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Zinc in PDB 8q3k: The Open State of the Asfv Apo-Rna Polymerase

Enzymatic activity of The Open State of the Asfv Apo-Rna Polymerase

All present enzymatic activity of The Open State of the Asfv Apo-Rna Polymerase:
2.7.7.6;

Other elements in 8q3k:

The structure of The Open State of the Asfv Apo-Rna Polymerase also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the The Open State of the Asfv Apo-Rna Polymerase (pdb code 8q3k). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Open State of the Asfv Apo-Rna Polymerase, PDB code: 8q3k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 1 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:175.8
occ:1.00
 NE2 A:HIS72 1.8 97.8 1.0
SG A:CYS69 2.0 83.5 1.0
SG A:CYS62 2.0 71.9 1.0
CD2 A:HIS72 2.2 94.1 1.0
SG A:CYS59 2.3 86.4 1.0
CB A:CYS59 3.0 79.9 1.0
CB A:CYS69 3.0 73.5 1.0
CE1 A:HIS72 3.1 86.4 1.0
CB A:CYS62 3.5 75.5 1.0
CG A:HIS72 3.5 77.9 1.0
ND1 A:HIS72 3.8 74.0 1.0
N A:CYS62 3.9 67.6 1.0
CA A:CYS69 4.0 73.3 1.0
CA A:CYS62 4.2 70.0 1.0
CA A:CYS59 4.4 76.8 1.0
C A:CYS62 4.5 69.8 1.0
C A:CYS69 4.7 72.3 1.0
CB A:THR61 4.7 79.9 1.0
CB A:HIS72 4.7 70.3 1.0
N A:MET70 4.8 71.6 1.0
CB A:HIS64 4.9 65.4 1.0
C A:THR61 4.9 70.8 1.0
N A:SER63 4.9 73.6 1.0
CA A:GLY51 5.0 78.6 1.0
O A:CYS62 5.0 69.3 1.0

Zinc binding site 2 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 2 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:208.7
occ:1.00
 SG A:CYS102 2.3 134.4 1.0
SG A:CYS137 2.3 146.9 1.0
SG A:CYS134 2.3 138.9 1.0
SG A:CYS99 2.3 118.5 1.0
CB A:CYS137 2.9 141.9 1.0
CB A:CYS102 3.2 122.8 1.0
CB A:CYS134 3.4 132.0 1.0
CB A:CYS99 3.5 114.6 1.0
N A:CYS102 3.5 124.6 1.0
CG2 A:VAL136 3.7 121.5 1.0
N A:CYS137 3.7 138.3 1.0
CA A:CYS102 3.8 123.4 1.0
CA A:CYS137 3.9 138.7 1.0
O A:CYS102 4.2 123.4 1.0
C A:CYS102 4.3 125.7 1.0
CB A:ASN101 4.4 123.1 1.0
C A:ASN101 4.5 123.1 1.0
C A:VAL136 4.5 121.8 1.0
CA A:CYS134 4.8 129.3 1.0
CA A:ASN101 4.8 122.1 1.0
CB A:ALA104 4.8 106.5 1.0
CA A:CYS99 4.9 113.0 1.0
O A:ALA104 4.9 102.8 1.0
C A:CYS137 4.9 138.1 1.0
N A:ASN101 4.9 120.9 1.0
O A:CYS137 4.9 137.8 1.0
CB A:VAL136 5.0 121.2 1.0

Zinc binding site 3 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 3 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:130.8
occ:1.00
 SG B:CYS1198 2.3 75.4 1.0
SG B:CYS1183 2.3 75.6 1.0
SG B:CYS1180 2.3 69.8 1.0
SG B:CYS1201 2.3 87.6 1.0
CB B:CYS1180 3.1 54.4 1.0
CB B:CYS1201 3.2 73.3 1.0
CB B:CYS1183 3.2 60.5 1.0
CB B:CYS1198 3.6 59.5 1.0
N B:CYS1183 3.6 49.5 1.0
N B:CYS1201 3.7 63.1 1.0
CA B:CYS1183 4.0 51.5 1.0
CA B:CYS1201 4.1 67.0 1.0
CB B:ASN1182 4.1 52.8 1.0
CB B:ASN1200 4.3 73.9 1.0
C B:ASN1182 4.4 47.8 1.0
CA B:CYS1180 4.5 42.0 1.0
ND2 B:ASN1182 4.6 62.9 1.0
C B:ASN1200 4.6 70.2 1.0
ND2 B:ASN1200 4.6 77.8 1.0
CA B:ASN1182 4.7 49.3 1.0
N B:ASN1182 4.8 50.2 1.0
O B:CYS1180 4.8 49.9 1.0
C B:CYS1180 4.8 37.8 1.0
C B:CYS1183 4.8 61.6 1.0
CG B:ASN1182 4.9 57.2 1.0
CA B:ASN1200 4.9 70.6 1.0
CA B:CYS1198 4.9 57.2 1.0
N B:ASN1200 4.9 75.0 1.0

Zinc binding site 4 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 4 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:246.8
occ:1.00
 SG I:CYS4 2.3 173.5 1.0
SG I:CYS26 2.3 192.5 1.0
SG I:CYS24 2.3 192.9 1.0
SG I:CYS7 2.3 178.9 1.0
CB I:CYS24 3.1 187.4 1.0
CB I:CYS26 3.4 190.9 1.0
O I:CYS7 3.6 179.4 1.0
CB I:CYS7 3.7 175.9 1.0
CB I:CYS4 3.9 172.6 1.0
N I:CYS26 4.0 192.3 1.0
CB I:SER9 4.2 164.7 1.0
N I:CYS7 4.3 177.3 1.0
C I:CYS7 4.3 177.8 1.0
CA I:CYS26 4.3 191.1 1.0
CA I:CYS7 4.3 176.6 1.0
CA I:CYS24 4.6 187.4 1.0
N I:SER25 4.7 183.9 1.0
C I:CYS24 4.9 188.1 1.0
C I:CYS26 4.9 190.6 1.0
OG I:SER9 4.9 163.3 1.0
O I:GLY27 5.0 178.7 1.0

Zinc binding site 5 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 5 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:207.8
occ:1.00
 SG I:CYS98 2.3 113.9 1.0
SG I:CYS73 2.3 121.6 1.0
SG I:CYS96 2.3 121.2 1.0
SG I:CYS76 2.3 132.5 1.0
CB I:CYS98 2.5 108.9 1.0
CB I:CYS76 3.2 124.6 1.0
CB I:CYS96 3.3 111.1 1.0
N I:CYS76 3.7 124.8 1.0
CB I:CYS73 3.7 118.5 1.0
CA I:CYS98 3.8 107.3 1.0
N I:CYS98 3.8 108.7 1.0
CA I:CYS76 4.1 123.9 1.0
CB I:ASN75 4.3 120.5 1.0
CB I:TYR100 4.4 104.7 1.0
C I:CYS98 4.6 106.0 1.0
CA I:CYS96 4.7 106.0 1.0
C I:ASN75 4.7 120.9 1.0
C I:CYS96 4.9 105.2 1.0
N I:TYR100 4.9 103.0 1.0
CA I:ASN75 4.9 120.3 1.0
N I:ARG97 5.0 102.7 1.0

Zinc binding site 6 out of 6 in 8q3k

Go back to Zinc Binding Sites List in 8q3k
Zinc binding site 6 out of 6 in the The Open State of the Asfv Apo-Rna Polymerase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Open State of the Asfv Apo-Rna Polymerase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:118.5
occ:1.00
 SG J:CYS65 2.3 63.4 1.0
SG J:CYS10 2.3 82.4 1.0
SG J:CYS66 2.3 66.0 1.0
SG J:CYS7 2.3 68.1 1.0
CB J:CYS10 3.0 53.6 1.0
N J:CYS66 3.3 49.6 1.0
CB J:CYS7 3.4 55.3 1.0
CB J:CYS65 3.5 58.2 1.0
N J:CYS10 3.6 48.9 1.0
CB J:CYS66 3.7 55.2 1.0
CA J:CYS66 3.7 49.8 1.0
CA J:CYS10 3.9 46.2 1.0
C J:CYS65 3.9 55.4 1.0
NE J:ARG63 4.1 54.4 1.0
CA J:CYS65 4.2 58.0 1.0
CB J:THR9 4.3 51.4 1.0
C J:THR9 4.5 52.0 1.0
CB J:ARG63 4.7 57.1 1.0
CD J:ARG63 4.7 55.4 1.0
O J:CYS65 4.7 62.8 1.0
N J:CYS65 4.7 55.8 1.0
CA J:THR9 4.8 43.1 1.0
CB J:PHE12 4.8 50.0 1.0
CA J:CYS7 4.8 48.2 1.0
N J:THR9 4.9 43.8 1.0

Reference:

S.Pilotto, M.Sykora, G.Cackett, C.Dulson, F.Werner. Structural Characterization of the Fully Recombinant Rna Polymerase From African Swine Fever Virus To Be Published.
Page generated: Fri Aug 22 12:31:35 2025

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