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Zinc in PDB 7nvy: Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position

Enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position

All present enzymatic activity of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position:
2.3.1.48; 2.7.7.6; 3.6.4.12;

Other elements in 7nvy:

The structure of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Zinc atom in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position (pdb code 7nvy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position, PDB code: 7nvy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 7nvy

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Zinc binding site 1 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn400

b:168.8
occ:1.00
 CB 3:CYS34 2.2 124.8 1.0
SG 3:CYS9 2.3 98.3 1.0
SG 3:CYS6 2.3 91.7 1.0
SG 3:CYS31 2.4 104.5 1.0
SG 3:CYS34 2.7 124.8 1.0
CB 3:CYS6 3.1 91.7 1.0
CA 3:CYS34 3.5 124.8 1.0
N 3:CYS34 3.9 124.8 1.0
CB 3:CYS31 4.0 104.5 1.0
CB 3:CYS9 4.0 98.3 1.0
N 3:CYS31 4.1 104.5 1.0
O 3:CYS31 4.3 104.5 1.0
N 3:CYS9 4.3 98.3 1.0
O 3:CYS9 4.5 98.3 1.0
CA 3:CYS31 4.5 104.5 1.0
CA 3:CYS9 4.6 98.3 1.0
CA 3:CYS6 4.6 91.7 1.0
C 3:CYS34 4.7 124.8 1.0
CD2 3:LEU30 4.8 97.6 1.0
C 3:CYS9 4.8 98.3 1.0
C 3:CYS31 4.8 104.5 1.0
C 3:LEU30 5.0 97.6 1.0
C 3:SER33 5.0 135.2 1.0
CA 3:LEU30 5.0 97.6 1.0

Zinc binding site 2 out of 17 in 7nvy

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Zinc binding site 2 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:111.7
occ:1.00
 NE2 3:HIS28 2.1 83.2 1.0
CE1 3:HIS28 2.1 83.2 1.0
CD2 3:HIS28 2.3 83.2 1.0
SG 3:CYS49 2.3 116.0 1.0
SG 3:CYS46 2.3 115.0 1.0
ND1 3:HIS28 2.3 83.2 1.0
CG 3:HIS28 2.4 83.2 1.0
SG 3:CYS26 2.5 74.9 1.0
CB 3:CYS49 3.4 116.0 1.0
CB 3:HIS28 3.6 83.2 1.0
CB 3:CYS46 3.7 115.0 1.0
CB 3:CYS26 3.9 74.9 1.0
N 3:CYS49 4.2 116.0 1.0
CA 3:CYS49 4.4 116.0 1.0
CA 3:HIS28 4.9 83.2 1.0

Zinc binding site 3 out of 17 in 7nvy

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Zinc binding site 3 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:90.3
occ:1.00
 CB 4:CYS285 2.1 38.1 1.0
SG 4:CYS268 2.3 36.0 1.0
SG 4:CYS285 2.4 38.1 1.0
SG 4:CYS271 2.5 40.1 1.0
SG 4:CYS282 2.5 46.3 1.0
CB 4:CYS271 3.2 40.1 1.0
CA 4:CYS285 3.4 38.1 1.0
CB 4:CYS268 3.6 36.0 1.0
N 4:CYS271 3.6 40.1 1.0
N 4:CYS285 3.8 38.1 1.0
CA 4:CYS271 4.0 40.1 1.0
CB 4:CYS282 4.1 46.3 1.0
CB 4:VAL270 4.5 33.9 1.0
OG1 4:THR284 4.5 42.1 1.0
C 4:THR284 4.5 42.1 1.0
C 4:CYS285 4.6 38.1 1.0
CG2 4:THR287 4.7 39.5 1.0
C 4:VAL270 4.7 33.9 1.0
O 4:THR284 4.8 42.1 1.0
O 4:CYS282 4.8 46.3 1.0
N 4:VAL270 4.9 33.9 1.0
CA 4:CYS268 4.9 36.0 1.0
CA 4:VAL270 4.9 33.9 1.0

Zinc binding site 4 out of 17 in 7nvy

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Zinc binding site 4 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn402

b:48.6
occ:1.00
 CE1 4:HIS258 1.4 53.0 1.0
ND1 4:HIS258 2.2 53.0 1.0
NE2 4:HIS258 2.3 53.0 1.0
SG 4:CYS276 2.6 45.1 1.0
SG 4:CYS257 2.7 62.4 1.0
CB 4:CYS257 2.7 62.4 1.0
CB 4:CYS276 2.8 45.1 1.0
SG 4:CYS255 2.9 62.5 1.0
CG 4:HIS258 3.3 53.0 1.0
CD2 4:HIS258 3.3 53.0 1.0
CA 4:CYS276 4.0 45.1 1.0
CA 4:CYS257 4.1 62.4 1.0
CB 4:CYS255 4.2 62.5 1.0
N 4:HIS258 4.3 53.0 1.0
CB 4:HIS258 4.5 53.0 1.0
N 4:CYS257 4.5 62.4 1.0
C 4:CYS257 4.5 62.4 1.0
N 4:CYS276 4.8 45.1 1.0
CA 4:HIS258 4.9 53.0 1.0

Zinc binding site 5 out of 17 in 7nvy

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Zinc binding site 5 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn401

b:116.0
occ:1.00
 SG 6:CYS371 2.3 29.4 1.0
SG 6:CYS368 2.3 29.4 1.0
SG 6:CYS348 2.3 21.3 1.0
SG 6:CYS345 2.3 28.3 1.0
CB 6:CYS345 3.2 28.3 1.0
CB 6:CYS368 3.3 29.4 1.0
CB 6:CYS371 3.3 29.4 1.0
CB 6:CYS348 3.3 21.3 1.0
N 6:CYS348 3.5 21.3 1.0
N 6:CYS368 3.6 29.4 1.0
CA 6:CYS368 4.0 29.4 1.0
CA 6:CYS348 4.0 21.3 1.0
N 6:CYS371 4.2 29.4 1.0
CA 6:CYS371 4.3 29.4 1.0
C 6:GLY347 4.4 22.6 1.0
CA 6:GLY347 4.5 22.6 1.0
N 6:GLY347 4.6 22.6 1.0
CA 6:CYS345 4.6 28.3 1.0
C 6:CYS368 4.7 29.4 1.0
C 6:PHE367 4.7 27.6 1.0
C 6:CYS345 4.8 28.3 1.0
O 6:CYS345 4.9 28.3 1.0
C 6:CYS348 4.9 21.3 1.0
CA 6:PHE367 4.9 27.6 1.0
O 6:CYS368 5.0 29.4 1.0

Zinc binding site 6 out of 17 in 7nvy

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Zinc binding site 6 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn402

b:22.4
occ:1.00
 CB 6:CYS385 2.1 23.0 1.0
SG 6:CYS360 2.3 27.2 1.0
SG 6:CYS363 2.4 27.3 1.0
SG 6:CYS382 2.5 23.3 1.0
SG 6:CYS385 2.7 23.0 1.0
CB 6:CYS360 3.1 27.2 1.0
CB 6:CYS363 3.3 27.3 1.0
CA 6:CYS385 3.3 23.0 1.0
CB 6:CYS382 3.4 23.3 1.0
N 6:CYS385 3.6 23.0 1.0
N 6:CYS363 4.2 27.3 1.0
CA 6:CYS363 4.4 27.3 1.0
C 6:CYS385 4.6 23.0 1.0
CE2 6:PHE367 4.6 27.6 1.0
CA 6:CYS360 4.6 27.2 1.0
CA 6:CYS382 4.8 23.3 1.0
C 6:GLY384 4.8 21.9 1.0
CZ 6:PHE367 4.9 27.6 1.0
CZ 6:PHE331 4.9 20.5 1.0

Zinc binding site 7 out of 17 in 7nvy

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Zinc binding site 7 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn403

b:255.1
occ:1.00
 SG 6:CYS294 2.2 79.7 1.0
SG 6:CYS305 2.3 67.8 1.0
SG 6:CYS308 2.3 91.9 1.0
SG 6:CYS291 2.4 70.8 1.0
CB 6:CYS294 3.0 79.7 1.0
N 6:CYS294 3.1 79.7 1.0
CB 6:CYS308 3.3 91.9 1.0
CB 6:CYS305 3.3 67.8 1.0
CA 6:CYS294 3.6 79.7 1.0
CB 6:CYS291 3.7 70.8 1.0
N 6:CYS308 4.0 91.9 1.0
C 6:GLN293 4.2 84.5 1.0
CA 6:CYS308 4.3 91.9 1.0
CB 6:GLN293 4.3 84.5 1.0
CA 6:CYS305 4.4 67.8 1.0
N 6:GLN293 4.6 84.5 1.0
CA 6:GLN293 4.6 84.5 1.0
CD1 6:LEU312 4.6 56.9 1.0
CD2 6:LEU312 4.6 56.9 1.0
C 6:CYS294 4.9 79.7 1.0
CG 6:LEU312 5.0 56.9 1.0
OH 6:TYR298 5.0 61.1 1.0

Zinc binding site 8 out of 17 in 7nvy

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Zinc binding site 8 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:32.1
occ:1.00
 NE2 A:HIS84 2.0 16.7 1.0
SG A:CYS71 2.3 24.9 1.0
SG A:CYS81 2.3 15.9 1.0
SG A:CYS74 2.3 24.6 1.0
CE1 A:HIS84 2.7 16.7 1.0
CB A:CYS74 3.1 24.6 1.0
CD2 A:HIS84 3.2 16.7 1.0
CB A:CYS81 3.5 15.9 1.0
CG2 A:THR73 3.7 21.6 1.0
CB A:CYS71 3.8 24.9 1.0
N A:CYS74 3.9 24.6 1.0
ND1 A:HIS84 3.9 16.7 1.0
CA A:CYS74 4.1 24.6 1.0
CG A:HIS84 4.2 16.7 1.0
CA A:CYS81 4.2 15.9 1.0
CD A:PRO82 4.4 12.8 1.0
N A:GLY83 4.7 13.5 1.0
CA A:GLY63 4.8 21.1 1.0
N A:PRO82 4.8 12.8 1.0
C A:CYS81 4.8 15.9 1.0
C A:THR73 4.9 21.6 1.0
O A:ARG61 5.0 22.7 1.0

Zinc binding site 9 out of 17 in 7nvy

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Zinc binding site 9 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:68.0
occ:1.00
 SG A:CYS114 2.3 41.5 1.0
SG A:CYS111 2.3 40.8 1.0
SG A:CYS154 2.3 56.8 1.0
SG A:CYS184 2.3 58.5 1.0
CB A:CYS154 3.2 56.8 1.0
CB A:CYS111 3.2 40.8 1.0
CB A:CYS114 3.4 41.5 1.0
N A:CYS114 3.7 41.5 1.0
CB A:CYS184 3.9 58.5 1.0
N A:CYS184 3.9 58.5 1.0
CA A:CYS114 4.1 41.5 1.0
N A:GLY185 4.2 52.8 1.0
NE2 A:GLN188 4.2 42.5 1.0
CA A:CYS184 4.4 58.5 1.0
CB A:PHE113 4.6 42.0 1.0
CA A:CYS154 4.6 56.8 1.0
CA A:CYS111 4.7 40.8 1.0
C A:CYS184 4.8 58.5 1.0
C A:PHE113 4.8 42.0 1.0
C A:CYS114 4.9 41.5 1.0
CD A:GLN188 4.9 42.5 1.0
N A:PHE113 4.9 42.0 1.0
C A:GLY183 4.9 77.5 1.0
CA A:GLY183 5.0 77.5 1.0

Zinc binding site 10 out of 17 in 7nvy

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Zinc binding site 10 out of 17 in the Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Rna Polymerase II Pre-Initiation Complex with Closed Promoter Dna in Proximal Position within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:8.9
occ:1.00
 SG B:CYS1140 2.3 13.1 1.0
SG B:CYS1137 2.3 18.2 1.0
SG B:CYS1122 2.3 9.6 1.0
SG B:CYS1119 2.4 16.5 1.0
CB B:CYS1119 2.7 16.5 1.0
CB B:CYS1140 3.2 13.1 1.0
CB B:CYS1122 3.4 9.6 1.0
CB B:CYS1137 3.6 18.2 1.0
N B:CYS1122 3.8 9.6 1.0
O B:CYS1122 4.1 9.6 1.0
CA B:CYS1122 4.1 9.6 1.0
CA B:CYS1119 4.3 16.5 1.0
OD1 B:ASN1142 4.3 18.0 1.0
CA B:CYS1140 4.4 13.1 1.0
N B:CYS1140 4.4 13.1 1.0
O B:ARG1138 4.5 16.2 1.0
C B:CYS1122 4.6 9.6 1.0
CB B:LEU1121 4.7 18.0 1.0
C B:LEU1121 4.8 18.0 1.0
C B:CYS1119 4.9 16.5 1.0
CA B:CYS1137 4.9 18.2 1.0

Reference:

S.Aibara, S.Schilbach, P.Cramer. Structures of Mammalian Rna Polymerase II Pre-Initiation Complexes. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902107
DOI: 10.1038/S41586-021-03554-8
Page generated: Wed Oct 30 07:59:54 2024

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