Zinc in PDB 6rfl: Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex

All present enzymatic activity of Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex:
2.1.1.56; 2.7.7.6; 3.6.1.15;

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase Complex (pdb code 6rfl). 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 the Complete Vaccinia Dna-Dependent Rna Polymerase Complex, PDB code: 6rfl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase 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 the Complete Vaccinia Dna-Dependent Rna Polymerase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:48.8 occ:1.00 SG B:CYS1103 2.2 25.5 1.0 SG B:CYS1090 2.3 25.4 1.0 SG B:CYS1087 2.3 25.7 1.0 SG B:CYS1106 2.3 25.5 1.0 CB B:CYS1106 3.3 25.5 1.0 CB B:CYS1087 3.4 25.7 1.0 CB B:CYS1103 3.5 25.5 1.0 CB B:CYS1090 3.6 25.4 1.0 N B:CYS1090 3.7 25.4 1.0 N B:CYS1106 4.0 25.5 1.0 CA B:CYS1106 4.2 25.5 1.0 CA B:CYS1090 4.2 25.4 1.0 CB B:ASN1089 4.3 26.4 1.0 CG B:PRO1113 4.3 25.5 1.0 CB B:PRO1113 4.6 25.5 1.0 C B:ASN1089 4.7 26.4 1.0 CA B:CYS1087 4.8 25.7 1.0 N B:ASN1089 4.8 26.4 1.0 CA B:ASN1089 4.8 26.4 1.0 CB B:ARG1105 4.8 24.3 1.0 ND2 B:ASN1089 4.9 26.4 1.0 CA B:CYS1103 4.9 25.5 1.0

Zinc binding site 2 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase 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 the Complete Vaccinia Dna-Dependent Rna Polymerase Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn801 b:53.4 occ:1.00 ND1 I:HIS328 2.0 37.0 1.0 SG I:CYS366 2.3 34.0 1.0 SG I:CYS326 2.3 40.9 1.0 SG I:CYS363 2.3 33.1 1.0 CE1 I:HIS328 2.9 37.0 1.0 CG I:HIS328 3.0 37.0 1.0 CB I:CYS326 3.2 40.9 1.0 CB I:CYS363 3.2 33.1 1.0 CB I:HIS328 3.4 37.0 1.0 N I:CYS366 3.5 34.0 1.0 CB I:CYS366 3.6 34.0 1.0 NE2 I:HIS328 3.9 37.0 1.0 CD2 I:HIS328 4.0 37.0 1.0 CB I:VAL365 4.1 36.1 1.0 CA I:CYS366 4.1 34.0 1.0 N I:HIS328 4.2 37.0 1.0 CA I:HIS328 4.4 37.0 1.0 C I:VAL365 4.6 36.1 1.0 N I:VAL365 4.6 36.1 1.0 CA I:CYS326 4.6 40.9 1.0 CA I:CYS363 4.6 33.1 1.0 CA I:VAL365 4.7 36.1 1.0 C I:CYS366 4.8 34.0 1.0 CG1 I:VAL365 4.8 36.1 1.0 N I:GLU327 4.9 42.1 1.0 C I:CYS326 5.0 40.9 1.0 CG2 I:VAL365 5.0 36.1 1.0 O I:CYS366 5.0 34.0 1.0

Zinc binding site 3 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase 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 the Complete Vaccinia Dna-Dependent Rna Polymerase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:46.2 occ:1.00 NE2 A:HIS62 2.0 21.9 1.0 SG A:CYS59 2.2 30.1 1.0 SG A:CYS49 2.2 30.8 1.0 SG A:CYS52 2.3 31.6 1.0 CD2 A:HIS62 3.0 21.9 1.0 CB A:CYS49 3.0 30.8 1.0 CE1 A:HIS62 3.0 21.9 1.0 CB A:CYS59 3.4 30.1 1.0 CB A:CYS52 3.4 31.6 1.0 N A:CYS52 3.8 31.6 1.0 ND1 A:HIS62 4.1 21.9 1.0 CG A:HIS62 4.1 21.9 1.0 CA A:CYS52 4.2 31.6 1.0 CA A:CYS59 4.4 30.1 1.0 CA A:CYS49 4.5 30.8 1.0 O A:LEU41 4.5 27.8 1.0 CB A:THR51 4.5 32.4 1.0 CA A:GLY42 4.7 29.1 1.0 N A:GLY61 4.7 27.6 1.0 O A:HOH1416 4.8 30.7 1.0 C A:THR51 4.8 32.4 1.0 N A:GLY53 4.9 29.8 1.0 C A:CYS52 4.9 31.6 1.0 N A:THR51 5.0 32.4 1.0 CG2 A:THR51 5.0 32.4 1.0 CA A:GLY61 5.0 27.6 1.0

Zinc binding site 4 out of 4 in the Structure of the Complete Vaccinia Dna-Dependent Rna Polymerase 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 the Complete Vaccinia Dna-Dependent Rna Polymerase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:60.9 occ:1.00 SG A:CYS130 2.3 51.6 1.0 SG A:CYS93 2.3 41.4 1.0 SG A:CYS135 2.3 52.4 1.0 SG A:CYS90 2.3 40.5 1.0 CB A:CYS135 3.2 52.4 1.0 CB A:CYS130 3.4 51.6 1.0 CB A:CYS90 3.5 40.5 1.0 CB A:CYS93 3.6 41.4 1.0 N A:CYS93 4.0 41.4 1.0 CB A:HIS92 4.3 43.5 1.0 CA A:CYS93 4.4 41.4 1.0 CB A:ASN132 4.4 50.4 1.0 CA A:CYS135 4.6 52.4 1.0 C A:HIS92 4.6 43.5 1.0 ND2 A:ASN132 4.7 50.4 1.0 N A:HIS92 4.8 43.5 1.0 CA A:CYS130 4.8 51.6 1.0 CA A:CYS90 4.8 40.5 1.0 CA A:HIS92 4.8 43.5 1.0 O A:CYS90 4.9 40.5 1.0 N A:MET136 5.0 54.4 1.0 C A:CYS90 5.0 40.5 1.0 C A:CYS135 5.0 52.4 1.0

C.Grimm, H.S.Hillen, K.Bedenk, J.Bartuli, S.Neyer, Q.Zhang, A.Huttenhofer, M.Erlacher, C.Dienemann, A.Schlosser, H.Urlaub, B.Bottcher, A.A.Szalay, P.Cramer, U.Fischer. Structural Basis of Poxvirus Transcription: Vaccinia Rna Polymerase Complexes. Cell V. 179 1537 2019.
ISSN: ISSN 1097-4172
PubMed: 31835032
DOI: 10.1016/J.CELL.2019.11.024