Zinc in PDB 7oop: Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)

Enzymatic activity of Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)

All present enzymatic activity of Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3):
2.7.7.6;

Other elements in 7oop:

The structure of Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) (pdb code 7oop). 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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3), PDB code: 7oop:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7oop

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Zinc binding site 1 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:67.6
occ:1.00
NE2 A:HIS84 2.0 33.5 1.0
SG A:CYS74 2.2 41.4 1.0
SG A:CYS81 2.2 35.3 1.0
SG A:CYS71 2.3 48.2 1.0
CD2 A:HIS84 2.5 33.5 1.0
CB A:CYS71 2.9 48.2 1.0
CE1 A:HIS84 3.3 33.5 1.0
O A:PRO82 3.7 26.5 1.0
CB A:CYS81 3.7 35.3 1.0
CB A:CYS74 3.8 41.4 1.0
CG A:HIS84 3.8 33.5 1.0
CA A:GLY63 3.9 37.5 1.0
N A:CYS74 4.0 41.4 1.0
ND1 A:HIS84 4.1 33.5 1.0
N A:GLY63 4.4 37.5 1.0
CA A:CYS71 4.4 48.2 1.0
CA A:CYS74 4.5 41.4 1.0
CA A:CYS81 4.5 35.3 1.0
CB A:THR73 4.5 41.9 1.0
C A:GLY63 4.6 37.5 1.0
C A:PRO82 4.8 26.5 1.0
C A:CYS81 4.8 35.3 1.0
OG1 A:THR73 5.0 41.9 1.0
N A:THR73 5.0 41.9 1.0

Zinc binding site 2 out of 8 in 7oop

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Zinc binding site 2 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:123.3
occ:1.00
SG A:CYS184 2.1 108.6 1.0
SG A:CYS111 2.3 91.8 1.0
SG A:CYS154 2.3 109.3 1.0
CB A:CYS154 2.7 109.3 1.0
SG A:CYS114 3.0 95.1 1.0
CB A:CYS184 3.1 108.6 1.0
CB A:CYS114 3.2 95.1 1.0
N A:CYS184 3.5 108.6 1.0
N A:CYS114 3.6 95.1 1.0
CB A:CYS111 3.7 91.8 1.0
CA A:CYS184 3.8 108.6 1.0
CA A:CYS114 4.0 95.1 1.0
CA A:CYS154 4.2 109.3 1.0
NE2 A:GLN188 4.2 96.9 1.0
C A:CYS184 4.3 108.6 1.0
N A:GLY185 4.4 107.5 1.0
CB A:PHE113 4.5 96.1 1.0
C A:GLY183 4.6 111.2 1.0
C A:PHE113 4.7 96.1 1.0
CD2 A:PHE113 4.8 96.1 1.0
N A:ARG186 4.9 104.9 1.0
N A:PHE113 4.9 96.1 1.0
CA A:GLY183 4.9 111.2 1.0
CA A:PHE113 4.9 96.1 1.0
N A:CYS154 4.9 109.3 1.0
C A:CYS154 5.0 109.3 1.0
CA A:CYS111 5.0 91.8 1.0

Zinc binding site 3 out of 8 in 7oop

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Zinc binding site 3 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:70.3
occ:1.00
SG B:CYS1122 2.3 36.2 1.0
SG B:CYS1119 2.3 36.2 1.0
SG B:CYS1137 2.3 45.7 1.0
SG B:CYS1140 2.3 50.2 1.0
CB B:CYS1119 2.8 36.2 1.0
CB B:CYS1137 3.1 45.7 1.0
CB B:CYS1140 3.1 50.2 1.0
CB B:CYS1122 3.6 36.2 1.0
N B:CYS1140 3.6 50.2 1.0
N B:CYS1122 4.0 36.2 1.0
CA B:CYS1140 4.0 50.2 1.0
OD1 B:ASN1142 4.1 48.2 1.0
CA B:CYS1119 4.4 36.2 1.0
CA B:CYS1122 4.4 36.2 1.0
CA B:CYS1137 4.5 45.7 1.0
C B:GLY1139 4.6 48.4 1.0
CB B:LEU1121 4.7 40.4 1.0
CG B:ASN1142 4.9 48.2 1.0
CA B:GLY1139 4.9 48.4 1.0
C B:CYS1137 5.0 45.7 1.0
C B:CYS1119 5.0 36.2 1.0

Zinc binding site 4 out of 8 in 7oop

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Zinc binding site 4 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:61.9
occ:1.00
SG C:CYS97 2.2 19.4 1.0
SG C:CYS90 2.2 40.7 1.0
SG C:CYS88 2.3 29.3 1.0
SG C:CYS94 2.3 24.5 1.0
CB C:CYS88 3.0 29.3 1.0
CB C:CYS97 3.1 19.4 1.0
CB C:CYS94 3.5 24.5 1.0
CB C:CYS90 3.6 40.7 1.0
N C:CYS94 3.6 24.5 1.0
N C:CYS97 4.0 19.4 1.0
CA C:CYS94 4.0 24.5 1.0
C C:PHE93 4.0 24.2 1.0
CA C:CYS97 4.1 19.4 1.0
O C:CYS94 4.2 24.5 1.0
CA C:CYS88 4.4 29.3 1.0
C C:CYS94 4.4 24.5 1.0
CA C:PHE93 4.5 24.2 1.0
O C:PHE93 4.6 24.2 1.0
O C:GLU91 4.6 49.5 1.0
N C:CYS90 4.6 40.7 1.0
CA C:CYS90 4.6 40.7 1.0
C C:GLU96 4.8 22.1 1.0
C C:CYS97 4.9 19.4 1.0
C C:CYS88 4.9 29.3 1.0

Zinc binding site 5 out of 8 in 7oop

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Zinc binding site 5 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:110.3
occ:1.00
SG I:CYS20 2.3 85.0 1.0
SG I:CYS17 2.3 82.4 1.0
SG I:CYS42 2.3 91.8 1.0
SG I:CYS39 2.3 88.8 1.0
CB I:CYS17 2.4 82.4 1.0
CB I:CYS39 2.5 88.8 1.0
CB I:CYS42 3.5 91.8 1.0
CA I:CYS17 3.8 82.4 1.0
CB I:CYS20 3.9 85.0 1.0
N I:CYS42 4.0 91.8 1.0
CA I:CYS39 4.0 88.8 1.0
N I:CYS20 4.2 85.0 1.0
CB I:TYR44 4.2 91.2 1.0
CA I:CYS42 4.3 91.8 1.0
CA I:CYS20 4.6 85.0 1.0
N I:CYS17 4.6 82.4 1.0
CD2 I:LEU24 4.6 85.4 1.0
C I:CYS42 4.7 91.8 1.0
O I:ASN22 4.7 77.4 1.0
C I:CYS17 4.7 82.4 1.0
N I:CYS39 4.8 88.8 1.0
C I:CYS39 4.8 88.8 1.0
N I:ASN22 4.8 77.4 1.0
N I:TYR44 4.9 91.2 1.0
CB I:ASN22 4.9 77.4 1.0
N I:ASN21 5.0 76.5 1.0
O I:CYS42 5.0 91.8 1.0

Zinc binding site 6 out of 8 in 7oop

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Zinc binding site 6 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:71.0
occ:1.00
SG I:CYS89 2.2 48.0 1.0
SG I:CYS86 2.3 50.0 1.0
SG I:CYS119 2.3 52.6 1.0
SG I:CYS114 2.3 40.0 1.0
CB I:CYS114 2.6 40.0 1.0
CB I:CYS86 3.1 50.0 1.0
CB I:CYS89 3.5 48.0 1.0
CB I:CYS119 3.5 52.6 1.0
CB I:HIS121 3.8 45.6 1.0
N I:CYS89 4.1 48.0 1.0
CA I:CYS114 4.1 40.0 1.0
N I:HIS121 4.2 45.6 1.0
CA I:CYS89 4.4 48.0 1.0
CA I:CYS86 4.5 50.0 1.0
CA I:HIS121 4.6 45.6 1.0
CB I:ALA116 4.7 51.3 1.0
N I:GLY120 4.7 46.4 1.0
CB I:LYS88 4.7 50.4 1.0
CB I:HIS91 4.8 50.8 1.0
CA I:CYS119 4.8 52.6 1.0
C I:CYS119 4.8 52.6 1.0
C I:CYS114 4.9 40.0 1.0
CG I:HIS121 4.9 45.6 1.0
C I:LYS88 4.9 50.4 1.0
N I:CYS114 4.9 40.0 1.0

Zinc binding site 7 out of 8 in 7oop

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Zinc binding site 7 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:21.1
occ:1.00
SG J:CYS10 2.2 13.5 1.0
SG J:CYS44 2.2 10.8 1.0
SG J:CYS7 2.3 21.2 1.0
SG J:CYS45 2.3 13.2 1.0
CB J:CYS7 3.0 21.2 1.0
N J:CYS45 3.4 13.2 1.0
CB J:CYS10 3.4 13.5 1.0
CB J:CYS44 3.4 10.8 1.0
CB J:CYS45 3.7 13.2 1.0
N J:CYS10 3.8 13.5 1.0
CA J:CYS45 3.8 13.2 1.0
C J:CYS44 3.9 10.8 1.0
CA J:CYS10 4.2 13.5 1.0
CA J:CYS44 4.2 10.8 1.0
NE J:ARG42 4.2 12.0 1.0
CA J:CYS7 4.5 21.2 1.0
CB J:THR9 4.6 12.3 1.0
O J:CYS44 4.6 10.8 1.0
CB J:LYS12 4.6 18.0 1.0
CB J:ARG42 4.7 12.0 1.0
N J:GLY11 4.8 18.0 1.0
NH2 J:ARG42 4.9 12.0 1.0
C J:THR9 4.9 12.3 1.0
N J:CYS44 4.9 10.8 1.0
N J:LYS12 4.9 18.0 1.0
N J:THR9 5.0 12.3 1.0
C J:CYS7 5.0 21.2 1.0
C J:CYS10 5.0 13.5 1.0
CD J:ARG42 5.0 12.0 1.0

Zinc binding site 8 out of 8 in 7oop

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Zinc binding site 8 out of 8 in the Pol II-Csb-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3)


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-Csa-DDB1-Uvssa-Paf-SPT6 (Structure 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:78.6
occ:1.00
SG L:CYS36 2.2 54.5 1.0
SG L:CYS22 2.2 47.7 1.0
SG L:CYS39 2.3 52.4 1.0
SG L:CYS19 2.3 42.9 1.0
CB L:CYS36 2.8 54.5 1.0
CB L:CYS19 3.1 42.9 1.0
CB L:CYS22 3.3 47.7 1.0
CB L:CYS39 3.6 52.4 1.0
N L:CYS39 3.7 52.4 1.0
N L:CYS22 4.0 47.7 1.0
CB L:TYR41 4.1 39.0 1.0
CA L:CYS39 4.1 52.4 1.0
OE1 L:GLU38 4.1 58.8 1.0
CA L:CYS22 4.2 47.7 1.0
CA L:CYS36 4.3 54.5 1.0
N L:TYR41 4.3 39.0 1.0
N L:GLY40 4.4 50.7 1.0
C L:CYS39 4.5 52.4 1.0
CA L:CYS19 4.5 42.9 1.0
CB L:GLU38 4.5 58.8 1.0
C L:GLU38 4.6 58.8 1.0
OG1 L:THR24 4.7 51.9 1.0
N L:GLU38 4.7 58.8 1.0
C L:CYS36 4.8 54.5 1.0
CA L:TYR41 4.8 39.0 1.0
CA L:GLU38 4.9 58.8 1.0
C L:CYS22 4.9 47.7 1.0
CB L:THR24 5.0 51.9 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: Fri Nov 5 16:56:17 2021

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