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

Enzymatic activity of Rna Pol II(G)

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

Zinc Binding Sites:

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 6drd

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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 6drd

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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 6drd

Go back to Zinc Binding Sites List in 6drd
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 6drd

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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 6drd

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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

Reference:

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
Page generated: Wed Dec 16 11:40:57 2020

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