1.0
NZ A:LYS288 4.3 44.0 1.0
CA A:CYS270 4.3 41.1 1.0
O A:CYS281 4.3 45.3 1.0
O A:GLU272 4.3 62.6 1.0
CE A:LYS288 4.3 41.4 1.0
CA A:CYS281 4.4 52.5 1.0
CD A:LYS288 4.4 44.5 1.0
N A:CYS286 4.5 46.0 1.0
CA A:CYS286 4.5 39.5 1.0
N A:CYS270 4.6 48.1 1.0
OE2 A:GLU272 4.6 65.4 1.0
CA A:PRO283 4.6 46.2 1.0
CD A:PRO283 4.8 44.7 1.0

Zinc binding site 2 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:47.9
occ:1.00
SG B:CYS270 2.2 45.1 1.0
SG B:CYS286 2.2 40.1 1.0
SG B:CYS281 2.3 48.3 1.0
CB B:CYS270 2.9 44.7 1.0
CB B:CYS286 3.2 42.9 1.0
O B:SER282 3.4 49.7 1.0
CB B:CYS281 3.6 44.2 1.0
C B:SER282 3.8 48.9 1.0
N B:SER282 4.0 41.2 1.0
NZ B:LYS288 4.0 37.5 1.0
CE B:LYS288 4.0 37.1 1.0
CA B:SER282 4.2 39.3 1.0
OE2 B:GLU272 4.2 59.7 1.0
O B:GLU272 4.2 61.6 1.0
CD B:LYS288 4.2 36.8 1.0
C B:CYS281 4.2 47.4 1.0
CA B:CYS270 4.4 44.4 1.0
N B:PRO283 4.4 48.4 1.0
CA B:CYS286 4.5 49.9 1.0
N B:CYS286 4.5 45.6 1.0
CA B:CYS281 4.5 49.3 1.0
CA B:PRO283 4.7 43.4 1.0
N B:CYS270 4.8 45.9 1.0
O B:CYS281 4.8 48.7 1.0
CG B:LYS288 4.9 33.9 1.0

Zinc binding site 3 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:64.6
occ:1.00
SG C:CYS286 1.8 31.4 1.0
SG C:CYS281 2.2 50.2 1.0
SG C:CYS270 2.4 73.5 1.0
CB C:CYS270 3.0 62.2 1.0
N C:SER282 3.2 48.1 1.0
O C:SER282 3.3 59.3 1.0
CB C:CYS281 3.4 52.7 1.0
C C:SER282 3.5 56.4 1.0
CB C:CYS286 3.5 52.4 1.0
CA C:SER282 3.7 49.2 1.0
C C:CYS281 3.9 58.8 1.0
N C:PRO283 4.1 56.8 1.0
CA C:CYS281 4.2 52.5 1.0
CA C:CYS286 4.3 53.0 1.0
N C:CYS286 4.3 51.0 1.0
CA C:CYS270 4.4 68.0 1.0
OE2 C:GLU272 4.5 74.6 1.0
NZ C:LYS288 4.5 56.4 1.0
O C:GLU272 4.5 74.2 1.0
CE C:LYS288 4.6 51.1 1.0
CA C:PRO283 4.6 51.7 1.0
N C:CYS270 4.7 76.8 1.0
O C:CYS281 4.8 63.8 1.0
CD C:LYS288 4.8 54.6 1.0
CD C:PRO283 4.8 53.9 1.0

Zinc binding site 4 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:55.0
occ:1.00
SG D:CYS281 2.2 49.6 1.0
CB D:CYS286 2.3 55.1 1.0
SG D:CYS270 2.4 57.9 1.0
SG D:CYS286 2.6 86.5 1.0
O D:SER282 3.3 50.2 1.0
CB D:CYS270 3.4 58.6 1.0
CA D:CYS286 3.5 69.6 1.0
N D:SER282 3.6 44.5 1.0
C D:SER282 3.6 53.1 1.0
CB D:CYS281 3.7 47.2 1.0
OE2 D:GLU272 4.0 90.9 1.0
CA D:SER282 4.1 43.0 1.0
N D:CYS286 4.1 57.4 1.0
N D:PRO283 4.1 52.2 1.0
CE D:LYS288 4.1 51.4 1.0
NZ D:LYS288 4.2 56.2 1.0
CD D:LYS288 4.3 51.6 1.0
CA D:PRO283 4.4 46.4 1.0
C D:CYS281 4.4 56.0 1.0
CA D:CYS281 4.6 47.5 1.0
C D:CYS286 4.7 58.9 1.0
CA D:CYS270 4.8 65.8 1.0
CG D:LYS288 4.8 56.3 1.0
CD D:GLU272 4.9 75.3 1.0
CD D:PRO283 5.0 47.2 1.0

Zinc binding site 5 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn402

b:91.3
occ:1.00
SG E:CYS286 2.2 69.3 1.0
SG E:CYS270 2.2 78.3 1.0
SG E:CYS281 2.4 69.1 1.0
CB E:CYS286 3.0 79.3 1.0
CB E:CYS270 3.2 94.7 1.0
O E:SER282 3.6 68.9 1.0
CB E:CYS281 3.6 78.6 1.0
C E:SER282 3.8 73.7 1.0
CE E:LYS288 4.0 1.0 1.0
N E:SER282 4.0 82.7 1.0
NZ E:LYS288 4.0 0.9 1.0
CA E:CYS286 4.2 82.7 1.0
N E:PRO283 4.2 78.6 1.0
CA E:SER282 4.3 73.5 1.0
N E:CYS286 4.3 76.6 1.0
C E:CYS281 4.3 82.9 1.0
CD E:LYS288 4.3 96.0 1.0
CA E:PRO283 4.5 75.9 1.0
CA E:CYS281 4.5 74.0 1.0
CA E:CYS270 4.6 98.2 1.0
O E:GLU272 4.7 0.1 1.0
O E:CYS281 4.9 86.6 1.0
CG E:LYS288 4.9 92.6 1.0
N E:CYS270 5.0 87.9 1.0
C E:CYS286 5.0 84.7 1.0

Zinc binding site 6 out of 6 in 5grb

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


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) Bound with Atpgammas within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn402

b:86.5
occ:1.00
SG F:CYS281 2.3 74.8 1.0
SG F:CYS286 2.4 69.3 1.0
SG F:CYS270 2.4 72.5 1.0
CB F:CYS286 2.9 74.3 1.0
O F:SER282 3.4 68.4 1.0
CB F:CYS270 3.5 86.0 1.0
C F:SER282 3.5 67.5 1.0
N F:SER282 3.6 76.2 1.0
CB F:CYS281 3.7 81.7 1.0
CA F:SER282 4.0 70.9 1.0
N F:PRO283 4.0 72.9 1.0
CA F:CYS286 4.1 80.9 1.0
N F:CYS286 4.2 78.6 1.0
CA F:PRO283 4.3 71.0 1.0
C F:CYS281 4.3 76.3 1.0
OE2 F:GLU272 4.3 98.3 1.0
CA F:CYS281 4.6 70.8 1.0
CG F:GLU272 4.8 0.1 1.0
CA F:CYS270 4.9 88.5 1.0
CD F:PRO283 5.0 73.2 1.0

Reference:

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
Page generated: Wed Dec 16 06:19:44 2020

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