Zinc in PDB 6rid: Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex

All present enzymatic activity of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex:
2.7.7.6;

The structure of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex (pdb code 6rid). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex, PDB code: 6rid:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:75.7 occ:1.00 NE2 A:HIS62 2.1 48.9 1.0 SG A:CYS52 2.2 60.1 1.0 SG A:CYS59 2.2 52.6 1.0 SG A:CYS49 2.3 59.7 1.0 CD2 A:HIS62 2.8 48.9 1.0 CB A:CYS49 3.0 59.7 1.0 CE1 A:HIS62 3.2 48.9 1.0 CB A:CYS59 3.4 52.6 1.0 CB A:CYS52 3.5 60.1 1.0 CG A:HIS62 4.0 48.9 1.0 N A:CYS52 4.1 60.1 1.0 ND1 A:HIS62 4.1 48.9 1.0 CA A:CYS59 4.3 52.6 1.0 CA A:CYS52 4.4 60.1 1.0 CA A:GLY42 4.5 55.5 1.0 CA A:CYS49 4.5 59.7 1.0 N A:GLY61 4.5 49.0 1.0 CB A:THR51 4.5 55.7 1.0 N A:ALA43 4.8 60.6 1.0 CA A:GLY61 4.8 49.0 1.0 C A:CYS59 4.9 52.6 1.0 N A:PHE60 4.9 45.6 1.0 N A:GLY42 5.0 55.5 1.0 C A:THR51 5.0 55.7 1.0

Zinc binding site 2 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:0.2 occ:1.00 SG A:CYS93 2.3 0.5 1.0 CB A:CYS135 2.3 0.6 1.0 SG A:CYS90 2.6 0.3 1.0 SG A:CYS130 2.6 0.0 1.0 SG A:CYS135 2.7 0.6 1.0 CB A:CYS130 3.5 0.0 1.0 N A:CYS93 3.5 0.5 1.0 CB A:CYS93 3.6 0.5 1.0 CA A:CYS135 3.6 0.6 1.0 CB A:CYS90 3.8 0.3 1.0 O A:CYS135 3.9 0.6 1.0 C A:CYS135 3.9 0.6 1.0 OE1 A:GLN137 4.0 0.6 1.0 CB A:HIS92 4.1 0.6 1.0 CA A:CYS93 4.2 0.5 1.0 C A:HIS92 4.4 0.6 1.0 CA A:HIS92 4.6 0.6 1.0 N A:HIS92 4.6 0.6 1.0 N A:CYS135 4.7 0.6 1.0 N A:MET136 4.9 0.1 1.0 CG A:HIS92 4.9 0.6 1.0 CA A:CYS130 5.0 0.0 1.0

Zinc binding site 3 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:77.2 occ:1.00 SG B:CYS1090 2.2 42.0 1.0 SG B:CYS1103 2.3 51.8 1.0 SG B:CYS1087 2.3 44.9 1.0 SG B:CYS1106 2.4 53.9 1.0 CB B:CYS1106 3.0 53.9 1.0 CB B:CYS1103 3.2 51.8 1.0 CB B:CYS1087 3.4 44.9 1.0 CB B:CYS1090 3.8 42.0 1.0 CG B:PRO1113 3.8 55.5 1.0 N B:CYS1106 3.9 53.9 1.0 CA B:CYS1106 4.0 53.9 1.0 N B:CYS1090 4.2 42.0 1.0 OD1 B:ASN1089 4.5 47.2 1.0 OD1 B:ASP1092 4.5 41.9 1.0 CD B:PRO1113 4.6 55.5 1.0 CA B:CYS1090 4.7 42.0 1.0 CA B:CYS1103 4.7 51.8 1.0 CB B:ASN1089 4.7 47.2 1.0 C B:ARG1105 4.8 48.1 1.0 CA B:CYS1087 4.8 44.9 1.0 CB B:ARG1105 4.9 48.1 1.0

Zinc binding site 4 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Elongation Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:28.3 occ:1.00 SG J:CYS10 2.2 13.1 1.0 SG J:CYS7 2.3 11.7 1.0 SG J:CYS40 2.3 14.4 1.0 SG J:CYS39 2.3 15.3 1.0 CB J:CYS7 3.2 11.7 1.0 N J:CYS40 3.2 14.4 1.0 CB J:CYS10 3.3 13.1 1.0 CB J:CYS39 3.4 15.3 1.0 N J:CYS10 3.5 13.1 1.0 CB J:CYS40 3.6 14.4 1.0 CA J:CYS40 3.7 14.4 1.0 C J:CYS39 3.8 15.3 1.0 CA J:CYS10 4.0 13.1 1.0 CA J:CYS39 4.1 15.3 1.0 CB J:THR9 4.3 10.9 1.0 CB J:ASN37 4.5 19.9 1.0 O J:CYS39 4.5 15.3 1.0 C J:THR9 4.6 10.9 1.0 CA J:CYS7 4.6 11.7 1.0 N J:CYS39 4.6 15.3 1.0 N J:THR9 4.7 10.9 1.0 N J:GLY11 4.8 13.7 1.0 CA J:THR9 4.8 10.9 1.0 C J:CYS10 4.8 13.1 1.0 CG2 J:THR9 4.8 10.9 1.0 OD1 J:ASN37 5.0 19.9 1.0 C J:CYS7 5.0 11.7 1.0

H.S.Hillen, J.Bartuli, C.Grimm, C.Dienemann, K.Bedenk, A.A.Szalay, U.Fischer, P.Cramer. Structural Basis of Poxvirus Transcription: Transcribing and Capping Vaccinia Complexes. Cell V. 179 1525 2019.
ISSN: ISSN 1097-4172
PubMed: 31835031
DOI: 10.1016/J.CELL.2019.11.023