Zinc in PDB 9fsr: Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- Mini)

Enzymatic activity of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- Mini)

All present enzymatic activity of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- Mini):
2.7.7.6;

Other elements in 9fsr:

The structure of Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) (pdb code 9fsr). 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 1 (OC1- Mini), PDB code: 9fsr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9fsr

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Zinc binding site 1 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:10.2
occ:1.00
 NE2 A:HIS82 2.1 2.4 1.0
SG A:CYS79 2.3 5.9 1.0
SG A:CYS72 2.3 4.3 1.0
SG A:CYS69 2.3 8.4 1.0
CD2 A:HIS82 3.0 2.4 1.0
CE1 A:HIS82 3.0 2.4 1.0
CB A:CYS69 3.1 8.4 1.0
CB A:CYS72 3.6 4.3 1.0
CB A:CYS79 3.8 5.9 1.0
N A:CYS72 3.9 4.3 1.0
ND1 A:HIS82 4.1 2.4 1.0
CG A:HIS82 4.1 2.4 1.0
CA A:CYS72 4.3 4.3 1.0
CA A:CYS79 4.4 5.9 1.0
CA A:CYS69 4.5 8.4 1.0
CB A:THR71 4.5 6.1 1.0
N A:GLY81 4.6 4.7 1.0
C A:THR71 4.7 6.1 1.0
O A:CYS69 4.8 8.4 1.0
C A:CYS69 4.8 8.4 1.0
N A:LEU80 4.8 1.2 1.0
C A:CYS72 4.9 4.3 1.0
C A:CYS79 4.9 5.9 1.0
N A:THR71 4.9 6.1 1.0
CA A:THR71 5.0 6.1 1.0
CA A:GLY81 5.0 4.7 1.0
CA A:GLY61 5.0 8.2 1.0

Zinc binding site 2 out of 9 in 9fsr

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Zinc binding site 2 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- Mini)


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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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:31.1
occ:1.00
 SG A:CYS109 2.3 17.1 1.0
SG A:CYS156 2.3 20.9 1.0
SG A:CYS112 2.3 18.3 1.0
SG A:CYS159 2.3 24.2 1.0
CB A:CYS156 3.0 20.9 1.0
CB A:CYS159 3.0 24.2 1.0
CB A:CYS109 3.3 17.1 1.0
CB A:CYS112 3.6 18.3 1.0
OG1 A:THR111 3.6 17.9 1.0
N A:CYS159 3.7 24.2 1.0
CA A:CYS159 4.0 24.2 1.0
N A:CYS112 4.2 18.3 1.0
CA A:CYS112 4.4 18.3 1.0
CA A:CYS156 4.5 20.9 1.0
CA A:CYS109 4.7 17.1 1.0
CB A:HIS158 4.7 21.7 1.0
O A:HIS114 4.8 17.1 1.0
ND1 A:HIS158 4.8 21.7 1.0
C A:HIS158 4.8 21.7 1.0
C A:CYS159 4.8 24.2 1.0
C A:CYS156 5.0 20.9 1.0
CB A:THR111 5.0 17.9 1.0

Zinc binding site 3 out of 9 in 9fsr

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Zinc binding site 3 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:9.5
occ:1.00
 SG B:CYS1080 2.3 7.3 1.0
SG B:CYS1083 2.3 6.1 1.0
SG B:CYS1092 2.3 6.0 1.0
SG B:CYS1095 2.3 6.5 1.0
CB B:CYS1080 3.0 7.3 1.0
CB B:CYS1083 3.3 6.1 1.0
CB B:CYS1095 3.5 6.5 1.0
CB B:CYS1092 3.6 6.0 1.0
N B:CYS1083 3.9 6.1 1.0
N B:CYS1095 4.0 6.5 1.0
CA B:CYS1083 4.2 6.1 1.0
CD1 B:TYR1094 4.4 5.6 1.0
CA B:CYS1095 4.4 6.5 1.0
CA B:CYS1080 4.5 7.3 1.0
CB B:TYR1094 4.5 5.6 1.0
CG B:TYR1094 4.8 5.6 1.0
CA B:CYS1092 4.9 6.0 1.0
C B:CYS1080 4.9 7.3 1.0
CB B:GLN1082 4.9 10.7 1.0
C B:TYR1094 4.9 5.6 1.0
O B:CYS1080 5.0 7.3 1.0
O B:CYS1092 5.0 6.0 1.0

Zinc binding site 4 out of 9 in 9fsr

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Zinc binding site 4 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:29.2
occ:1.00
 CB J:CYS5 2.0 19.8 1.0
SG J:CYS5 2.3 19.8 1.0
SG J:CYS25 2.3 22.3 1.0
SG J:CYS8 2.3 18.9 1.0
CB J:CYS25 3.0 22.3 1.0
CA J:CYS5 3.5 19.8 1.0
SG J:CYS28 3.7 22.4 1.0
CB J:CYS8 3.8 18.9 1.0
O J:ASN10 3.8 18.2 1.0
N J:CYS8 3.9 18.9 1.0
CA J:CYS25 4.0 22.3 1.0
N J:ASN10 4.1 18.2 1.0
N J:CYS5 4.1 19.8 1.0
CA J:CYS8 4.2 18.9 1.0
C J:CYS5 4.2 19.8 1.0
CD2 J:LEU12 4.3 21.4 1.0
CB J:ASN10 4.3 18.2 1.0
N J:GLY9 4.4 18.7 1.0
O J:CYS5 4.4 19.8 1.0
C J:ASN10 4.5 18.2 1.0
C J:CYS8 4.5 18.9 1.0
CA J:ASN10 4.5 18.2 1.0
CB J:CYS28 4.8 22.4 1.0
C J:GLY7 4.9 17.7 1.0
N J:GLY7 4.9 17.7 1.0
N J:CYS25 5.0 22.3 1.0
C J:CYS25 5.0 22.3 1.0

Zinc binding site 5 out of 9 in 9fsr

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Zinc binding site 5 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:18.6
occ:1.00
 SG P:CYS39 2.3 11.3 1.0
SG P:CYS19 2.3 7.0 1.0
SG P:CYS22 2.3 8.7 1.0
SG P:CYS36 2.3 9.0 1.0
CB P:CYS19 3.1 7.0 1.0
CB P:CYS39 3.1 11.3 1.0
CB P:CYS22 3.3 8.7 1.0
CB P:CYS36 3.4 9.0 1.0
N P:CYS39 4.0 11.3 1.0
CA P:CYS39 4.2 11.3 1.0
OG1 P:THR24 4.2 6.8 1.0
O P:GLY20 4.3 6.8 1.0
CA P:CYS22 4.4 8.7 1.0
CA P:CYS19 4.5 7.0 1.0
N P:CYS22 4.5 8.7 1.0
CA P:CYS36 4.6 9.0 1.0
C P:CYS19 4.9 7.0 1.0
N P:HIS23 5.0 8.9 1.0
N P:ARG37 5.0 12.5 1.0
CB P:TYR41 5.0 5.2 1.0

Zinc binding site 6 out of 9 in 9fsr

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Zinc binding site 6 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn101

b:10.4
occ:1.00
 SG Q:CYS44 2.3 15.0 1.0
SG Q:CYS10 2.3 8.5 1.0
SG Q:CYS7 2.3 15.0 1.0
SG Q:CYS45 2.3 0.6 1.0
CB Q:CYS7 3.2 15.0 1.0
N Q:CYS45 3.5 0.6 1.0
CB Q:CYS45 3.5 0.6 1.0
CA Q:CYS45 3.6 0.6 1.0
CB Q:CYS10 3.7 8.5 1.0
O Q:THR9 3.8 6.0 1.0
C Q:CYS44 3.8 15.0 1.0
CB Q:CYS44 3.9 15.0 1.0
OG1 Q:THR9 4.0 6.0 1.0
O Q:CYS44 4.2 15.0 1.0
C Q:THR9 4.3 6.0 1.0
CA Q:CYS44 4.5 15.0 1.0
N Q:GLY11 4.6 9.1 1.0
CB Q:LYS12 4.6 4.5 1.0
CA Q:CYS7 4.7 15.0 1.0
N Q:CYS10 4.7 8.5 1.0
CA Q:CYS10 4.7 8.5 1.0
NE Q:ARG42 4.8 4.7 1.0
N Q:LYS12 4.9 4.5 1.0

Zinc binding site 7 out of 9 in 9fsr

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Zinc binding site 7 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn601

b:29.4
occ:1.00
 OD1 S:ASP9 2.1 22.2 1.0
SG S:CYS10 2.3 22.9 1.0
SG S:CYS7 2.3 21.2 1.0
CG S:ASP9 3.3 22.2 1.0
CB S:CYS10 3.4 22.9 1.0
N S:CYS10 3.8 22.9 1.0
CB S:CYS7 3.9 21.2 1.0
OD2 S:ASP9 3.9 22.2 1.0
N S:ASP9 3.9 22.2 1.0
CA S:CYS10 4.2 22.9 1.0
C S:ASP9 4.3 22.2 1.0
CA S:ASP9 4.4 22.2 1.0
CB S:ASP9 4.4 22.2 1.0
CD S:PRO8 4.5 18.0 1.0
SG S:CYS31 4.6 20.3 1.0
N S:PRO8 4.6 18.0 1.0
OD2 S:ASP30 4.6 22.5 1.0
OD1 S:ASP30 4.7 22.5 1.0
C S:CYS7 4.9 21.2 1.0
C S:CYS10 4.9 22.9 1.0
CA S:CYS7 4.9 21.2 1.0
CG S:ASP30 4.9 22.5 1.0

Zinc binding site 8 out of 9 in 9fsr

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Zinc binding site 8 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn501

b:39.0
occ:1.00
 NE2 Z:HIS313 2.0 26.1 1.0
NE2 Z:HIS319 2.1 31.0 1.0
SG Z:CYS221 2.3 25.8 1.0
SG Z:CYS317 2.3 26.2 1.0
CE1 Z:HIS319 2.4 31.0 1.0
CE1 Z:HIS313 2.9 26.1 1.0
CD2 Z:HIS313 3.1 26.1 1.0
OG Z:SER223 3.2 26.4 1.0
CB Z:CYS221 3.2 25.8 1.0
CD2 Z:HIS319 3.4 31.0 1.0
CB Z:CYS317 3.6 26.2 1.0
ND1 Z:HIS319 3.7 31.0 1.0
CB Z:SER223 3.8 26.4 1.0
ND1 Z:HIS313 4.1 26.1 1.0
CG Z:HIS319 4.1 31.0 1.0
CG Z:HIS313 4.2 26.1 1.0
O Z:CYS317 4.4 26.2 1.0
CD Z:PRO189 4.7 27.9 1.0
CA Z:CYS221 4.7 25.8 1.0
CG Z:PRO189 4.7 27.9 1.0
N Z:SER223 4.7 26.4 1.0
CA Z:CYS317 4.8 26.2 1.0
C Z:CYS317 4.9 26.2 1.0
CA Z:SER223 4.9 26.4 1.0

Zinc binding site 9 out of 9 in 9fsr

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Zinc binding site 9 out of 9 in the Rna Polymerase III Class III Open Mini Pre-Initiation Complex 1 (OC1- 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 1 (OC1- Mini) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn502

b:23.1
occ:1.00
 SG Z:CYS380 2.3 25.1 1.0
SG Z:CYS383 2.3 25.8 1.0
SG Z:CYS357 2.3 30.3 1.0
CB Z:CYS357 3.3 30.3 1.0
CB Z:CYS383 3.8 25.8 1.0
CB Z:CYS380 3.8 25.1 1.0
CD2 W:LEU344 4.1 25.8 1.0
CB Z:TYR360 4.2 27.3 1.0
N Z:CYS357 4.2 30.3 1.0
SG Z:CYS354 4.3 27.8 1.0
CA Z:CYS357 4.4 30.3 1.0
CB Z:CYS354 4.4 27.8 1.0
CD1 W:LEU344 4.7 25.8 1.0
NE2 W:GLN338 4.8 27.5 1.0
N Z:CYS383 4.8 25.8 1.0
CG Z:TYR360 4.8 27.3 1.0
CB Z:VAL356 4.8 27.2 1.0
CA Z:CYS383 4.9 25.8 1.0
CD1 Z:TYR360 5.0 27.3 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 01:07:28 2025

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