Zinc in PDB 7opd: Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)

Enzymatic activity of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)

All present enzymatic activity of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5):
2.3.2.27; 2.3.2.32; 2.7.7.6;

Other elements in 7opd:

The structure of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) (pdb code 7opd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5), PDB code: 7opd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7opd

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Zinc binding site 1 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:73.6
occ:1.00
 NE2 A:HIS84 2.0 37.7 1.0
SG A:CYS74 2.2 43.6 1.0
SG A:CYS81 2.2 38.4 1.0
SG A:CYS71 2.3 49.4 1.0
CD2 A:HIS84 2.5 37.7 1.0
CB A:CYS71 2.9 49.4 1.0
CE1 A:HIS84 3.3 37.7 1.0
O A:PRO82 3.7 32.1 1.0
CB A:CYS81 3.8 38.4 1.0
CB A:CYS74 3.8 43.6 1.0
CG A:HIS84 3.8 37.7 1.0
CA A:GLY63 3.9 44.7 1.0
N A:CYS74 4.0 43.6 1.0
ND1 A:HIS84 4.1 37.7 1.0
N A:GLY63 4.4 44.7 1.0
CA A:CYS71 4.4 49.4 1.0
CA A:CYS74 4.5 43.6 1.0
CA A:CYS81 4.5 38.4 1.0
CB A:THR73 4.5 42.6 1.0
C A:GLY63 4.6 44.7 1.0
C A:PRO82 4.8 32.1 1.0
C A:CYS81 4.8 38.4 1.0
OG1 A:THR73 5.0 42.6 1.0
N A:THR73 5.0 42.6 1.0

Zinc binding site 2 out of 8 in 7opd

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Zinc binding site 2 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:139.6
occ:1.00
 SG A:CYS184 2.1 113.8 1.0
SG A:CYS111 2.3 97.2 1.0
SG A:CYS154 2.3 111.9 1.0
CB A:CYS154 2.7 111.9 1.0
SG A:CYS114 3.0 102.0 1.0
CB A:CYS184 3.1 113.8 1.0
CB A:CYS114 3.3 102.0 1.0
N A:CYS184 3.5 113.8 1.0
N A:CYS114 3.6 102.0 1.0
CB A:CYS111 3.7 97.2 1.0
CA A:CYS184 3.8 113.8 1.0
CA A:CYS114 4.0 102.0 1.0
CA A:CYS154 4.2 111.9 1.0
NE2 A:GLN188 4.2 102.2 1.0
C A:CYS184 4.3 113.8 1.0
N A:GLY185 4.4 112.1 1.0
CB A:PHE113 4.4 99.0 1.0
C A:GLY183 4.6 108.0 1.0
C A:PHE113 4.7 99.0 1.0
CD2 A:PHE113 4.8 99.0 1.0
N A:ARG186 4.9 106.7 1.0
N A:PHE113 4.9 99.0 1.0
CA A:GLY183 4.9 108.0 1.0
CA A:PHE113 4.9 99.0 1.0
N A:CYS154 4.9 111.9 1.0
C A:CYS154 5.0 111.9 1.0
CA A:CYS111 5.0 97.2 1.0

Zinc binding site 3 out of 8 in 7opd

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Zinc binding site 3 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:83.3
occ:1.00
 SG B:CYS1122 2.3 39.9 1.0
SG B:CYS1119 2.3 41.8 1.0
SG B:CYS1137 2.3 53.6 1.0
SG B:CYS1140 2.3 51.7 1.0
CB B:CYS1119 2.8 41.8 1.0
CB B:CYS1137 3.1 53.6 1.0
CB B:CYS1140 3.1 51.7 1.0
CB B:CYS1122 3.6 39.9 1.0
N B:CYS1140 3.6 51.7 1.0
CA B:CYS1140 4.0 51.7 1.0
N B:CYS1122 4.0 39.9 1.0
OD1 B:ASN1142 4.1 54.8 1.0
CA B:CYS1119 4.3 41.8 1.0
CA B:CYS1122 4.4 39.9 1.0
CA B:CYS1137 4.5 53.6 1.0
C B:GLY1139 4.6 52.1 1.0
CB B:LEU1121 4.7 40.5 1.0
CG B:ASN1142 4.9 54.8 1.0
CA B:GLY1139 4.9 52.1 1.0
C B:CYS1137 5.0 53.6 1.0
C B:CYS1119 5.0 41.8 1.0

Zinc binding site 4 out of 8 in 7opd

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Zinc binding site 4 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:123.5
occ:1.00
 SG C:CYS97 2.2 41.5 1.0
SG C:CYS90 2.2 65.4 1.0
SG C:CYS88 2.2 57.8 1.0
SG C:CYS94 2.3 49.6 1.0
CB C:CYS88 3.0 57.8 1.0
CB C:CYS97 3.1 41.5 1.0
CB C:CYS94 3.5 49.6 1.0
CB C:CYS90 3.6 65.4 1.0
N C:CYS94 3.6 49.6 1.0
N C:CYS97 4.0 41.5 1.0
CA C:CYS94 4.0 49.6 1.0
C C:PHE93 4.0 40.0 1.0
CA C:CYS97 4.1 41.5 1.0
O C:CYS94 4.2 49.6 1.0
CA C:CYS88 4.4 57.8 1.0
C C:CYS94 4.4 49.6 1.0
CA C:PHE93 4.5 40.0 1.0
O C:PHE93 4.6 40.0 1.0
O C:GLU91 4.6 69.3 1.0
N C:CYS90 4.6 65.4 1.0
CA C:CYS90 4.6 65.4 1.0
C C:GLU96 4.8 44.7 1.0
C C:CYS97 4.9 41.5 1.0
C C:CYS88 4.9 57.8 1.0

Zinc binding site 5 out of 8 in 7opd

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Zinc binding site 5 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:132.6
occ:1.00
 SG I:CYS20 2.3 97.6 1.0
SG I:CYS42 2.3 104.2 1.0
SG I:CYS17 2.3 100.9 1.0
SG I:CYS39 2.3 103.8 1.0
CB I:CYS17 2.4 100.9 1.0
CB I:CYS39 2.5 103.8 1.0
CB I:CYS42 3.5 104.2 1.0
CA I:CYS17 3.8 100.9 1.0
CB I:CYS20 3.9 97.6 1.0
N I:CYS42 4.0 104.2 1.0
CA I:CYS39 4.0 103.8 1.0
N I:CYS20 4.2 97.6 1.0
CB I:TYR44 4.2 106.3 1.0
CA I:CYS42 4.3 104.2 1.0
CA I:CYS20 4.6 97.6 1.0
N I:CYS17 4.6 100.9 1.0
CD2 I:LEU24 4.6 102.0 1.0
C I:CYS42 4.7 104.2 1.0
O I:ASN22 4.7 92.5 1.0
C I:CYS17 4.7 100.9 1.0
N I:CYS39 4.8 103.8 1.0
C I:CYS39 4.8 103.8 1.0
N I:ASN22 4.8 92.5 1.0
N I:TYR44 4.9 106.3 1.0
CB I:ASN22 4.9 92.5 1.0
N I:ASN21 5.0 92.8 1.0
O I:CYS42 5.0 104.2 1.0

Zinc binding site 6 out of 8 in 7opd

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Zinc binding site 6 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:94.4
occ:1.00
 SG I:CYS89 2.2 68.1 1.0
SG I:CYS86 2.3 61.9 1.0
SG I:CYS119 2.3 64.3 1.0
SG I:CYS114 2.3 53.6 1.0
CB I:CYS114 2.6 53.6 1.0
CB I:CYS86 3.1 61.9 1.0
CB I:CYS89 3.5 68.1 1.0
CB I:CYS119 3.5 64.3 1.0
CB I:HIS121 3.8 57.0 1.0
N I:CYS89 4.1 68.1 1.0
CA I:CYS114 4.1 53.6 1.0
N I:HIS121 4.2 57.0 1.0
CA I:CYS89 4.4 68.1 1.0
CA I:CYS86 4.5 61.9 1.0
CA I:HIS121 4.6 57.0 1.0
CB I:ALA116 4.7 64.0 1.0
N I:GLY120 4.7 59.6 1.0
CB I:LYS88 4.7 66.2 1.0
CB I:HIS91 4.8 63.0 1.0
CA I:CYS119 4.8 64.3 1.0
C I:CYS119 4.8 64.3 1.0
C I:CYS114 4.9 53.6 1.0
CG I:HIS121 4.9 57.0 1.0
C I:LYS88 4.9 66.2 1.0
N I:CYS114 4.9 53.6 1.0

Zinc binding site 7 out of 8 in 7opd

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Zinc binding site 7 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:36.2
occ:1.00
 SG J:CYS10 2.2 9.7 1.0
SG J:CYS44 2.2 9.7 1.0
SG J:CYS7 2.3 41.6 1.0
SG J:CYS45 2.3 14.2 1.0
CB J:CYS7 3.0 41.6 1.0
N J:CYS45 3.4 14.2 1.0
CB J:CYS44 3.4 9.7 1.0
CB J:CYS10 3.4 9.7 1.0
CB J:CYS45 3.7 14.2 1.0
N J:CYS10 3.8 9.7 1.0
CA J:CYS45 3.8 14.2 1.0
C J:CYS44 3.9 9.7 1.0
CA J:CYS10 4.2 9.7 1.0
CA J:CYS44 4.2 9.7 1.0
NE J:ARG42 4.2 8.2 1.0
CA J:CYS7 4.5 41.6 1.0
CB J:THR9 4.6 13.4 1.0
O J:CYS44 4.6 9.7 1.0
CB J:LYS12 4.6 14.3 1.0
CB J:ARG42 4.7 8.2 1.0
N J:GLY11 4.8 15.1 1.0
NH2 J:ARG42 4.9 8.2 1.0
C J:THR9 4.9 13.4 1.0
N J:CYS44 4.9 9.7 1.0
N J:LYS12 4.9 14.3 1.0
N J:THR9 5.0 13.4 1.0
C J:CYS7 5.0 41.6 1.0
C J:CYS10 5.0 9.7 1.0
CD J:ARG42 5.0 8.2 1.0

Zinc binding site 8 out of 8 in 7opd

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Zinc binding site 8 out of 8 in the Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pol II-Csb-CRL4CSA-Uvssa-SPT6-Paf (Structure 5) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:96.7
occ:1.00
 SG L:CYS36 2.2 56.7 1.0
SG L:CYS22 2.2 51.3 1.0
SG L:CYS39 2.3 58.5 1.0
SG L:CYS19 2.3 46.0 1.0
CB L:CYS36 2.8 56.7 1.0
CB L:CYS19 3.1 46.0 1.0
CB L:CYS22 3.3 51.3 1.0
CB L:CYS39 3.6 58.5 1.0
N L:CYS39 3.7 58.5 1.0
N L:CYS22 4.0 51.3 1.0
CB L:TYR41 4.1 45.1 1.0
CA L:CYS39 4.1 58.5 1.0
OE1 L:GLU38 4.1 66.6 1.0
CA L:CYS22 4.2 51.3 1.0
CA L:CYS36 4.3 56.7 1.0
N L:TYR41 4.3 45.1 1.0
N L:GLY40 4.4 57.1 1.0
C L:CYS39 4.5 58.5 1.0
CA L:CYS19 4.5 46.0 1.0
CB L:GLU38 4.5 66.6 1.0
C L:GLU38 4.6 66.6 1.0
OG1 L:THR24 4.7 56.1 1.0
N L:GLU38 4.7 66.6 1.0
C L:CYS36 4.8 56.7 1.0
CA L:TYR41 4.8 45.1 1.0
CA L:GLU38 4.9 66.6 1.0
C L:CYS22 4.9 51.3 1.0
CB L:THR24 5.0 56.1 1.0

Reference:

G.Kokic, F.R.Wagner, A.Chernev, H.Urlaub, P.Cramer. Structural Basis of Human Transcription-Dna Repair Coupling. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 34526721
DOI: 10.1038/S41586-021-03906-4
Page generated: Wed Oct 30 08:40:45 2024

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