Zinc in PDB 9fss: Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)

Enzymatic activity of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)

All present enzymatic activity of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini):
2.7.7.6;

Other elements in 9fss:

The structure of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) (pdb code 9fss). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini), PDB code: 9fss:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 1 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:5.5
occ:1.00
 NE2 A:HIS82 2.1 6.1 1.0
SG A:CYS69 2.3 6.6 1.0
SG A:CYS72 2.3 4.6 1.0
SG A:CYS79 2.3 9.5 1.0
CB A:CYS72 2.5 4.6 1.0
CE1 A:HIS82 2.9 6.1 1.0
CD2 A:HIS82 3.2 6.1 1.0
N A:CYS72 3.3 4.6 1.0
CB A:CYS79 3.4 9.5 1.0
CA A:CYS72 3.4 4.6 1.0
CB A:CYS69 3.7 6.6 1.0
CA A:CYS79 4.1 9.5 1.0
ND1 A:HIS82 4.1 6.1 1.0
CG A:HIS82 4.3 6.1 1.0
C A:CYS72 4.3 4.6 1.0
N A:GLY73 4.5 9.5 1.0
C A:THR71 4.6 6.3 1.0
C A:CYS79 4.7 9.5 1.0
N A:GLY81 4.8 9.4 1.0
CB A:THR71 4.8 6.3 1.0
N A:LEU80 4.8 8.0 1.0
CA A:CYS69 4.9 6.6 1.0
O A:LYS74 4.9 7.8 1.0
N A:CYS69 5.0 6.6 1.0

Zinc binding site 2 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 2 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:32.6
occ:1.00
 SG A:CYS156 2.3 22.6 1.0
SG A:CYS109 2.3 16.7 1.0
SG A:CYS159 2.3 24.0 1.0
SG A:CYS112 2.3 15.7 1.0
OG1 A:THR111 2.9 20.1 1.0
CB A:CYS159 3.0 24.0 1.0
CB A:CYS156 3.1 22.6 1.0
CB A:CYS109 3.3 16.7 1.0
N A:CYS159 3.5 24.0 1.0
CB A:CYS112 3.6 15.7 1.0
CA A:CYS159 3.9 24.0 1.0
N A:CYS112 4.0 15.7 1.0
CA A:CYS112 4.3 15.7 1.0
CB A:THR111 4.3 20.1 1.0
CB A:HIS158 4.4 20.9 1.0
CA A:CYS156 4.6 22.6 1.0
C A:HIS158 4.6 20.9 1.0
CA A:CYS109 4.7 16.7 1.0
N A:GLY160 4.8 25.3 1.0
C A:THR111 4.8 20.1 1.0
C A:CYS159 4.8 24.0 1.0
N A:THR111 4.9 20.1 1.0
CA A:HIS158 4.9 20.9 1.0
CA A:THR111 4.9 20.1 1.0
C A:CYS109 4.9 16.7 1.0
N A:HIS158 4.9 20.9 1.0
C A:CYS112 4.9 15.7 1.0
C A:CYS156 5.0 22.6 1.0

Zinc binding site 3 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 3 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:37.0
occ:1.00
 SG B:CYS1092 2.3 6.4 1.0
SG B:CYS1083 2.3 6.7 1.0
SG B:CYS1095 2.3 6.4 1.0
SG B:CYS1080 2.3 6.5 1.0
CB B:CYS1080 2.9 6.5 1.0
CB B:CYS1095 3.3 6.4 1.0
CB B:CYS1083 3.4 6.7 1.0
CB B:CYS1092 3.5 6.4 1.0
N B:CYS1083 3.8 6.7 1.0
N B:CYS1095 3.9 6.4 1.0
CA B:CYS1083 4.2 6.7 1.0
CA B:CYS1095 4.2 6.4 1.0
CA B:CYS1080 4.3 6.5 1.0
CB B:TYR1094 4.4 6.8 1.0
OE1 B:GLN1082 4.5 7.4 1.0
O B:CYS1080 4.6 6.5 1.0
C B:CYS1080 4.7 6.5 1.0
CB B:GLN1082 4.7 7.4 1.0
CD2 B:TYR1094 4.8 6.8 1.0
C B:GLN1082 4.9 7.4 1.0
C B:TYR1094 4.9 6.8 1.0
CA B:CYS1092 4.9 6.4 1.0
N B:GLN1082 4.9 7.4 1.0

Zinc binding site 4 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 4 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:38.9
occ:1.00
 CB J:CYS5 1.8 26.6 1.0
OD1 J:ASN10 1.8 26.1 1.0
SG J:CYS5 2.3 26.6 1.0
SG J:CYS8 2.8 25.9 1.0
CG J:ASN10 2.9 26.1 1.0
SG J:CYS25 3.1 26.0 1.0
CA J:CYS5 3.2 26.6 1.0
N J:CYS8 3.3 25.9 1.0
N J:ASN10 3.4 26.1 1.0
O J:ASN10 3.4 26.1 1.0
N J:GLY9 3.5 25.6 1.0
C J:CYS8 3.6 25.9 1.0
ND2 J:ASN10 3.6 26.1 1.0
CA J:CYS8 3.8 25.9 1.0
CB J:CYS25 3.8 26.0 1.0
N J:CYS5 3.8 26.6 1.0
CB J:CYS8 3.9 25.9 1.0
C J:CYS5 3.9 26.6 1.0
CA J:ASN10 4.0 26.1 1.0
O J:CYS5 4.0 26.6 1.0
CB J:ASN10 4.0 26.1 1.0
C J:ASN10 4.0 26.1 1.0
C J:GLY9 4.2 25.6 1.0
O J:CYS8 4.2 25.9 1.0
CA J:GLY9 4.3 25.6 1.0
SG J:CYS28 4.5 26.4 1.0
C J:GLY7 4.5 26.9 1.0
N J:GLY7 4.6 26.9 1.0
CA J:CYS25 4.6 26.0 1.0
OG1 J:THR27 4.7 26.4 1.0
CA J:GLY7 4.8 26.9 1.0
N J:PRO6 4.9 28.7 1.0
CD2 J:LEU12 4.9 26.8 1.0

Zinc binding site 5 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 5 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:35.4
occ:1.00
 SG P:CYS22 2.3 19.7 1.0
SG P:CYS36 2.3 20.2 1.0
SG P:CYS39 2.3 21.2 1.0
SG P:CYS19 2.3 17.1 1.0
CB P:CYS39 3.0 21.2 1.0
CB P:CYS19 3.1 17.1 1.0
CB P:CYS36 3.3 20.2 1.0
CB P:CYS22 3.6 19.7 1.0
OE2 P:GLU38 3.6 22.8 1.0
N P:CYS39 3.8 21.2 1.0
O P:GLY20 3.8 17.3 1.0
CA P:CYS39 4.0 21.2 1.0
OG1 P:THR24 4.1 16.7 1.0
CD P:GLU38 4.2 22.8 1.0
CA P:CYS19 4.5 17.1 1.0
OE2 P:GLU21 4.6 17.9 1.0
N P:CYS22 4.6 19.7 1.0
CA P:CYS36 4.7 20.2 1.0
CA P:CYS22 4.7 19.7 1.0
C P:CYS19 4.8 17.1 1.0
CG P:GLU38 4.8 22.8 1.0
CB P:TYR41 4.8 17.7 1.0
C P:CYS39 4.8 21.2 1.0
OE1 P:GLU38 4.9 22.8 1.0
C P:GLY20 5.0 17.3 1.0
N P:GLY20 5.0 17.3 1.0

Zinc binding site 6 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 6 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn101

b:12.2
occ:1.00
 SG Q:CYS7 2.3 9.7 1.0
SG Q:CYS10 2.3 8.3 1.0
SG Q:CYS44 2.3 8.9 1.0
SG Q:CYS45 2.3 18.2 1.0
N Q:CYS45 3.1 18.2 1.0
CB Q:CYS7 3.2 9.7 1.0
CB Q:CYS10 3.3 8.3 1.0
CA Q:CYS45 3.5 18.2 1.0
C Q:CYS44 3.5 8.9 1.0
CB Q:CYS45 3.5 18.2 1.0
CB Q:CYS44 3.6 8.9 1.0
O Q:THR9 3.7 12.8 1.0
O Q:CYS44 3.9 8.9 1.0
CA Q:CYS44 4.1 8.9 1.0
OG1 Q:THR9 4.2 12.8 1.0
C Q:THR9 4.3 12.8 1.0
NE Q:ARG42 4.4 9.7 1.0
CA Q:CYS10 4.5 8.3 1.0
N Q:GLY11 4.6 15.7 1.0
CD Q:ARG42 4.6 9.7 1.0
CA Q:CYS7 4.6 9.7 1.0
N Q:CYS10 4.6 8.3 1.0
CB Q:ARG42 4.7 9.7 1.0
N Q:CYS44 4.8 8.9 1.0
C Q:CYS45 5.0 18.2 1.0

Zinc binding site 7 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 7 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn601

b:30.7
occ:1.00
 SG S:CYS10 2.3 25.3 1.0
CB S:CYS10 3.4 25.3 1.0
OD2 S:ASP30 3.7 32.1 1.0
SG S:CYS31 4.4 24.4 1.0
CG S:ASP30 4.5 32.1 1.0
N S:GLY11 4.6 27.6 1.0
CA S:CYS10 4.7 25.3 1.0
SG S:CYS7 4.7 27.5 1.0
O S:ASP30 4.8 32.1 1.0
C S:CYS10 4.9 25.3 1.0

Zinc binding site 8 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 8 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn501

b:47.2
occ:1.00
 CG Z:HIS313 2.2 36.5 1.0
OH Z:TYR311 2.3 36.8 1.0
CD2 Z:HIS313 2.4 36.5 1.0
CE2 Z:TYR311 2.4 36.8 1.0
CZ Z:TYR311 2.6 36.8 1.0
CB Z:HIS313 2.7 36.5 1.0
ND1 Z:HIS313 2.7 36.5 1.0
NE2 Z:HIS313 3.0 36.5 1.0
CE1 Z:HIS313 3.2 36.5 1.0
CD2 Z:TYR311 3.6 36.8 1.0
CA Z:HIS313 3.8 36.5 1.0
N Z:HIS313 3.8 36.5 1.0
CE1 Z:TYR311 3.9 36.8 1.0
O Z:CYS312 3.9 36.9 1.0
C Z:CYS312 3.9 36.9 1.0
CE1 Z:HIS319 4.4 38.9 1.0
CB Z:ALA250 4.4 36.2 1.0
ND1 Z:HIS319 4.5 38.9 1.0
CG Z:TYR311 4.6 36.8 1.0
CD1 Z:TYR311 4.7 36.8 1.0
CA Z:CYS312 4.8 36.9 1.0
CG2 Z:ILE219 4.8 34.5 1.0
OE1 Z:GLN314 4.8 37.4 1.0
C Z:HIS313 4.8 36.5 1.0
CD1 Z:ILE219 5.0 34.5 1.0
O Z:CYS317 5.0 38.9 1.0

Zinc binding site 9 out of 9 in 9fss

Go back to Zinc Binding Sites List in 9fss
Zinc binding site 9 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 2 (OC2- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn502

b:24.8
occ:1.00
 N Z:THR361 2.5 34.0 1.0
CB Z:THR361 2.6 34.0 1.0
CG1 W:VAL376 2.7 37.0 1.0
OG1 Z:THR361 2.7 34.0 1.0
CE2 Z:TYR360 2.9 35.6 1.0
CA Z:THR361 3.0 34.0 1.0
CZ Z:TYR360 3.0 35.6 1.0
CD2 Z:TYR360 3.0 35.6 1.0
CE1 Z:TYR360 3.2 35.6 1.0
C W:VAL376 3.2 37.0 1.0
CG Z:TYR360 3.2 35.6 1.0
O W:VAL376 3.2 37.0 1.0
CD1 Z:TYR360 3.3 35.6 1.0
N W:TYR377 3.3 35.0 1.0
CA W:TYR377 3.4 35.0 1.0
CB W:VAL376 3.4 37.0 1.0
O Z:THR361 3.4 34.0 1.0
C Z:THR361 3.6 34.0 1.0
C Z:TYR360 3.6 35.6 1.0
OH Z:TYR360 3.7 35.6 1.0
CA W:VAL376 3.9 37.0 1.0
CA Z:TYR360 4.0 35.6 1.0
CG2 Z:THR361 4.0 34.0 1.0
CB Z:TYR360 4.2 35.6 1.0
CB W:TYR377 4.3 35.0 1.0
C W:TYR377 4.4 35.0 1.0
O Z:TYR360 4.7 35.6 1.0
O W:TYR377 4.8 35.0 1.0
CG2 W:VAL376 4.8 37.0 1.0
O W:ARG382 4.8 41.5 1.0
N Z:ALA362 4.9 32.3 1.0
N W:VAL376 5.0 37.0 1.0

Reference:

S.Z.Shah, T.N.Perry, A.Graziadei, V.Cecatiello, T.Kaliyappan, A.D.Misiaszek, C.W.Muller, E.P.Ramsay, A.Vannini. Structural Insights Into Distinct Mechanisms of Rna Polymerase II and III Recruitment to Snrna Promoters. Nat Commun V. 16 141 2025.
ISSN: ESSN 2041-1723
PubMed: 39747245
DOI: 10.1038/S41467-024-55553-8
Page generated: Sun Feb 9 01:07:30 2025

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy