Zinc in PDB 7ap8: Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2

All present enzymatic activity of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2:
2.7.7.6;

The structure of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 (pdb code 7ap8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2, PDB code: 7ap8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1302 b:145.8 occ:1.00 NE2 A:HIS62 2.1 119.5 1.0 SG A:CYS52 2.3 127.4 1.0 SG A:CYS59 2.3 125.2 1.0 SG A:CYS49 2.3 134.7 1.0 HB3 A:CYS49 2.7 134.7 1.0 CB A:CYS49 2.8 134.7 1.0 HB2 A:CYS49 2.9 134.7 1.0 CE1 A:HIS62 2.9 119.5 1.0 HE1 A:HIS62 3.0 119.5 1.0 H A:CYS52 3.1 127.4 1.0 CD2 A:HIS62 3.1 119.5 1.0 HB2 A:CYS59 3.3 125.2 1.0 HB3 A:CYS52 3.3 127.4 1.0 HD2 A:HIS62 3.4 119.5 1.0 CB A:CYS52 3.4 127.4 1.0 CB A:CYS59 3.5 125.2 1.0 HA2 A:GLY42 3.6 128.0 1.0 HB A:THR51 3.7 122.8 1.0 N A:CYS52 3.8 127.4 1.0 ND1 A:HIS62 4.0 119.5 1.0 H A:GLY61 4.1 121.2 1.0 HB3 A:CYS59 4.1 125.2 1.0 CG A:HIS62 4.2 119.5 1.0 CA A:CYS52 4.2 127.4 1.0 HB2 A:CYS52 4.2 127.4 1.0 HA A:CYS59 4.2 125.2 1.0 H A:LYS54 4.3 132.5 1.0 CA A:CYS49 4.3 134.7 1.0 H A:THR51 4.4 122.8 1.0 H A:GLY53 4.4 133.3 1.0 CA A:CYS59 4.5 125.2 1.0 H A:ALA43 4.5 137.0 1.0 HB2 A:LYS54 4.5 132.5 1.0 HA2 A:GLY61 4.5 121.2 1.0 CA A:GLY42 4.5 128.0 1.0 CB A:THR51 4.6 122.8 1.0 HA A:CYS49 4.7 134.7 1.0 HD1 A:HIS62 4.8 119.5 1.0 N A:GLY61 4.8 121.2 1.0 N A:GLY53 4.8 133.3 1.0 C A:CYS49 4.9 134.7 1.0 H A:CYS49 4.9 134.7 1.0 HA3 A:GLY42 4.9 128.0 1.0 C A:THR51 4.9 122.8 1.0 C A:CYS52 4.9 127.4 1.0 HB1 B:ALA1095 4.9 119.2 1.0 N A:ALA43 5.0 137.0 1.0

Zinc binding site 2 out of 4 in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1303 b:207.1 occ:1.00 SG A:CYS130 2.3 165.8 1.0 SG A:CYS93 2.3 165.3 1.0 SG A:CYS135 2.3 169.8 1.0 SG A:CYS90 2.3 158.8 1.0 HB3 A:CYS135 3.0 169.8 1.0 HB2 A:CYS130 3.1 165.8 1.0 CB A:CYS135 3.1 169.8 1.0 HB2 A:HIS92 3.1 164.0 1.0 CB A:CYS130 3.2 165.8 1.0 HB2 A:CYS135 3.2 169.8 1.0 HB3 A:CYS130 3.5 165.8 1.0 H A:CYS93 3.5 165.3 1.0 HB3 A:CYS90 3.6 158.8 1.0 CB A:CYS90 3.6 158.8 1.0 HB3 A:ASN132 3.8 163.8 1.0 CB A:CYS93 3.8 165.3 1.0 N A:CYS93 3.9 165.3 1.0 HB3 A:CYS93 4.0 165.3 1.0 H A:HIS92 4.0 164.0 1.0 CB A:HIS92 4.1 164.0 1.0 HB2 A:CYS90 4.1 158.8 1.0 HD22 A:ASN132 4.1 163.8 1.0 HB2 A:GLN137 4.3 165.4 1.0 HB3 A:HIS92 4.4 164.0 1.0 C A:HIS92 4.4 164.0 1.0 CA A:CYS93 4.5 165.3 1.0 HB2 A:CYS93 4.5 165.3 1.0 CA A:CYS135 4.6 169.8 1.0 O A:CYS90 4.6 158.8 1.0 N A:HIS92 4.6 164.0 1.0 CA A:HIS92 4.6 164.0 1.0 H A:GLN137 4.6 165.4 1.0 CA A:CYS130 4.6 165.8 1.0 HD2 A:HIS92 4.6 164.0 1.0 CB A:ASN132 4.7 163.8 1.0 HB2 A:ASN132 4.7 163.8 1.0 HA A:CYS130 4.7 165.8 1.0 H A:MET136 4.8 166.1 1.0 H A:ASN132 4.9 163.8 1.0 H A:LEU95 4.9 156.8 1.0 CA A:CYS90 4.9 158.8 1.0 C A:CYS90 4.9 158.8 1.0 HB2 A:LEU95 4.9 156.8 1.0 ND2 A:ASN132 4.9 163.8 1.0 H A:GLY94 4.9 158.3 1.0 HA A:CYS135 5.0 169.8 1.0 HE1 A:TYR139 5.0 160.1 1.0

Zinc binding site 3 out of 4 in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1201 b:146.7 occ:1.00 SG B:CYS1103 2.3 116.7 1.0 SG B:CYS1090 2.3 115.3 1.0 SG B:CYS1106 2.3 121.8 1.0 SG B:CYS1087 2.3 115.6 1.0 H B:CYS1090 3.0 115.3 1.0 HB2 B:CYS1106 3.1 121.8 1.0 HB3 B:CYS1087 3.2 115.6 1.0 CB B:CYS1087 3.3 115.6 1.0 HB3 B:CYS1090 3.3 115.3 1.0 CB B:CYS1106 3.3 121.8 1.0 H B:CYS1106 3.3 121.8 1.0 CB B:CYS1090 3.4 115.3 1.0 HB2 B:CYS1087 3.4 115.6 1.0 HB3 B:ASN1089 3.4 116.9 1.0 CB B:CYS1103 3.5 116.7 1.0 HB2 B:CYS1103 3.6 116.7 1.0 HB3 B:CYS1103 3.6 116.7 1.0 N B:CYS1090 3.7 115.3 1.0 HG3 B:PRO1113 3.7 122.0 1.0 HB3 B:ARG1105 3.8 120.0 1.0 N B:CYS1106 4.0 121.8 1.0 HB2 B:ASP1092 4.0 114.0 1.0 HB3 B:CYS1106 4.1 121.8 1.0 HD22 B:ASN1089 4.1 116.9 1.0 CA B:CYS1090 4.1 115.3 1.0 HB2 B:CYS1090 4.2 115.3 1.0 H B:ASP1092 4.3 114.0 1.0 CA B:CYS1106 4.3 121.8 1.0 H B:ASN1089 4.3 116.9 1.0 HD2 B:ARG1105 4.3 120.0 1.0 CB B:ASN1089 4.4 116.9 1.0 CG B:PRO1113 4.6 122.0 1.0 H B:GLY1091 4.6 112.5 1.0 HA B:CYS1106 4.6 121.8 1.0 ND2 B:ASN1089 4.7 116.9 1.0 HB3 B:PRO1113 4.7 122.0 1.0 CA B:CYS1087 4.7 115.6 1.0 HG2 B:PRO1113 4.7 122.0 1.0 HB2 B:PRO1113 4.7 122.0 1.0 C B:ASN1089 4.8 116.9 1.0 CB B:ARG1105 4.8 120.0 1.0 C B:CYS1090 4.8 115.3 1.0 CA B:CYS1103 4.9 116.7 1.0 N B:GLY1091 4.9 112.5 1.0 CB B:PRO1113 4.9 122.0 1.0 N B:ASN1089 4.9 116.9 1.0 CA B:ASN1089 4.9 116.9 1.0 HB2 B:ASN1089 4.9 116.9 1.0 HA B:CYS1090 5.0 115.3 1.0 CG B:ASN1089 5.0 116.9 1.0 CB B:ASP1092 5.0 114.0 1.0

Zinc binding site 4 out of 4 in the Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Atomic Structure of the Poxvirus Initially Transcribing Complex in Conformation 2 within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn801 b:258.4 occ:1.00 HD1 I:HIS328 1.6 229.6 1.0 ND1 I:HIS328 2.1 229.6 1.0 SG I:CYS366 2.3 198.8 1.0 SG I:CYS363 2.3 203.2 1.0 SG I:CYS326 2.3 229.0 1.0 HB3 I:HIS328 2.5 229.6 1.0 CG I:HIS328 2.7 229.6 1.0 H I:CYS366 2.8 198.8 1.0 CE1 I:HIS328 3.0 229.6 1.0 HB3 I:CYS363 3.0 203.2 1.0 CB I:CYS363 3.0 203.2 1.0 HB2 I:CYS363 3.1 203.2 1.0 CB I:HIS328 3.1 229.6 1.0 HB3 I:CYS326 3.2 229.0 1.0 HE1 I:HIS328 3.3 229.6 1.0 CB I:CYS326 3.3 229.0 1.0 H I:HIS328 3.4 229.6 1.0 HB I:VAL365 3.5 208.4 1.0 CB I:CYS366 3.6 198.8 1.0 N I:CYS366 3.6 198.8 1.0 HB2 I:CYS326 3.6 229.0 1.0 HB3 I:CYS366 3.7 198.8 1.0 HB2 I:HIS328 3.7 229.6 1.0 CD2 I:HIS328 3.8 229.6 1.0 NE2 I:HIS328 3.8 229.6 1.0 CA I:CYS366 4.1 198.8 1.0 N I:HIS328 4.1 229.6 1.0 HD2 I:PHE353 4.2 219.3 1.0 CA I:HIS328 4.2 229.6 1.0 H I:VAL365 4.3 208.4 1.0 HB2 I:CYS366 4.4 198.8 1.0 CB I:VAL365 4.4 208.4 1.0 C I:CYS366 4.5 198.8 1.0 CA I:CYS363 4.5 203.2 1.0 HD2 I:HIS328 4.5 229.6 1.0 O I:CYS366 4.6 198.8 1.0 H I:ARG364 4.6 203.0 1.0 C I:VAL365 4.6 208.4 1.0 HG12 I:VAL365 4.7 208.4 1.0 H I:GLN329 4.7 228.2 1.0 N I:VAL365 4.7 208.4 1.0 HE3 A:LYS357 4.7 178.1 1.0 CA I:CYS326 4.7 229.0 1.0 H I:ILE368 4.8 175.7 1.0 CD2 I:PHE353 4.8 219.3 1.0 CA I:VAL365 4.8 208.4 1.0 HB I:ILE368 4.9 175.7 1.0 HA I:CYS363 4.9 203.2 1.0 HG2 I:GLN329 4.9 228.2 1.0 HA I:HIS328 4.9 229.6 1.0 H I:GLU327 5.0 229.0 1.0 HE2 I:PHE353 5.0 219.3 1.0 N I:ARG364 5.0 203.0 1.0 HA I:CYS366 5.0 198.8 1.0 C I:HIS328 5.0 229.6 1.0 C I:CYS326 5.0 229.0 1.0

C.Grimm, J.Bartuli, B.Boettcher, A.A.Szalay, U.Fischer. Structural Basis of the Complete Poxvirus Transcription Initiation Process Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-021-00655-W