Zinc in PDB 7nvr: Human Mediator with Rna Polymerase II Pre-Initiation Complex

Enzymatic activity of Human Mediator with Rna Polymerase II Pre-Initiation Complex

All present enzymatic activity of Human Mediator with Rna Polymerase II Pre-Initiation Complex:
2.3.1.48; 2.7.11.22; 2.7.11.23; 2.7.7.6; 3.6.4.12;

Other elements in 7nvr:

The structure of Human Mediator with Rna Polymerase II Pre-Initiation Complex also contains other interesting chemical elements:

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

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the Human Mediator with Rna Polymerase II Pre-Initiation Complex (pdb code 7nvr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the Human Mediator with Rna Polymerase II Pre-Initiation Complex, PDB code: 7nvr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 7nvr

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Zinc binding site 1 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

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

b:148.8
occ:1.00
SG 3:CYS6 2.3 115.8 1.0
SG 3:CYS9 2.3 135.5 1.0
SG 3:CYS31 2.4 134.4 1.0
CB 3:CYS34 2.4 136.7 1.0
SG 3:CYS34 2.6 136.7 1.0
CB 3:CYS6 3.2 115.8 1.0
CA 3:CYS34 3.7 136.7 1.0
CB 3:CYS9 4.0 135.5 1.0
N 3:CYS9 4.1 135.5 1.0
CB 3:CYS31 4.2 134.4 1.0
N 3:CYS34 4.2 136.7 1.0
O 3:CYS9 4.3 135.5 1.0
N 3:CYS31 4.5 134.4 1.0
NZ 3:LYS13 4.5 128.3 1.0
O 3:CYS31 4.5 134.4 1.0
CA 3:CYS9 4.5 135.5 1.0
CA 3:CYS6 4.6 115.8 1.0
C 3:CYS9 4.8 135.5 1.0
CA 3:CYS31 4.8 134.4 1.0
C 3:CYS34 4.9 136.7 1.0
CB 3:ARG8 4.9 129.6 1.0

Zinc binding site 2 out of 18 in 7nvr

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Zinc binding site 2 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

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

b:133.0
occ:1.00
NE2 3:HIS28 2.1 116.2 1.0
CE1 3:HIS28 2.1 116.2 1.0
CD2 3:HIS28 2.3 116.2 1.0
SG 3:CYS49 2.3 113.5 1.0
SG 3:CYS46 2.3 110.0 1.0
ND1 3:HIS28 2.3 116.2 1.0
CG 3:HIS28 2.4 116.2 1.0
SG 3:CYS26 2.5 105.5 1.0
CB 3:CYS49 3.3 113.5 1.0
CB 3:HIS28 3.6 116.2 1.0
CB 3:CYS46 3.7 110.0 1.0
CB 3:CYS26 3.9 105.5 1.0
N 3:CYS49 4.3 113.5 1.0
CA 3:CYS49 4.4 113.5 1.0
CA 3:HIS28 4.9 116.2 1.0

Zinc binding site 3 out of 18 in 7nvr

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Zinc binding site 3 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

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

b:191.5
occ:1.00
CB 4:CYS285 2.2 157.4 1.0
SG 4:CYS268 2.3 165.2 1.0
SG 4:CYS285 2.4 157.4 1.0
SG 4:CYS271 2.5 170.4 1.0
SG 4:CYS282 2.5 152.6 1.0
CB 4:CYS271 3.2 170.4 1.0
CA 4:CYS285 3.4 157.4 1.0
CB 4:CYS268 3.6 165.2 1.0
N 4:CYS271 3.6 170.4 1.0
N 4:CYS285 3.8 157.4 1.0
CA 4:CYS271 4.0 170.4 1.0
CB 4:CYS282 4.1 152.6 1.0
CB 4:VAL270 4.5 159.7 1.0
C 4:THR284 4.5 158.5 1.0
OG1 4:THR284 4.5 158.5 1.0
C 4:CYS285 4.6 157.4 1.0
CG2 4:THR287 4.7 147.1 1.0
C 4:VAL270 4.7 159.7 1.0
O 4:THR284 4.8 158.5 1.0
O 4:CYS282 4.9 152.6 1.0
N 4:VAL270 4.9 159.7 1.0
CA 4:CYS268 4.9 165.2 1.0
CA 4:VAL270 5.0 159.7 1.0

Zinc binding site 4 out of 18 in 7nvr

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Zinc binding site 4 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:199.4
occ:1.00
CE1 4:HIS258 1.5 176.3 1.0
ND1 4:HIS258 2.2 176.3 1.0
NE2 4:HIS258 2.3 176.3 1.0
SG 4:CYS276 2.5 172.0 1.0
CB 4:CYS276 2.7 172.0 1.0
SG 4:CYS257 2.7 176.3 1.0
CB 4:CYS257 2.8 176.3 1.0
SG 4:CYS255 2.9 175.3 1.0
CG 4:HIS258 3.3 176.3 1.0
CD2 4:HIS258 3.3 176.3 1.0
CA 4:CYS276 3.9 172.0 1.0
CA 4:CYS257 4.1 176.3 1.0
CB 4:CYS255 4.2 175.3 1.0
N 4:HIS258 4.4 176.3 1.0
CB 4:HIS258 4.5 176.3 1.0
N 4:CYS257 4.5 176.3 1.0
C 4:CYS257 4.6 176.3 1.0
N 4:CYS276 4.7 172.0 1.0
CA 4:HIS258 4.9 176.3 1.0
C 4:CYS276 4.9 172.0 1.0

Zinc binding site 5 out of 18 in 7nvr

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Zinc binding site 5 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:210.8
occ:1.00
SG 6:CYS371 2.3 192.6 1.0
SG 6:CYS368 2.3 188.2 1.0
SG 6:CYS348 2.3 191.6 1.0
SG 6:CYS345 2.4 180.7 1.0
CB 6:CYS345 3.2 180.7 1.0
CB 6:CYS368 3.3 188.2 1.0
CB 6:CYS371 3.3 192.6 1.0
CB 6:CYS348 3.3 191.6 1.0
N 6:CYS348 3.5 191.6 1.0
N 6:CYS368 3.6 188.2 1.0
CA 6:CYS368 4.0 188.2 1.0
CA 6:CYS348 4.0 191.6 1.0
N 6:CYS371 4.2 192.6 1.0
CA 6:CYS371 4.3 192.6 1.0
C 6:GLY347 4.4 187.9 1.0
CA 6:GLY347 4.5 187.9 1.0
N 6:GLY347 4.6 187.9 1.0
CA 6:CYS345 4.6 180.7 1.0
C 6:CYS368 4.7 188.2 1.0
C 6:PHE367 4.7 180.2 1.0
C 6:CYS345 4.8 180.7 1.0
O 6:CYS345 4.9 180.7 1.0
C 6:CYS348 4.9 191.6 1.0
CA 6:PHE367 4.9 180.2 1.0
O 6:CYS368 5.0 188.2 1.0

Zinc binding site 6 out of 18 in 7nvr

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Zinc binding site 6 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:188.8
occ:1.00
CB 6:CYS385 2.1 176.8 1.0
SG 6:CYS360 2.3 172.3 1.0
SG 6:CYS363 2.4 179.0 1.0
SG 6:CYS382 2.5 177.5 1.0
SG 6:CYS385 2.7 176.8 1.0
CB 6:CYS360 3.2 172.3 1.0
CA 6:CYS385 3.3 176.8 1.0
CB 6:CYS363 3.3 179.0 1.0
CB 6:CYS382 3.4 177.5 1.0
N 6:CYS385 3.6 176.8 1.0
N 6:CYS363 4.3 179.0 1.0
CA 6:CYS363 4.4 179.0 1.0
CE2 6:PHE367 4.5 180.2 1.0
C 6:CYS385 4.6 176.8 1.0
CA 6:CYS360 4.6 172.3 1.0
CZ 6:PHE367 4.8 180.2 1.0
CA 6:CYS382 4.8 177.5 1.0
C 6:GLY384 4.8 184.4 1.0
CZ 6:PHE331 4.9 188.7 1.0
N 6:CYS360 5.0 172.3 1.0

Zinc binding site 7 out of 18 in 7nvr

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Zinc binding site 7 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:177.6
occ:1.00
SG 6:CYS294 2.2 148.9 1.0
SG 6:CYS305 2.3 138.2 1.0
SG 6:CYS308 2.3 138.4 1.0
SG 6:CYS291 2.4 146.8 1.0
CB 6:CYS294 3.0 148.9 1.0
N 6:CYS294 3.1 148.9 1.0
CB 6:CYS308 3.3 138.4 1.0
CB 6:CYS305 3.3 138.2 1.0
CA 6:CYS294 3.6 148.9 1.0
CB 6:CYS291 3.7 146.8 1.0
N 6:CYS308 4.0 138.4 1.0
C 6:GLN293 4.2 155.4 1.0
CA 6:CYS308 4.3 138.4 1.0
CB 6:GLN293 4.3 155.4 1.0
CA 6:CYS305 4.4 138.2 1.0
N 6:GLN293 4.6 155.4 1.0
CA 6:GLN293 4.6 155.4 1.0
CD1 6:LEU312 4.6 147.0 1.0
CD2 6:LEU312 4.6 147.0 1.0
C 6:CYS294 5.0 148.9 1.0
CG 6:LEU312 5.0 147.0 1.0
OH 6:TYR298 5.0 142.6 1.0

Zinc binding site 8 out of 18 in 7nvr

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Zinc binding site 8 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:137.8
occ:1.00
NE2 A:HIS84 2.0 62.7 1.0
SG A:CYS71 2.2 64.5 1.0
SG A:CYS74 2.3 58.1 1.0
SG A:CYS81 2.3 44.4 1.0
CE1 A:HIS84 3.0 62.7 1.0
CD2 A:HIS84 3.0 62.7 1.0
OG1 A:THR73 3.4 68.4 1.0
CB A:CYS74 3.4 58.1 1.0
CB A:CYS81 3.4 44.4 1.0
CB A:CYS71 3.7 64.5 1.0
N A:CYS74 3.8 58.1 1.0
CA A:CYS74 4.1 58.1 1.0
ND1 A:HIS84 4.1 62.7 1.0
CG A:HIS84 4.2 62.7 1.0
CA A:CYS81 4.2 44.4 1.0
CD A:PRO82 4.5 43.5 1.0
C A:CYS74 4.6 58.1 1.0
CA A:GLY63 4.6 71.7 1.0
N A:GLY76 4.7 49.4 1.0
CB A:THR73 4.8 68.4 1.0
N A:ALA75 4.8 59.2 1.0
C A:CYS81 4.8 44.4 1.0
N A:GLY83 4.8 50.4 1.0
CA A:CYS71 4.9 64.5 1.0
N A:PRO82 4.9 43.5 1.0
C A:THR73 4.9 68.4 1.0
O A:GLY76 4.9 49.4 1.0

Zinc binding site 9 out of 18 in 7nvr

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Zinc binding site 9 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


Mono view


Stereo pair view

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

b:143.9
occ:1.00
SG A:CYS111 2.3 104.7 1.0
SG A:CYS114 2.3 110.7 1.0
SG A:CYS154 2.3 104.1 1.0
SG A:CYS184 2.3 102.9 1.0
CB A:CYS114 3.2 110.7 1.0
CB A:CYS111 3.2 104.7 1.0
CB A:CYS154 3.3 104.1 1.0
N A:CYS114 3.6 110.7 1.0
N A:CYS184 3.9 102.9 1.0
CB A:CYS184 3.9 102.9 1.0
CA A:CYS114 4.0 110.7 1.0
NE2 A:GLN188 4.0 103.3 1.0
N A:GLY185 4.2 102.6 1.0
CA A:CYS184 4.4 102.9 1.0
CB A:PHE113 4.6 101.4 1.0
CA A:CYS154 4.7 104.1 1.0
CA A:CYS111 4.7 104.7 1.0
C A:CYS114 4.7 110.7 1.0
C A:PHE113 4.7 101.4 1.0
C A:GLY183 4.8 103.3 1.0
C A:CYS184 4.8 102.9 1.0
CA A:GLY183 4.9 103.3 1.0
N A:PHE113 4.9 101.4 1.0
CD A:GLN188 4.9 103.3 1.0
N A:SER115 4.9 117.2 1.0
CA A:PHE113 5.0 101.4 1.0

Zinc binding site 10 out of 18 in 7nvr

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Zinc binding site 10 out of 18 in the Human Mediator with Rna Polymerase II Pre-Initiation Complex


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Stereo pair view

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

b:103.3
occ:1.00
SG B:CYS1119 2.3 40.9 1.0
SG B:CYS1122 2.3 45.4 1.0
CB B:CYS1140 2.4 50.3 1.0
SG B:CYS1137 2.4 52.1 1.0
SG B:CYS1140 2.5 50.3 1.0
CB B:CYS1119 3.0 40.9 1.0
CB B:CYS1137 3.6 52.1 1.0
OD1 B:ASN1142 3.6 51.2 1.0
CB B:CYS1122 3.8 45.4 1.0
N B:CYS1122 3.8 45.4 1.0
CA B:CYS1140 3.9 50.3 1.0
O B:CYS1122 4.1 45.4 1.0
CA B:CYS1122 4.3 45.4 1.0
CA B:CYS1119 4.4 40.9 1.0
CG B:ASN1142 4.5 51.2 1.0
N B:CYS1140 4.5 50.3 1.0
CB B:LEU1121 4.5 43.7 1.0
ND2 B:ASN1142 4.6 51.2 1.0
O B:CYS1137 4.6 52.1 1.0
C B:CYS1122 4.7 45.4 1.0
C B:CYS1140 4.8 50.3 1.0
CA B:CYS1137 4.9 52.1 1.0
C B:LEU1121 4.9 43.7 1.0
C B:CYS1119 4.9 40.9 1.0
N B:LEU1121 5.0 43.7 1.0

Reference:

S.Rengachari, S.Schilbach, S.Aibara, C.Dienemann, P.Cramer. Structure of Human Mediator-Rna Polymerase II Pre-Initiation Complex. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33902108
DOI: 10.1038/S41586-021-03555-7
Page generated: Mon Jul 12 17:29:33 2021

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