Zinc in PDB 6drd: Rna Pol II(G)

All present enzymatic activity of Rna Pol II(G):
2.7.7.48; 2.7.7.6;

The binding sites of Zinc atom in the Rna Pol II(G) (pdb code 6drd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Rna Pol II(G), PDB code: 6drd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Rna Pol II(G)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Pol II(G) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn301 b:0.2 occ:1.00 N C:CYS94 2.2 78.6 1.0 SG C:CYS97 2.5 73.2 1.0 SG C:CYS94 2.5 78.6 1.0 SG C:CYS90 2.5 89.8 1.0 CB C:CYS94 2.9 78.6 1.0 SG C:CYS88 2.9 84.2 1.0 CA C:CYS94 3.0 78.6 1.0 C C:PHE93 3.2 78.5 1.0 CA C:PHE93 3.4 78.5 1.0 O C:CYS94 3.6 78.6 1.0 C C:CYS94 3.7 78.6 1.0 CB C:CYS90 3.7 89.8 1.0 N C:PHE93 4.1 78.5 1.0 CB C:CYS97 4.1 73.2 1.0 CB C:CYS88 4.1 84.2 1.0 O C:PHE93 4.3 78.5 1.0 O C:GLU92 4.3 87.2 1.0 C C:GLU92 4.5 87.2 1.0 N C:CYS90 4.7 89.8 1.0 N C:CYS97 4.7 73.2 1.0 CB C:PHE93 4.7 78.5 1.0 CA C:CYS90 4.8 89.8 1.0 CA C:CYS97 4.9 73.2 1.0 N C:PRO95 5.0 77.5 1.0

Zinc binding site 2 out of 5 in the Rna Pol II(G)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Pol II(G) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn201 b:0.5 occ:1.00 SG I:CYS17 2.5 69.7 1.0 SG I:CYS39 2.5 73.3 1.0 CB I:CYS20 2.6 68.6 1.0 SG I:CYS42 2.7 84.8 1.0 SG I:CYS20 2.8 68.6 1.0 CB I:CYS17 3.4 69.7 1.0 CB I:CYS39 3.4 73.3 1.0 CB I:CYS42 3.8 84.8 1.0 CA I:CYS20 3.9 68.6 1.0 OD1 I:ASN22 4.1 64.0 1.0 N I:CYS42 4.1 84.8 1.0 C I:CYS20 4.3 68.6 1.0 CB I:ASN22 4.5 64.0 1.0 CA I:CYS42 4.6 84.8 1.0 N I:CYS20 4.6 68.6 1.0 N I:ASN21 4.6 66.0 1.0 N I:ASN22 4.6 64.0 1.0 CG I:ASN22 4.7 64.0 1.0 CA I:CYS17 4.8 69.7 1.0 O I:GLN18 4.8 71.1 1.0 C I:ASN41 4.8 86.8 1.0 CA I:CYS39 4.9 73.3 1.0 O I:CYS20 4.9 68.6 1.0 N I:ASN41 5.0 86.8 1.0

Zinc binding site 3 out of 5 in the Rna Pol II(G)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Pol II(G) within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn202 b:0.5 occ:1.00 SG I:CYS119 2.4 68.3 1.0 SG I:CYS86 2.4 65.3 1.0 SG I:CYS114 2.5 54.0 1.0 CB I:CYS89 2.8 73.7 1.0 CB I:CYS86 2.9 65.3 1.0 SG I:CYS89 3.4 73.7 1.0 CB I:CYS114 3.5 54.0 1.0 CB I:CYS119 3.7 68.3 1.0 CA I:CYS89 4.0 73.7 1.0 CB I:HIS91 4.0 60.4 1.0 N I:CYS89 4.2 73.7 1.0 CA I:CYS86 4.3 65.3 1.0 N I:HIS91 4.5 60.4 1.0 C I:CYS89 4.5 73.7 1.0 O I:THR115 4.6 54.7 1.0 CA I:HIS91 4.8 60.4 1.0 O I:HIS91 4.9 60.4 1.0 N I:GLY90 4.9 64.5 1.0 CA I:CYS114 4.9 54.0 1.0 CA I:CYS119 5.0 68.3 1.0

Zinc binding site 4 out of 5 in the Rna Pol II(G)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Pol II(G) within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn101 b:96.5 occ:1.00 SG J:CYS10 2.2 38.9 1.0 SG J:CYS44 2.4 44.1 1.0 SG J:CYS45 2.5 44.4 1.0 SG J:CYS7 2.7 37.1 1.0 N J:CYS45 2.8 44.4 1.0 CB J:CYS44 2.8 44.1 1.0 C J:CYS44 3.1 44.1 1.0 CA J:CYS45 3.2 44.4 1.0 CB J:CYS45 3.4 44.4 1.0 CA J:CYS44 3.5 44.1 1.0 CB J:CYS7 3.6 37.1 1.0 O J:CYS44 3.7 44.1 1.0 CB J:CYS10 3.8 38.9 1.0 N J:CYS10 4.2 38.9 1.0 N J:CYS44 4.3 44.1 1.0 CA J:CYS10 4.6 38.9 1.0 CB J:ARG42 4.6 45.9 1.0 C J:CYS45 4.7 44.4 1.0 CB J:LYS12 4.7 38.3 1.0 NH1 J:ARG42 4.9 45.9 1.0 CB J:THR9 5.0 37.4 1.0

Zinc binding site 5 out of 5 in the Rna Pol II(G)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Pol II(G) within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn101 b:0.7 occ:1.00 N L:CYS22 2.2 75.8 1.0 SG L:CYS22 2.4 75.8 1.0 SG L:CYS19 2.4 73.6 1.0 CB L:CYS39 2.5 80.8 1.0 CB L:CYS22 2.6 75.8 1.0 SG L:CYS39 2.7 80.8 1.0 CA L:CYS22 2.9 75.8 1.0 CB L:GLU21 3.1 75.5 1.0 C L:GLU21 3.1 75.5 1.0 CB L:CYS19 3.4 73.6 1.0 CA L:GLU21 3.4 75.5 1.0 N L:GLU21 3.5 75.5 1.0 CG L:GLU21 3.7 75.5 1.0 C L:CYS22 3.9 75.8 1.0 CA L:CYS39 4.0 80.8 1.0 N L:HIS23 4.1 72.9 1.0 O L:GLU21 4.2 75.5 1.0 CB L:TYR41 4.4 75.0 1.0 N L:CYS39 4.6 80.8 1.0 CA L:CYS19 4.7 73.6 1.0 N L:GLY20 4.8 73.9 1.0 C L:GLY20 4.8 73.9 1.0 C L:CYS39 4.9 80.8 1.0 C L:CYS19 4.9 73.6 1.0 O L:CYS22 4.9 75.8 1.0 CD2 L:TYR41 5.0 75.0 1.0

M.Jishage, X.Yu, Y.Shi, S.J.Ganesan, W.Y.Chen, A.Sali, B.T.Chait, F.J.Asturias, R.G.Roeder. Architecture of Pol II(G) and Molecular Mechanism of Transcription Regulation By GDOWN1. Nat. Struct. Mol. Biol. V. 25 859 2018.
ISSN: ESSN 1545-9985
PubMed: 30190596
DOI: 10.1038/S41594-018-0118-5