Zinc in PDB 8xxp: Asfv Rnap Core Complex

All present enzymatic activity of Asfv Rnap Core Complex:
2.7.7.6;

The structure of Asfv Rnap Core Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Asfv Rnap Core Complex (pdb code 8xxp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Asfv Rnap Core Complex, PDB code: 8xxp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:103.3 occ:1.00 NE2 A:HIS72 2.1 53.8 1.0 SG A:CYS59 2.3 67.2 1.0 SG A:CYS69 2.3 55.9 1.0 SG A:CYS62 2.3 57.0 1.0 CD2 A:HIS72 2.8 51.0 1.0 CB A:CYS59 3.0 60.5 1.0 CE1 A:HIS72 3.2 48.0 1.0 CB A:CYS69 3.3 55.6 1.0 CB A:CYS62 3.6 55.6 1.0 CA A:CYS69 3.9 56.6 1.0 CG A:HIS72 4.0 48.8 1.0 N A:CYS62 4.1 54.8 1.0 ND1 A:HIS72 4.2 52.0 1.0 N A:GLY71 4.3 58.5 1.0 CA A:GLY51 4.4 56.2 1.0 CA A:CYS62 4.4 55.9 1.0 CA A:CYS59 4.5 62.0 1.0 C A:CYS69 4.5 61.8 1.0 N A:MET70 4.6 63.2 1.0 CA A:GLY71 4.7 50.0 1.0 CB A:THR61 4.7 51.8 1.0 C A:GLY71 4.9 56.1 1.0 N A:GLY51 5.0 53.8 1.0

Zinc binding site 2 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:136.4 occ:1.00 SG A:CYS99 2.3 85.0 1.0 SG A:CYS137 2.3 106.8 1.0 SG A:CYS102 2.3 93.5 1.0 SG A:CYS134 2.3 105.0 1.0 CB A:CYS134 3.1 102.6 1.0 CB A:CYS99 3.3 84.7 1.0 CB A:CYS137 3.4 107.6 1.0 CB A:CYS102 3.5 89.7 1.0 N A:CYS102 3.8 85.7 1.0 N A:CYS137 3.9 105.1 1.0 CA A:CYS137 4.2 106.0 1.0 CA A:CYS102 4.2 88.4 1.0 CB A:ASN101 4.5 88.2 1.0 CA A:CYS134 4.6 104.3 1.0 CA A:CYS99 4.7 83.9 1.0 C A:CYS137 4.7 106.3 1.0 C A:ASN101 4.7 85.9 1.0 CB A:VAL136 4.8 107.0 1.0 C A:CYS102 4.8 89.9 1.0 CB A:ALA104 4.8 84.2 1.0 N A:GLY103 4.8 85.0 1.0 N A:ASN101 4.9 87.2 1.0 CB A:ALA139 4.9 97.6 1.0 C A:VAL136 4.9 107.1 1.0 CA A:ASN101 4.9 86.8 1.0 N A:ALA104 4.9 85.1 1.0 N A:LYS138 5.0 105.1 1.0

Zinc binding site 3 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1301 b:91.7 occ:1.00 SG B:CYS1201 2.3 70.8 1.0 SG B:CYS1180 2.3 52.1 1.0 SG B:CYS1198 2.3 70.8 1.0 SG B:CYS1183 2.3 54.6 1.0 CB B:CYS1180 3.0 47.1 1.0 CB B:CYS1183 3.4 53.0 1.0 CB B:CYS1198 3.5 60.5 1.0 N B:CYS1201 3.7 64.1 1.0 N B:CYS1183 3.8 54.7 1.0 CB B:CYS1201 3.8 72.2 1.0 CB B:ASN1200 4.1 63.9 1.0 CA B:CYS1201 4.2 67.7 1.0 CA B:CYS1183 4.2 48.2 1.0 CB B:ASN1182 4.3 46.0 1.0 C B:ASN1182 4.4 56.0 1.0 CA B:CYS1180 4.4 40.1 1.0 C B:CYS1201 4.6 64.5 1.0 C B:ASN1200 4.6 67.1 1.0 O B:CYS1201 4.6 74.7 1.0 CA B:ASN1200 4.7 62.5 1.0 CA B:ASN1182 4.8 45.6 1.0 N B:ASN1200 4.8 61.6 1.0 ND2 B:ASN1200 4.8 68.7 1.0 ND2 B:ASN1182 4.8 52.4 1.0 N B:ASN1182 4.9 50.1 1.0 CA B:ALA1205 4.9 53.5 1.0 CA B:CYS1198 4.9 60.8 1.0

Zinc binding site 4 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:157.4 occ:1.00 SG G:CYS24 2.3 123.4 1.0 SG G:CYS7 2.3 117.5 1.0 SG G:CYS26 2.3 122.9 1.0 SG G:CYS4 2.3 111.6 1.0 CB G:CYS4 3.2 108.8 1.0 CB G:CYS7 3.3 112.0 1.0 CB G:CYS24 3.6 120.0 1.0 CB G:CYS26 3.6 124.2 1.0 N G:CYS7 3.8 112.9 1.0 N G:CYS26 4.0 124.5 1.0 CA G:CYS7 4.1 112.0 1.0 OG G:SER25 4.5 123.2 1.0 CB G:SER9 4.5 106.6 1.0 CA G:CYS26 4.5 125.2 1.0 CB G:ALA6 4.5 114.4 1.0 C G:CYS7 4.6 112.7 1.0 N G:SER25 4.6 121.7 1.0 CA G:CYS4 4.7 108.5 1.0 C G:ALA6 4.7 115.1 1.0 OG G:SER9 4.7 106.6 1.0 N G:SER9 4.8 107.3 1.0 CA G:CYS24 4.9 119.8 1.0 N G:SER8 4.9 107.8 1.0 CB G:GLU28 4.9 122.5 1.0 CA G:ALA6 5.0 114.6 1.0

Zinc binding site 5 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn202 b:123.8 occ:1.00 SG G:CYS73 2.3 90.2 1.0 SG G:CYS76 2.3 97.5 1.0 SG G:CYS98 2.3 81.0 1.0 SG G:CYS96 2.3 88.5 1.0 CB G:CYS96 3.0 72.1 1.0 CB G:CYS76 3.2 92.7 1.0 CB G:CYS73 3.3 89.9 1.0 CB G:CYS98 3.5 78.6 1.0 N G:CYS76 3.7 95.2 1.0 CA G:CYS76 4.0 93.7 1.0 N G:CYS98 4.2 76.9 1.0 CA G:CYS98 4.4 78.0 1.0 CA G:CYS96 4.5 70.6 1.0 C G:CYS76 4.5 95.9 1.0 CB G:TYR100 4.6 77.0 1.0 N G:HIS77 4.7 96.7 1.0 CB G:ASN75 4.7 91.6 1.0 CD1 G:LEU78 4.7 85.6 1.0 CA G:CYS73 4.7 90.6 1.0 C G:ASN75 4.8 93.7 1.0 N G:ARG97 4.8 75.5 1.0 C G:CYS96 4.8 75.0 1.0

Zinc binding site 6 out of 6 in the Asfv Rnap Core Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Asfv Rnap Core Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:67.5 occ:1.00 SG H:CYS10 2.3 43.2 1.0 SG H:CYS66 2.3 46.1 1.0 SG H:CYS65 2.3 40.4 1.0 SG H:CYS7 2.3 37.4 1.0 CB H:CYS7 3.0 14.2 1.0 N H:CYS66 3.3 37.2 1.0 CB H:CYS10 3.3 28.4 1.0 CB H:CYS65 3.3 32.4 1.0 CB H:CYS66 3.6 42.0 1.0 CA H:CYS66 3.6 25.8 1.0 N H:CYS10 3.7 27.8 1.0 C H:CYS65 3.8 41.4 1.0 NE H:ARG63 3.9 43.0 1.0 CA H:CYS10 4.1 25.7 1.0 CA H:CYS65 4.1 32.9 1.0 O H:CYS65 4.5 47.2 1.0 CA H:CYS7 4.5 21.6 1.0 CB H:PHE12 4.6 26.5 1.0 CD H:ARG63 4.6 41.6 1.0 CB H:THR9 4.6 31.9 1.0 N H:GLY11 4.7 19.6 1.0 C H:CYS10 4.7 26.3 1.0 CB H:ARG63 4.7 44.1 1.0 N H:CYS65 4.7 35.0 1.0 N H:PHE12 4.8 26.8 1.0 C H:THR9 4.8 37.8 1.0 NH2 H:ARG63 4.8 44.1 1.0 CZ H:ARG63 4.9 43.9 1.0

G.Zhu, F.Xi, W.Zeng, Y.Zhao, W.Cao, C.Liu, F.Yang, Y.Ru, S.Xiao, S.Zhang, H.Liu, H.Tian, F.Yang, B.Lu, S.Sun, H.Song, B.Sun, X.Zhao, L.Tang, K.Li, J.He, J.Guo, Y.Zhu, Z.Zhu, F.Sun, H.Zheng. Structural Basis of Rna Polymerase Complexes in African Swine Fever Virus. Nat Commun V. 16 501 2025.
ISSN: ESSN 2041-1723
PubMed: 39779680
DOI: 10.1038/S41467-024-55683-Z