Zinc in PDB 8x77: Enterovirus Proteinase with Host Factor

Protein crystallography data

The structure of Enterovirus Proteinase with Host Factor, PDB code: 8x77 was solved by X.Gao, S.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 3.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 148.954, 57.479, 198.622, 90, 110.88, 90
R / Rfree (%) 27.4 / 29.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Enterovirus Proteinase with Host Factor (pdb code 8x77). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Enterovirus Proteinase with Host Factor, PDB code: 8x77:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8x77

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Zinc binding site 1 out of 4 in the Enterovirus Proteinase with Host Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Enterovirus Proteinase with Host Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:9.0
occ:0.14
 ND1 F:HIS118 1.4 5.9 1.0
SG F:CYS116 1.5 8.4 1.0
CG F:HIS118 2.2 6.2 1.0
SG F:CYS56 2.3 7.6 1.0
SG F:CYS58 2.4 5.0 1.0
CB F:CYS56 2.5 18.3 1.0
CB F:HIS118 2.6 11.7 1.0
CE1 F:HIS118 2.6 5.4 1.0
N F:HIS118 3.0 18.5 1.0
CA F:HIS118 3.4 9.4 1.0
CB F:CYS116 3.4 12.4 1.0
CD2 F:HIS118 3.4 5.9 1.0
NE2 F:HIS118 3.6 5.4 1.0
N F:GLN117 3.9 6.2 1.0
CA F:CYS56 4.0 8.3 1.0
CB F:CYS58 4.0 24.1 1.0
C F:CYS116 4.1 8.9 1.0
C F:GLN117 4.1 15.1 1.0
C F:HIS118 4.2 11.5 1.0
CB F:ALA54 4.3 45.3 1.0
CA F:CYS116 4.4 11.0 1.0
N F:CYS56 4.5 26.2 1.0
CA F:GLN117 4.5 16.7 1.0
N F:GLY119 4.6 14.8 1.0
O F:CYS116 4.6 11.6 1.0
CB F:GLN117 4.8 35.7 1.0
C F:CYS56 4.9 8.3 1.0
N F:CYS58 4.9 10.1 1.0
O F:HIS118 4.9 26.8 1.0

Zinc binding site 2 out of 4 in 8x77

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Zinc binding site 2 out of 4 in the Enterovirus Proteinase with Host Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Enterovirus Proteinase with Host Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:104.6
occ:0.30
 ND1 E:HIS118 1.2 83.1 1.0
SG E:CYS116 1.8 74.5 1.0
CG E:HIS118 1.9 87.6 1.0
CB E:HIS118 2.3 86.9 1.0
N E:HIS118 2.5 96.5 1.0
CE1 E:HIS118 2.5 91.6 1.0
SG E:CYS58 2.5 108.4 1.0
SG E:CYS56 2.8 81.6 1.0
CB E:CYS56 2.9 74.0 1.0
CA E:HIS118 2.9 82.8 1.0
CD2 E:HIS118 3.1 85.7 1.0
NE2 E:HIS118 3.3 100.6 1.0
CB E:CYS116 3.5 87.1 1.0
C E:GLN117 3.5 104.6 1.0
N E:GLN117 3.6 87.2 1.0
C E:CYS116 3.8 73.4 1.0
C E:HIS118 3.9 82.0 1.0
CA E:GLN117 4.0 118.6 1.0
CB E:CYS58 4.2 88.8 1.0
CB E:GLN117 4.3 126.2 1.0
CA E:CYS116 4.3 86.2 1.0
O E:CYS116 4.3 78.8 1.0
N E:GLY119 4.3 88.8 1.0
CA E:CYS56 4.4 89.5 1.0
CB E:ALA54 4.4 90.5 1.0
O E:GLN117 4.6 96.2 1.0
O E:HIS118 4.7 91.2 1.0
N E:CYS56 4.9 105.4 1.0

Zinc binding site 3 out of 4 in 8x77

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Zinc binding site 3 out of 4 in the Enterovirus Proteinase with Host Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Enterovirus Proteinase with Host Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:162.5
occ:0.31
 SG H:CYS116 2.0 151.0 1.0
CB H:HIS118 2.1 154.4 1.0
N H:HIS118 2.6 152.2 1.0
ND1 H:HIS118 2.6 146.7 1.0
CA H:HIS118 2.6 155.3 1.0
CG H:HIS118 2.6 150.9 1.0
SG H:CYS56 2.8 159.0 1.0
CB H:CYS56 3.0 136.6 1.0
CB H:ALA54 3.0 163.7 1.0
C H:HIS118 3.0 158.5 1.0
N H:GLY119 3.4 151.2 1.0
CB H:CYS116 3.4 152.8 1.0
SG H:CYS58 3.6 144.5 1.0
O H:HIS118 3.7 167.8 1.0
C H:CYS116 3.8 158.6 1.0
C H:GLN117 3.8 155.0 1.0
CE1 H:HIS118 3.9 145.6 1.0
O H:CYS116 3.9 156.7 1.0
CA H:ALA54 4.0 167.5 1.0
CD2 H:HIS118 4.0 159.1 1.0
N H:GLN117 4.0 165.0 1.0
CA H:CYS116 4.1 158.0 1.0
N H:CYS56 4.2 138.4 1.0
CA H:CYS56 4.2 136.5 1.0
O H:GLY119 4.5 150.6 1.0
CA H:GLN117 4.5 150.3 1.0
CA H:GLY119 4.5 154.1 1.0
NE2 H:HIS118 4.6 151.7 1.0
C H:ALA54 4.6 169.4 1.0
N H:ARG55 4.7 161.5 1.0
N H:CYS116 4.8 158.9 1.0
O H:GLN117 4.8 167.4 1.0
C H:GLY119 4.8 152.6 1.0
CG H:GLN117 4.9 172.7 1.0
CB H:CYS58 5.0 132.4 1.0

Zinc binding site 4 out of 4 in 8x77

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Zinc binding site 4 out of 4 in the Enterovirus Proteinase with Host Factor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Enterovirus Proteinase with Host Factor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:68.6
occ:0.45
 ND1 C:HIS118 1.5 55.9 1.0
SG C:CYS116 1.6 63.7 1.0
CG C:HIS118 2.2 57.6 1.0
SG C:CYS56 2.4 57.5 1.0
SG C:CYS58 2.4 62.1 1.0
CB C:HIS118 2.4 59.0 1.0
CB C:CYS56 2.4 59.6 1.0
CE1 C:HIS118 2.8 55.0 1.0
N C:HIS118 2.8 54.9 1.0
CA C:HIS118 3.1 65.0 1.0
CD2 C:HIS118 3.4 57.7 1.0
CB C:CYS116 3.4 76.8 1.0
NE2 C:HIS118 3.6 56.1 1.0
C C:CYS116 3.9 74.3 1.0
C C:GLN117 3.9 63.8 1.0
CA C:CYS56 3.9 62.2 1.0
O C:CYS116 3.9 68.8 1.0
C C:HIS118 4.0 62.5 1.0
N C:GLN117 4.0 89.7 1.0
CB C:CYS58 4.0 60.3 1.0
CB C:ALA54 4.2 86.8 1.0
CA C:GLN117 4.3 81.7 1.0
N C:CYS56 4.4 70.8 1.0
CA C:CYS116 4.4 67.3 1.0
N C:GLY119 4.4 63.1 1.0
CB C:GLN117 4.5 91.4 1.0
O C:HIS118 4.8 80.5 1.0
C C:CYS56 4.8 61.8 1.0
N C:CYS58 4.8 75.6 1.0
O C:GLN117 4.9 62.1 1.0

Reference:

X.Gao, B.Wang, K.Zhu, L.Wang, B.Qin, K.Shang, W.Ding, J.Wang, S.Cui. The EV71 2A Protease Occupies the Central Cleft of SETD3 and Disrupts SETD3-Actin Interaction. Nat Commun V. 15 4176 2024.
ISSN: ESSN 2041-1723
PubMed: 38755176
DOI: 10.1038/S41467-024-48504-W
Page generated: Thu Oct 31 13:50:47 2024

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