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Zinc in PDB 5z3q: Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)

Enzymatic activity of Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)

All present enzymatic activity of Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom):
2.7.7.48; 3.4.22.28; 3.4.22.29; 3.6.1.15;

Protein crystallography data

The structure of Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom), PDB code: 5z3q was solved by H.Guan, J.Tian, C.Zhang, B.Qin, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.62 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.698, 84.073, 172.562, 90.00, 94.21, 90.00
R / Rfree (%) 20.2 / 26.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) (pdb code 5z3q). 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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom), PDB code: 5z3q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5z3q

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Zinc binding site 1 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:62.7
occ:1.00
SG B:CYS281 2.1 59.7 1.0
SG B:CYS269 2.3 70.8 1.0
SG B:CYS286 2.5 62.0 1.0
SG B:CYS272 2.5 82.1 1.0
HB3 B:CYS286 2.5 72.4 1.0
CB B:CYS286 3.0 60.3 1.0
HB2 B:CYS269 3.1 85.5 1.0
CB B:CYS269 3.1 71.3 1.0
HB3 B:CYS269 3.2 85.5 1.0
HB3 B:CYS281 3.3 65.8 1.0
CB B:CYS281 3.4 54.8 1.0
HB2 B:CYS286 3.4 72.4 1.0
O B:CYS282 3.5 50.8 1.0
CB B:CYS272 3.6 82.7 1.0
HD2 B:LYS288 3.6 73.5 1.0
HB2 B:CYS272 3.6 99.3 1.0
HB3 B:CYS272 3.6 99.3 1.0
H B:CYS286 3.8 67.4 1.0
HE3 B:LYS288 3.8 84.7 1.0
C B:CYS282 4.0 53.2 1.0
HZ2 B:LYS288 4.0 0.4 1.0
HB2 B:CYS281 4.0 65.8 1.0
HA B:PRO283 4.0 65.2 1.0
N B:CYS282 4.2 55.0 1.0
CA B:CYS286 4.2 59.1 1.0
HG3 B:LYS288 4.2 83.0 1.0
C B:CYS281 4.3 53.5 1.0
HA B:CYS282 4.3 70.9 1.0
H B:CYS282 4.3 65.9 1.0
CD B:LYS288 4.3 61.2 1.0
N B:CYS286 4.3 56.1 1.0
CA B:CYS281 4.4 55.0 1.0
CE B:LYS288 4.4 70.6 1.0
CA B:CYS282 4.4 59.1 1.0
N B:PRO283 4.5 49.6 1.0
CA B:CYS269 4.6 68.5 1.0
NZ B:LYS288 4.6 87.0 1.0
HD3 B:PRO283 4.7 61.5 1.0
HA B:CYS281 4.7 66.0 1.0
HB B:VAL285 4.7 64.0 1.0
H B:CYS269 4.7 79.2 1.0
CA B:PRO283 4.8 54.4 1.0
HA B:CYS286 4.8 70.9 1.0
O B:CYS281 4.8 52.5 1.0
CG B:LYS288 4.8 69.2 1.0
HA B:CYS269 4.9 82.2 1.0
HZ1 B:LYS288 5.0 0.4 1.0

Zinc binding site 2 out of 6 in 5z3q

Go back to Zinc Binding Sites List in 5z3q
Zinc binding site 2 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:56.5
occ:1.00
SG A:CYS286 2.2 47.6 1.0
SG A:CYS272 2.3 58.9 1.0
SG A:CYS281 2.3 57.9 1.0
SG A:CYS269 2.4 58.4 1.0
CB A:CYS286 3.1 42.2 1.0
CB A:CYS281 3.2 34.3 1.0
CB A:CYS272 3.2 58.6 1.0
HE3 A:LYS288 3.3 77.9 1.0
CB A:CYS269 3.3 56.8 1.0
HZ2 A:LYS288 3.5 82.7 1.0
O A:CYS282 3.7 40.5 1.0
HD2 A:LYS288 3.9 59.4 1.0
H A:CYS286 3.9 51.0 1.0
N A:CYS282 3.9 52.7 1.0
H A:CYS282 4.0 63.3 1.0
C A:CYS282 4.0 40.2 1.0
CE A:LYS288 4.0 64.9 1.0
NZ A:LYS288 4.1 68.9 1.0
O A:HOH537 4.1 54.7 1.0
HA A:CYS282 4.1 67.0 1.0
C A:CYS281 4.2 46.5 1.0
HZ1 A:LYS288 4.2 82.7 1.0
HA A:PRO283 4.2 57.3 1.0
CA A:CYS281 4.3 51.1 1.0
CA A:CYS282 4.3 55.9 1.0
CA A:CYS286 4.4 47.3 1.0
N A:CYS286 4.5 42.5 1.0
CD A:LYS288 4.5 49.5 1.0
HG3 A:LYS288 4.5 58.0 1.0
HA A:CYS281 4.5 61.3 1.0
N A:PRO283 4.6 42.7 1.0
CA A:CYS272 4.7 59.0 1.0
O A:CYS281 4.8 57.0 1.0
CA A:CYS269 4.8 48.9 1.0
HB A:VAL285 4.9 51.2 1.0
HD3 A:PRO283 4.9 61.5 1.0
HE2 A:LYS288 4.9 77.9 1.0
CA A:PRO283 4.9 47.8 1.0
HZ3 A:LYS288 4.9 82.7 1.0
HA A:CYS272 4.9 70.8 1.0
H A:CYS269 4.9 64.0 1.0
HA A:CYS286 5.0 56.7 1.0

Zinc binding site 3 out of 6 in 5z3q

Go back to Zinc Binding Sites List in 5z3q
Zinc binding site 3 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:72.2
occ:1.00
SG D:CYS272 2.2 70.8 1.0
SG D:CYS286 2.3 53.5 1.0
SG D:CYS281 2.4 68.0 1.0
SG D:CYS269 2.5 73.8 1.0
HZ2 D:LYS288 2.7 83.2 1.0
HB3 D:CYS286 3.1 72.4 1.0
HB2 D:CYS272 3.2 98.7 1.0
HB2 D:CYS269 3.2 97.6 1.0
HB3 D:CYS269 3.2 97.6 1.0
CB D:CYS269 3.2 81.4 1.0
CB D:CYS272 3.2 82.3 1.0
HZ1 D:LYS288 3.2 83.2 1.0
CB D:CYS286 3.3 60.4 1.0
NZ D:LYS288 3.4 69.3 1.0
HB3 D:CYS272 3.5 98.7 1.0
HB3 D:CYS281 3.5 74.0 1.0
CB D:CYS281 3.6 61.7 1.0
O D:CYS282 3.6 56.1 1.0
HB2 D:CYS286 3.8 72.4 1.0
HA D:PRO283 3.9 82.0 1.0
C D:CYS282 3.9 54.0 1.0
N D:CYS282 4.0 63.1 1.0
HZ3 D:LYS288 4.0 83.2 1.0
H D:CYS282 4.0 75.7 1.0
HA D:CYS282 4.0 78.5 1.0
H D:CYS286 4.1 60.7 1.0
HE3 D:LYS288 4.1 82.1 1.0
HG3 D:LYS288 4.2 72.3 1.0
HG2 D:LYS288 4.2 72.3 1.0
CA D:CYS282 4.2 65.5 1.0
C D:CYS281 4.2 70.0 1.0
HB2 D:CYS281 4.3 74.0 1.0
CE D:LYS288 4.4 68.4 1.0
N D:PRO283 4.5 66.0 1.0
CA D:CYS281 4.5 60.0 1.0
CA D:CYS286 4.6 46.7 1.0
CA D:CYS272 4.6 86.3 1.0
CG D:LYS288 4.6 60.2 1.0
N D:CYS286 4.6 50.6 1.0
CA D:PRO283 4.6 68.4 1.0
CA D:CYS269 4.7 79.9 1.0
HA D:CYS281 4.8 72.0 1.0
HA D:CYS272 4.8 0.6 1.0
O D:CYS281 4.8 75.6 1.0
O D:HOH512 4.9 51.7 1.0
H D:CYS272 4.9 0.1 1.0
H D:CYS269 5.0 93.3 1.0

Zinc binding site 4 out of 6 in 5z3q

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Zinc binding site 4 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:65.2
occ:1.00
SG C:CYS269 2.2 63.2 1.0
SG C:CYS286 2.3 68.8 1.0
SG C:CYS281 2.5 62.9 1.0
SG C:CYS272 2.5 69.4 1.0
HB3 C:CYS286 2.8 70.9 1.0
CB C:CYS269 3.0 66.7 1.0
HB3 C:CYS269 3.0 80.0 1.0
HB2 C:CYS269 3.0 80.0 1.0
HE3 C:LYS288 3.1 96.0 1.0
CB C:CYS286 3.1 59.1 1.0
HB3 C:CYS281 3.2 77.7 1.0
O C:CYS282 3.5 48.2 1.0
CB C:CYS281 3.5 64.8 1.0
HB2 C:CYS272 3.6 94.0 1.0
HB2 C:CYS286 3.6 70.9 1.0
CB C:CYS272 3.6 78.3 1.0
HB3 C:CYS272 3.7 94.0 1.0
C C:CYS282 3.8 50.6 1.0
H C:CYS282 3.8 70.0 1.0
N C:CYS282 3.8 58.3 1.0
HA C:PRO283 3.9 75.6 1.0
CE C:LYS288 4.0 80.0 1.0
HA C:CYS282 4.0 74.1 1.0
H C:CYS286 4.1 75.0 1.0
CA C:CYS282 4.2 61.8 1.0
C C:CYS281 4.2 67.6 1.0
HB2 C:CYS281 4.2 77.7 1.0
HG3 C:LYS288 4.3 92.3 1.0
N C:PRO283 4.4 52.0 1.0
CA C:CYS281 4.4 65.9 1.0
CA C:CYS269 4.4 74.8 1.0
CA C:CYS286 4.4 60.7 1.0
HZ1 C:LYS288 4.5 0.2 1.0
HE2 C:LYS288 4.5 96.0 1.0
HZ2 C:LYS288 4.5 0.2 1.0
N C:CYS286 4.6 62.5 1.0
NZ C:LYS288 4.6 87.7 1.0
CA C:PRO283 4.6 63.0 1.0
HA C:CYS269 4.7 89.7 1.0
HA C:CYS281 4.7 79.0 1.0
HD2 C:LYS288 4.7 91.0 1.0
H C:CYS269 4.8 86.1 1.0
O C:CYS281 4.8 61.1 1.0
CD C:LYS288 4.9 75.8 1.0
HB C:VAL285 4.9 79.9 1.0
HD3 C:PRO283 5.0 68.1 1.0
HA C:CYS286 5.0 72.9 1.0

Zinc binding site 5 out of 6 in 5z3q

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Zinc binding site 5 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:94.6
occ:1.00
HG E:CYS269 1.5 0.1 1.0
HB3 E:CYS286 2.3 98.2 1.0
SG E:CYS272 2.4 0.6 1.0
SG E:CYS286 2.4 78.9 1.0
SG E:CYS281 2.5 88.4 1.0
SG E:CYS269 2.6 0.4 1.0
CB E:CYS286 2.8 81.8 1.0
HB2 E:CYS286 3.1 98.2 1.0
HZ2 E:LYS288 3.3 0.4 1.0
HB3 E:CYS281 3.3 0.3 1.0
HB3 E:CYS272 3.3 0.2 1.0
HB2 E:CYS269 3.4 0.9 1.0
CB E:CYS272 3.4 0.3 1.0
HB3 E:CYS269 3.4 0.9 1.0
CB E:CYS269 3.4 0.9 1.0
HE3 E:LYS288 3.5 0.7 1.0
CB E:CYS281 3.5 98.6 1.0
HB2 E:CYS272 3.6 0.2 1.0
O E:CYS282 3.8 82.2 1.0
H E:CYS282 3.8 0.8 1.0
N E:CYS282 3.9 90.7 1.0
NZ E:LYS288 3.9 0.5 1.0
C E:CYS282 3.9 82.7 1.0
HZ1 E:LYS288 4.0 0.4 1.0
HD2 E:LYS288 4.0 0.9 1.0
CE E:LYS288 4.1 93.9 1.0
HA E:CYS282 4.1 0.3 1.0
CA E:CYS286 4.1 86.0 1.0
H E:CYS286 4.1 0.7 1.0
HA E:PRO283 4.2 0.1 1.0
C E:CYS281 4.2 97.7 1.0
HB2 E:CYS281 4.2 0.3 1.0
CA E:CYS282 4.2 88.6 1.0
HB E:VAL285 4.4 0.1 1.0
N E:CYS286 4.4 87.3 1.0
CA E:CYS281 4.5 0.9 1.0
N E:PRO283 4.5 84.5 1.0
CD E:LYS288 4.6 88.3 1.0
HA E:CYS286 4.6 0.2 1.0
HD3 E:PRO283 4.7 0.2 1.0
HZ3 E:LYS288 4.7 0.4 1.0
HA E:CYS281 4.7 0.2 1.0
CA E:CYS272 4.7 0.5 1.0
HG12 E:VAL285 4.8 0.1 1.0
HA E:CYS272 4.8 0.8 1.0
HG3 E:LYS288 4.8 0.2 1.0
O E:CYS281 4.8 99.9 1.0
CA E:PRO283 4.9 83.4 1.0
CA E:CYS269 4.9 0.6 1.0
HE2 E:LYS288 5.0 0.7 1.0

Zinc binding site 6 out of 6 in 5z3q

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Zinc binding site 6 out of 6 in the Crystal Structure of A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom)


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 A Soluble Fragment of Poliovirus 2C Atpase (2.55 Angstrom) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn401

b:0.2
occ:1.00
O H:HOH507 2.4 0.8 1.0
O H:CYS282 2.8 0.2 1.0
SG H:CYS269 2.9 0.6 1.0
SG H:CYS281 3.0 0.2 1.0
HA H:PRO283 3.1 0.3 1.0
HB H:VAL285 3.4 0.2 1.0
C H:CYS282 3.6 0.9 1.0
H H:CYS282 3.7 0.5 1.0
CA H:PRO283 3.9 0.9 1.0
N H:PRO283 4.0 0.1 1.0
N H:CYS282 4.3 0.9 1.0
CB H:VAL285 4.4 0.3 1.0
H H:VAL285 4.5 0.1 1.0
O H:VAL285 4.5 0.2 1.0
CA H:CYS282 4.6 0.7 1.0
CB H:CYS269 4.6 0.4 1.0
HB3 H:PRO283 4.6 0.6 1.0
HG23 H:VAL285 4.7 0.3 1.0
HB2 H:CYS269 4.8 0.7 1.0
CB H:CYS281 4.8 0.8 1.0
HD3 H:PRO283 4.8 0.1 1.0
HG21 H:VAL285 4.8 0.3 1.0
HB3 H:CYS269 4.8 0.7 1.0
C H:PRO283 4.8 0.2 1.0
HA H:CYS282 4.9 0.1 1.0
CB H:PRO283 4.9 0.3 1.0
CG2 H:VAL285 4.9 0.4 1.0
HB3 H:CYS281 5.0 1.0 1.0

Reference:

H.Guan, J.Tian, C.Zhang, B.Qin, S.Cui. Crystal Structure of A Soluble Fragment of Poliovirus 2CATPASE Plos Pathog. V. 14 07304 2018.
ISSN: ESSN 1553-7374
PubMed: 30231078
DOI: 10.1371/JOURNAL.PPAT.1007304
Page generated: Wed Dec 16 11:24:58 2020

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