Zinc in PDB 6rie: Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping Complex

All present enzymatic activity of Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping Complex:
2.1.1.56; 2.7.7.6;

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

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping Complex (pdb code 6rie). 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 Co- Transcriptional Capping Complex, PDB code: 6rie:
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 Co- Transcriptional Capping 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 Co- Transcriptional Capping Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:58.5 occ:1.00 NE2 A:HIS62 2.1 34.1 1.0 SG A:CYS59 2.2 35.7 1.0 SG A:CYS52 2.2 43.2 1.0 SG A:CYS49 2.3 46.1 1.0 CB A:CYS49 2.9 46.1 1.0 CD2 A:HIS62 2.9 34.1 1.0 CE1 A:HIS62 3.1 34.1 1.0 CB A:CYS59 3.3 35.7 1.0 CB A:CYS52 3.9 43.2 1.0 CG A:HIS62 4.1 34.1 1.0 N A:CYS52 4.1 43.2 1.0 ND1 A:HIS62 4.1 34.1 1.0 CA A:GLY42 4.2 41.5 1.0 CA A:CYS59 4.3 35.7 1.0 CA A:CYS49 4.4 46.1 1.0 CA A:CYS52 4.6 43.2 1.0 N A:GLY61 4.7 33.0 1.0 N A:ALA43 4.7 45.5 1.0 N A:GLY42 4.9 41.5 1.0 CB A:THR51 4.9 42.3 1.0 C A:GLY42 4.9 41.5 1.0 CA A:GLY61 4.9 33.0 1.0 C A:CYS59 4.9 35.7 1.0

Zinc binding site 2 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping 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 Co- Transcriptional Capping Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:0.1 occ:1.00 SG A:CYS93 2.3 76.3 1.0 SG A:CYS130 2.4 79.8 1.0 SG A:CYS90 2.5 74.9 1.0 SG A:CYS135 2.5 85.9 1.0 CB A:CYS135 2.7 85.9 1.0 CB A:CYS130 3.1 79.8 1.0 CB A:CYS93 3.2 76.3 1.0 N A:CYS93 3.5 76.3 1.0 CB A:CYS90 3.6 74.9 1.0 CA A:CYS93 3.9 76.3 1.0 OD1 A:ASN132 4.0 82.4 1.0 CA A:CYS135 4.2 85.9 1.0 ND2 A:ASN132 4.5 82.4 1.0 CB A:HIS92 4.5 75.3 1.0 CG A:ASN132 4.5 82.4 1.0 CA A:CYS130 4.6 79.8 1.0 C A:HIS92 4.7 75.3 1.0 O A:CYS93 4.7 76.3 1.0 C A:CYS93 4.8 76.3 1.0 CD2 A:HIS92 4.8 75.3 1.0 N A:CYS135 4.9 85.9 1.0 C A:CYS135 4.9 85.9 1.0 CA A:HIS92 5.0 75.3 1.0 N A:HIS92 5.0 75.3 1.0

Zinc binding site 3 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping 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 Co- Transcriptional Capping Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:64.0 occ:1.00 SG B:CYS1090 2.3 33.5 1.0 SG B:CYS1087 2.3 33.3 1.0 SG B:CYS1103 2.3 36.6 1.0 SG B:CYS1106 2.4 38.7 1.0 CB B:CYS1087 3.2 33.3 1.0 CB B:CYS1106 3.2 38.7 1.0 CB B:CYS1103 3.4 36.6 1.0 N B:CYS1090 3.8 33.5 1.0 OD1 B:ASP1092 3.9 28.8 1.0 O B:CYS1090 3.9 33.5 1.0 CB B:CYS1090 3.9 33.5 1.0 N B:CYS1106 4.0 38.7 1.0 CA B:CYS1106 4.2 38.7 1.0 CA B:CYS1090 4.3 33.5 1.0 CG B:PRO1113 4.4 39.3 1.0 CB B:ASN1089 4.4 35.2 1.0 C B:CYS1090 4.6 33.5 1.0 CA B:CYS1087 4.7 33.3 1.0 CA B:CYS1103 4.8 36.6 1.0 C B:ASN1089 4.8 35.2 1.0 CB B:PRO1113 4.9 39.3 1.0 CG B:ASP1092 4.9 28.8 1.0 CB B:ARG1105 5.0 35.6 1.0 N B:ASN1089 5.0 35.2 1.0 CA B:ASN1089 5.0 35.2 1.0

Zinc binding site 4 out of 4 in the Structure of Vaccinia Virus Dna-Dependent Rna Polymerase Co- Transcriptional Capping 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 Co- Transcriptional Capping Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:42.7 occ:1.00 SG J:CYS10 2.2 19.5 1.0 SG J:CYS40 2.3 20.1 1.0 SG J:CYS39 2.3 21.9 1.0 SG J:CYS7 2.3 17.0 1.0 CB J:CYS10 3.0 19.5 1.0 CB J:CYS7 3.2 17.0 1.0 N J:CYS40 3.2 20.1 1.0 CB J:CYS39 3.3 21.9 1.0 N J:CYS10 3.5 19.5 1.0 CB J:CYS40 3.6 20.1 1.0 CA J:CYS40 3.8 20.1 1.0 C J:CYS39 3.8 21.9 1.0 CA J:CYS10 3.9 19.5 1.0 CA J:CYS39 4.1 21.9 1.0 CB J:THR9 4.4 16.8 1.0 CB J:ASN37 4.4 26.8 1.0 C J:THR9 4.5 16.8 1.0 CA J:CYS7 4.6 17.0 1.0 O J:CYS39 4.6 21.9 1.0 N J:CYS39 4.6 21.9 1.0 OD1 J:ASN37 4.7 26.8 1.0 N J:THR9 4.7 16.8 1.0 C J:CYS10 4.8 19.5 1.0 N J:GLY11 4.8 18.0 1.0 CA J:THR9 4.8 16.8 1.0 C J:CYS7 4.9 17.0 1.0 CG J:ASN37 4.9 26.8 1.0 CG2 J:THR9 5.0 16.8 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