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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Go back to Zinc Binding Sites List in 7opd
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy