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Zinc in PDB 8urb: Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex (pdb code 8urb). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex, PDB code: 8urb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8urb

Go back to Zinc Binding Sites List in 8urb
Zinc binding site 1 out of 2 in the Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:68.4
occ:1.00
ND1 A:HIS290 2.1 29.2 1.0
HG A:CYS305 2.2 23.2 1.0
SG A:CYS296 2.3 58.2 1.0
SG A:CYS305 2.3 43.4 1.0
SG A:CYS301 2.3 43.7 1.0
HE1 A:HIS290 2.8 24.3 1.0
CE1 A:HIS290 2.8 27.7 1.0
HG A:CYS296 2.9 34.9 1.0
HG A:CYS301 2.9 28.5 1.0
CG A:HIS290 3.3 24.2 1.0
HA A:CYS296 3.3 34.1 1.0
HB2 A:HIS290 3.4 22.8 1.0
CB A:CYS296 3.4 31.7 1.0
HB3 A:CYS296 3.5 34.8 1.0
O A:CYS301 3.5 30.0 1.0
HB2 A:CYS305 3.5 20.9 1.0
H A:HIS290 3.6 23.0 1.0
CB A:CYS305 3.6 18.2 1.0
CB A:CYS301 3.8 27.3 1.0
HB3 A:CYS301 3.8 29.6 1.0
CB A:HIS290 3.9 16.2 1.0
CA A:CYS296 3.9 32.2 1.0
NE2 A:HIS290 4.0 27.0 1.0
C A:CYS301 4.0 20.6 1.0
HB3 A:CYS305 4.1 21.2 1.0
H A:CYS305 4.3 22.6 1.0
CD2 A:HIS290 4.3 27.9 1.0
HB2 A:CYS296 4.3 34.0 1.0
N A:HIS290 4.3 26.1 1.0
CA A:CYS301 4.4 17.0 1.0
HB2 A:CYS301 4.5 28.3 1.0
HA A:CYS301 4.5 27.2 1.0
H A:SER297 4.5 37.6 1.0
HA A:ILE302 4.5 24.1 1.0
HB3 A:HIS290 4.6 23.2 1.0
N A:CYS296 4.6 29.6 1.0
HA A:CYS293 4.7 23.4 1.0
CA A:HIS290 4.7 22.0 1.0
HE2 A:HIS290 4.7 24.4 1.0
HA A:TYR289 4.8 19.3 1.0
N A:ILE302 4.8 18.1 1.0
CA A:CYS305 4.8 16.2 1.0
N A:CYS305 4.8 19.0 1.0
H A:CYS296 4.8 32.5 1.0
HD1 A:HIS304 4.9 19.5 1.0

Zinc binding site 2 out of 2 in 8urb

Go back to Zinc Binding Sites List in 8urb
Zinc binding site 2 out of 2 in the Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Porcine Epidemic Diarrhea Virus Complete Core Polymerase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:79.4
occ:1.00
ND1 A:HIS637 2.1 32.1 1.0
SG A:CYS482 2.3 41.6 1.0
SG A:CYS641 2.3 46.5 1.0
SG A:CYS640 2.3 58.8 1.0
HG A:CYS482 2.4 32.6 1.0
HB3 A:HIS637 2.8 29.6 1.0
HG A:CYS641 3.0 37.8 1.0
CE1 A:HIS637 3.0 35.6 1.0
CG A:HIS637 3.1 30.3 1.0
HE1 A:HIS637 3.2 30.6 1.0
HG A:CYS640 3.3 44.3 1.0
HB2 A:CYS640 3.3 44.6 1.0
CB A:HIS637 3.4 27.7 1.0
CB A:CYS640 3.4 41.8 1.0
HE1 A:TYR566 3.6 19.5 1.0
CB A:CYS482 3.7 32.0 1.0
HB2 A:CYS482 3.7 32.3 1.0
CB A:CYS641 3.7 33.3 1.0
HB2 A:CYS641 3.7 37.5 1.0
H A:CYS482 3.7 32.1 1.0
C A:CYS640 4.0 43.9 1.0
HB2 A:HIS637 4.1 30.1 1.0
N A:CYS641 4.1 38.0 1.0
N A:CYS482 4.1 32.4 1.0
HA A:HIS637 4.1 28.1 1.0
NE2 A:HIS637 4.1 35.6 1.0
HB3 A:CYS640 4.2 45.0 1.0
CD2 A:HIS637 4.2 33.0 1.0
H A:CYS641 4.3 39.2 1.0
HD1 A:TYR566 4.3 22.7 1.0
CA A:CYS640 4.3 40.2 1.0
O A:CYS640 4.3 52.1 1.0
CE1 A:TYR566 4.3 12.4 1.0
CA A:HIS637 4.4 23.0 1.0
HB3 A:CYS482 4.4 32.5 1.0
HB3 A:CYS641 4.4 37.8 1.0
HA2 A:GLY481 4.4 26.2 1.0
CA A:CYS482 4.4 35.1 1.0
CA A:CYS641 4.5 35.6 1.0
HH A:TYR523 4.6 26.8 1.0
H A:CYS640 4.6 45.7 1.0
HA A:CYS482 4.7 32.8 1.0
CD1 A:TYR566 4.7 17.4 1.0
HA A:CYS641 4.8 37.9 1.0
C A:GLY481 4.8 27.5 1.0
N A:CYS640 4.9 46.8 1.0
HE2 A:HIS637 4.9 29.6 1.0
OH A:TYR523 5.0 32.8 1.0

Reference:

T.K.Anderson, P.J.Hoferle, K.W.Lee, J.J.Coon, R.N.Kirchdoerfer. An Alphacoronavirus Polymerase Structure Reveals Conserved Co-Factor Functions. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993498
DOI: 10.1101/2023.03.15.532841
Page generated: Thu Dec 28 13:45:32 2023

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