Zinc in PDB 7nvx: Tfiih in A Post-Translocated State (with Adp-BEF3)

Enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3)

All present enzymatic activity of Tfiih in A Post-Translocated State (with Adp-BEF3):
3.6.4.12;

Other elements in 7nvx:

The structure of Tfiih in A Post-Translocated State (with Adp-BEF3) also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Magnesium (Mg) 1 atom
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Tfiih in A Post-Translocated State (with Adp-BEF3) (pdb code 7nvx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Tfiih in A Post-Translocated State (with Adp-BEF3), PDB code: 7nvx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 1 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn400

b:93.1
occ:1.00
 CB 3:CYS34 2.2 72.9 1.0
SG 3:CYS6 2.3 69.7 1.0
SG 3:CYS9 2.4 70.5 1.0
SG 3:CYS31 2.4 69.7 1.0
SG 3:CYS34 2.6 72.9 1.0
CB 3:CYS6 3.2 69.7 1.0
CA 3:CYS34 3.5 72.9 1.0
N 3:CYS34 3.9 72.9 1.0
CB 3:CYS9 4.0 70.5 1.0
CB 3:CYS31 4.1 69.7 1.0
N 3:CYS9 4.2 70.5 1.0
O 3:CYS9 4.2 70.5 1.0
N 3:CYS31 4.5 69.7 1.0
CA 3:CYS9 4.5 70.5 1.0
O 3:CYS31 4.6 69.7 1.0
NZ 3:LYS13 4.6 66.1 1.0
CA 3:CYS6 4.7 69.7 1.0
C 3:CYS34 4.7 72.9 1.0
CA 3:CYS31 4.7 69.7 1.0
C 3:CYS9 4.7 70.5 1.0
CB 3:ARG8 5.0 64.9 1.0

Zinc binding site 2 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 2 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Zn401

b:119.2
occ:1.00
 NE2 3:HIS28 2.1 73.2 1.0
CE1 3:HIS28 2.1 73.2 1.0
CD2 3:HIS28 2.2 73.2 1.0
SG 3:CYS49 2.3 76.9 1.0
ND1 3:HIS28 2.3 73.2 1.0
SG 3:CYS46 2.3 78.2 1.0
CG 3:HIS28 2.4 73.2 1.0
SG 3:CYS26 2.5 63.5 1.0
CB 3:CYS49 3.3 76.9 1.0
CB 3:HIS28 3.5 73.2 1.0
CB 3:CYS46 3.8 78.2 1.0
CB 3:CYS26 3.9 63.5 1.0
N 3:CYS49 4.3 76.9 1.0
CA 3:CYS49 4.4 76.9 1.0
CA 3:HIS28 4.9 73.2 1.0

Zinc binding site 3 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 3 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn401

b:101.6
occ:1.00
 CB 4:CYS285 2.1 50.8 1.0
SG 4:CYS268 2.3 40.3 1.0
SG 4:CYS271 2.4 42.7 1.0
SG 4:CYS285 2.5 50.8 1.0
SG 4:CYS282 2.5 55.8 1.0
CB 4:CYS271 3.1 42.7 1.0
CA 4:CYS285 3.3 50.8 1.0
N 4:CYS271 3.5 42.7 1.0
CB 4:CYS268 3.6 40.3 1.0
N 4:CYS285 3.7 50.8 1.0
CA 4:CYS271 3.9 42.7 1.0
CB 4:CYS282 4.2 55.8 1.0
CB 4:VAL270 4.4 41.0 1.0
OG1 4:THR284 4.4 49.4 1.0
C 4:CYS285 4.5 50.8 1.0
CG2 4:THR287 4.6 49.5 1.0
C 4:THR284 4.6 49.4 1.0
C 4:VAL270 4.6 41.0 1.0
O 4:CYS282 4.7 55.8 1.0
CA 4:VAL270 4.9 41.0 1.0
N 4:VAL270 5.0 41.0 1.0
CA 4:CYS268 5.0 40.3 1.0

Zinc binding site 4 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 4 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn402

b:74.8
occ:1.00
 CD2 4:HIS258 1.8 59.0 1.0
NE2 4:HIS258 2.1 59.0 1.0
CB 4:CYS276 2.4 53.0 1.0
SG 4:CYS276 2.4 53.0 1.0
CB 4:CYS257 2.5 53.7 1.0
SG 4:CYS255 2.6 50.6 1.0
SG 4:CYS257 2.7 53.7 1.0
CG 4:HIS258 3.0 59.0 1.0
CE1 4:HIS258 3.3 59.0 1.0
ND1 4:HIS258 3.7 59.0 1.0
CB 4:CYS255 3.7 50.6 1.0
CA 4:CYS257 3.7 53.7 1.0
CA 4:CYS276 3.8 53.0 1.0
N 4:HIS258 3.9 59.0 1.0
CB 4:HIS258 4.0 59.0 1.0
N 4:CYS257 4.0 53.7 1.0
C 4:CYS257 4.1 53.7 1.0
N 4:CYS276 4.4 53.0 1.0
CA 4:HIS258 4.6 59.0 1.0
C 4:CYS276 4.8 53.0 1.0
OD1 4:ASN260 4.9 56.4 1.0

Zinc binding site 5 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 5 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn401

b:106.8
occ:1.00
 SG 6:CYS345 2.3 33.6 1.0
SG 6:CYS348 2.3 23.0 1.0
SG 6:CYS371 2.3 23.7 1.0
SG 6:CYS368 2.3 31.6 1.0
CB 6:CYS345 3.1 33.6 1.0
CB 6:CYS348 3.3 23.0 1.0
CB 6:CYS371 3.3 23.7 1.0
CB 6:CYS368 3.5 31.6 1.0
N 6:CYS348 3.5 23.0 1.0
N 6:CYS368 3.7 31.6 1.0
CA 6:CYS348 4.0 23.0 1.0
N 6:CYS371 4.0 23.7 1.0
CA 6:CYS368 4.2 31.6 1.0
CA 6:CYS371 4.2 23.7 1.0
C 6:GLY347 4.4 27.5 1.0
CA 6:CYS345 4.5 33.6 1.0
CA 6:GLY347 4.6 27.5 1.0
N 6:GLY347 4.6 27.5 1.0
C 6:CYS348 4.8 23.0 1.0
C 6:PHE367 4.8 34.2 1.0
C 6:CYS368 4.8 31.6 1.0
C 6:CYS345 4.9 33.6 1.0

Zinc binding site 6 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 6 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn402

b:71.3
occ:1.00
 CB 6:CYS385 2.0 55.5 1.0
SG 6:CYS360 2.3 49.3 1.0
SG 6:CYS363 2.4 64.0 1.0
SG 6:CYS382 2.5 38.3 1.0
SG 6:CYS385 2.7 55.5 1.0
CB 6:CYS360 3.1 49.3 1.0
CA 6:CYS385 3.2 55.5 1.0
CB 6:CYS363 3.3 64.0 1.0
CB 6:CYS382 3.4 38.3 1.0
N 6:CYS385 3.6 55.5 1.0
N 6:CYS363 4.3 64.0 1.0
CA 6:CYS363 4.4 64.0 1.0
CE2 6:PHE367 4.4 34.2 1.0
C 6:CYS385 4.5 55.5 1.0
CA 6:CYS360 4.6 49.3 1.0
C 6:GLY384 4.8 40.6 1.0
CA 6:CYS382 4.8 38.3 1.0
CZ 6:PHE367 4.8 34.2 1.0
N 6:CYS360 5.0 49.3 1.0
CZ 6:PHE331 5.0 43.8 1.0
N 6:GLN364 5.0 57.2 1.0

Zinc binding site 7 out of 7 in 7nvx

Go back to Zinc Binding Sites List in 7nvx
Zinc binding site 7 out of 7 in the Tfiih in A Post-Translocated State (with Adp-BEF3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Tfiih in A Post-Translocated State (with Adp-BEF3) within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn403

b:78.2
occ:1.00
 SG 6:CYS294 2.2 37.4 1.0
SG 6:CYS308 2.3 38.8 1.0
SG 6:CYS305 2.3 45.1 1.0
SG 6:CYS291 2.4 33.6 1.0
CB 6:CYS305 3.1 45.1 1.0
CB 6:CYS294 3.1 37.4 1.0
N 6:CYS294 3.1 37.4 1.0
CB 6:CYS308 3.3 38.8 1.0
CA 6:CYS294 3.6 37.4 1.0
CB 6:CYS291 3.7 33.6 1.0
N 6:CYS308 4.0 38.8 1.0
CB 6:GLN293 4.2 37.5 1.0
C 6:GLN293 4.2 37.5 1.0
CA 6:CYS305 4.3 45.1 1.0
CA 6:CYS308 4.3 38.8 1.0
CA 6:GLN293 4.5 37.5 1.0
N 6:GLN293 4.5 37.5 1.0
CD1 6:LEU312 4.6 39.9 1.0
CD2 6:LEU312 4.8 39.9 1.0
OH 6:TYR298 5.0 37.1 1.0
CG 6:LEU312 5.0 39.9 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 07:58:21 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy