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

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

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

Other elements in 9fso:

The structure of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) (pdb code 9fso). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1), PDB code: 9fso:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 9fso

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:62.3
occ:1.00
 NE2 A:HIS82 2.1 18.3 1.0
SG A:CYS72 2.3 32.5 1.0
SG A:CYS79 2.3 27.3 1.0
SG A:CYS69 2.3 34.1 1.0
CD2 A:HIS82 2.8 18.3 1.0
CB A:CYS69 3.2 34.1 1.0
CE1 A:HIS82 3.2 18.3 1.0
CB A:CYS79 3.9 27.3 1.0
CB A:CYS72 3.9 32.5 1.0
N A:CYS72 3.9 32.5 1.0
CG A:HIS82 4.0 18.3 1.0
O A:CYS72 4.1 32.5 1.0
ND1 A:HIS82 4.2 18.3 1.0
CA A:CYS72 4.4 32.5 1.0
CB A:THR71 4.6 28.1 1.0
CA A:CYS79 4.6 27.3 1.0
CA A:CYS69 4.6 34.1 1.0
C A:CYS72 4.7 32.5 1.0
CA A:GLY61 4.7 27.0 1.0
N A:GLY81 4.8 20.1 1.0
C A:THR71 4.8 28.1 1.0
N A:GLY61 4.9 27.0 1.0

Zinc binding site 2 out of 9 in 9fso

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:104.8
occ:1.00
 ND1 A:HIS158 2.1 76.3 1.0
SG A:CYS159 2.3 72.2 1.0
SG A:CYS156 2.3 72.9 1.0
SG A:CYS112 2.3 65.6 1.0
CE1 A:HIS158 2.7 76.3 1.0
CB A:CYS112 3.1 65.6 1.0
CG A:HIS158 3.3 76.3 1.0
N A:CYS159 3.4 72.2 1.0
CB A:CYS159 3.5 72.2 1.0
CB A:CYS156 3.9 72.9 1.0
CB A:HIS158 3.9 76.3 1.0
NE2 A:HIS158 4.0 76.3 1.0
CA A:CYS159 4.0 72.2 1.0
C A:HIS158 4.1 76.3 1.0
N A:HIS158 4.2 76.3 1.0
CD2 A:HIS158 4.3 76.3 1.0
CA A:HIS158 4.3 76.3 1.0
CA A:CYS112 4.5 65.6 1.0
SG A:CYS109 4.5 60.7 1.0
N A:GLY160 4.6 68.7 1.0
O A:CYS156 4.6 72.9 1.0
C A:CYS156 4.6 72.9 1.0
C A:CYS159 4.8 72.2 1.0
N A:CYS112 4.8 65.6 1.0
CA A:CYS156 4.8 72.9 1.0
CB A:CYS109 4.8 60.7 1.0
ND1 A:HIS114 4.9 58.6 1.0
CB A:HIS114 4.9 58.6 1.0

Zinc binding site 3 out of 9 in 9fso

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Zinc binding site 3 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:45.9
occ:1.00
 SG B:CYS1092 2.3 24.2 1.0
SG B:CYS1083 2.3 24.6 1.0
SG B:CYS1080 2.3 24.7 1.0
SG B:CYS1095 2.3 34.1 1.0
CB B:CYS1080 3.1 24.7 1.0
CB B:CYS1092 3.4 24.2 1.0
CB B:CYS1083 3.5 24.6 1.0
CB B:CYS1095 3.8 34.1 1.0
N B:CYS1083 3.9 24.6 1.0
N B:CYS1095 4.2 34.1 1.0
CB B:TYR1094 4.2 20.9 1.0
CA B:CYS1083 4.3 24.6 1.0
CA B:CYS1080 4.5 24.7 1.0
CB B:GLN1082 4.6 31.7 1.0
CD2 B:TYR1094 4.6 20.9 1.0
CA B:CYS1095 4.7 34.1 1.0
C B:TYR1094 4.8 20.9 1.0
CA B:CYS1092 4.8 24.2 1.0
O B:LEU1085 4.8 19.4 1.0
C B:CYS1080 4.9 24.7 1.0
O B:CYS1080 4.9 24.7 1.0
CG B:TYR1094 4.9 20.9 1.0
C B:GLN1082 4.9 31.7 1.0
CA B:TYR1094 4.9 20.9 1.0

Zinc binding site 4 out of 9 in 9fso

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Zinc binding site 4 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:104.4
occ:1.00
 SG J:CYS8 2.3 58.4 1.0
SG J:CYS25 2.3 65.7 1.0
CG2 J:THR27 2.3 61.8 1.0
ND2 J:ASN10 2.9 56.0 1.0
CB J:ASN10 3.2 56.0 1.0
CG J:ASN10 3.4 56.0 1.0
CB J:THR27 3.6 61.8 1.0
N J:THR27 3.9 61.8 1.0
CB J:CYS8 4.0 58.4 1.0
CB J:CYS25 4.0 65.7 1.0
N J:CYS28 4.1 63.5 1.0
CA J:THR27 4.2 61.8 1.0
OD1 J:ASN26 4.2 62.2 1.0
CA J:ASN10 4.4 56.0 1.0
OD1 J:ASN10 4.4 56.0 1.0
C J:THR27 4.4 61.8 1.0
N J:ASN10 4.5 56.0 1.0
SG J:CYS28 4.5 63.5 1.0
N J:ASN26 4.6 62.2 1.0
CZ E:PHE139 4.7 60.7 1.0
OG1 J:THR27 4.7 61.8 1.0
CB J:CYS28 4.7 63.5 1.0
CB J:CYS5 4.8 57.3 1.0

Zinc binding site 5 out of 9 in 9fso

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Zinc binding site 5 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn101

b:60.5
occ:1.00
 SG P:CYS36 2.3 22.8 1.0
SG P:CYS19 2.3 23.5 1.0
SG P:CYS22 2.3 25.5 1.0
SG P:CYS39 2.3 34.4 1.0
CB P:CYS36 3.1 22.8 1.0
CB P:CYS19 3.2 23.5 1.0
CB P:CYS22 3.6 25.5 1.0
CB P:CYS39 3.7 34.4 1.0
N P:CYS22 3.7 25.5 1.0
N P:CYS39 3.9 34.4 1.0
OG1 P:THR24 4.1 27.1 1.0
CA P:CYS22 4.2 25.5 1.0
CA P:CYS39 4.3 34.4 1.0
CB P:TYR41 4.5 20.6 1.0
CA P:CYS36 4.5 22.8 1.0
C P:CYS39 4.7 34.4 1.0
CA P:CYS19 4.7 23.5 1.0
CB P:GLU21 4.7 28.0 1.0
O P:CYS39 4.7 34.4 1.0
N P:HIS23 4.8 29.3 1.0
C P:GLU21 4.8 28.0 1.0
N P:GLU21 4.8 28.0 1.0
C P:CYS22 4.8 25.5 1.0
N P:TYR41 5.0 20.6 1.0

Zinc binding site 6 out of 9 in 9fso

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Zinc binding site 6 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn101

b:40.9
occ:1.00
 SG Q:CYS45 2.3 17.5 1.0
SG Q:CYS10 2.3 16.7 1.0
SG Q:CYS44 2.3 17.8 1.0
SG Q:CYS7 2.3 11.8 1.0
CB Q:CYS10 3.4 16.7 1.0
CB Q:CYS7 3.5 11.8 1.0
O Q:CYS44 3.6 17.8 1.0
C Q:CYS44 3.6 17.8 1.0
CB Q:CYS45 3.6 17.5 1.0
N Q:CYS45 3.7 17.5 1.0
N Q:CYS10 3.7 16.7 1.0
CA Q:CYS45 3.8 17.5 1.0
CB Q:CYS44 3.8 17.8 1.0
CA Q:CYS10 4.1 16.7 1.0
CA Q:CYS44 4.3 17.8 1.0
CB Q:THR9 4.5 13.8 1.0
NE Q:ARG42 4.5 15.8 1.0
C Q:THR9 4.8 13.8 1.0
N Q:GLY11 4.8 19.7 1.0
C Q:CYS10 4.8 16.7 1.0
CB Q:LYS12 4.8 15.4 1.0
N Q:THR9 4.8 13.8 1.0
CA Q:CYS7 4.8 11.8 1.0
CA Q:THR9 4.9 13.8 1.0

Zinc binding site 7 out of 9 in 9fso

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Zinc binding site 7 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Zn700

b:61.4
occ:1.00
 SG S:CYS31 2.3 35.6 1.0
SG S:CYS28 2.3 30.2 1.0
SG S:CYS7 2.3 42.1 1.0
CB S:CYS7 3.1 42.1 1.0
CB S:CYS31 3.2 35.6 1.0
CB S:CYS10 3.2 49.4 1.0
CB S:CYS28 3.4 30.2 1.0
SG S:CYS10 3.6 49.4 1.0
N S:CYS10 3.7 49.4 1.0
OG S:SER12 3.9 44.4 1.0
N S:CYS31 4.0 35.6 1.0
CA S:CYS10 4.0 49.4 1.0
CA S:CYS31 4.1 35.6 1.0
CB S:ASP9 4.6 44.9 1.0
CA S:CYS7 4.6 42.1 1.0
C S:CYS10 4.6 49.4 1.0
C S:ASP9 4.7 44.9 1.0
C S:ASP30 4.7 40.2 1.0
CA S:CYS28 4.8 30.2 1.0
N S:GLY11 4.8 49.3 1.0
C S:CYS31 4.8 35.6 1.0
N S:ASP9 4.9 44.9 1.0
CA S:ASP9 5.0 44.9 1.0
CB S:CYS33 5.0 26.4 1.0
CB S:ASP30 5.0 40.2 1.0

Zinc binding site 8 out of 9 in 9fso

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Zinc binding site 8 out of 9 in the Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn501

b:123.6
occ:1.00
 NE2 Z:HIS319 2.0 92.3 1.0
NE2 Z:HIS313 2.1 89.2 1.0
SG Z:CYS221 2.3 87.4 1.0
SG Z:CYS317 2.3 86.5 1.0
CE1 Z:HIS319 2.3 92.3 1.0
CE1 Z:HIS313 2.9 89.2 1.0
CB Z:CYS221 3.0 87.4 1.0
OG Z:SER223 3.2 82.7 1.0
CD2 Z:HIS313 3.2 89.2 1.0
CD2 Z:HIS319 3.4 92.3 1.0
ND1 Z:HIS319 3.6 92.3 1.0
CB Z:SER223 3.6 82.7 1.0
CB Z:CYS317 3.8 86.5 1.0
ND1 Z:HIS313 4.1 89.2 1.0
CG Z:HIS319 4.1 92.3 1.0
CG Z:HIS313 4.2 89.2 1.0
CD Z:PRO189 4.3 84.8 1.0
CG Z:PRO189 4.5 84.8 1.0
CA Z:CYS221 4.5 87.4 1.0
N Z:SER223 4.6 82.7 1.0
O Z:CYS317 4.7 86.5 1.0
CA Z:SER223 4.8 82.7 1.0
CA Z:CYS317 4.9 86.5 1.0
C Z:CYS221 5.0 87.4 1.0
C Z:CYS317 5.0 86.5 1.0

Zinc binding site 9 out of 9 in 9fso

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Rna Polymerase III Class III Open Pre-Initiation Complex 1 (OC1) within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn502

b:107.5
occ:1.00
 SG Z:CYS383 2.3 88.2 1.0
SG Z:CYS380 2.3 85.7 1.0
N Z:CYS383 2.7 88.2 1.0
CB Z:VAL382 3.0 85.0 1.0
CB Z:CYS383 3.2 88.2 1.0
C Z:VAL382 3.3 85.0 1.0
CA Z:CYS383 3.4 88.2 1.0
CG1 Z:VAL382 3.5 85.0 1.0
NE2 W:GLN338 3.5 84.8 1.0
CA Z:VAL382 3.6 85.0 1.0
CD1 W:LEU344 3.8 80.4 1.0
N Z:VAL382 4.0 85.0 1.0
CG2 Z:VAL382 4.1 85.0 1.0
CB Z:CYS380 4.1 85.7 1.0
SG Z:CYS357 4.2 87.1 1.0
O Z:VAL382 4.3 85.0 1.0
CD W:GLN338 4.7 84.8 1.0
O Z:CYS380 4.8 85.7 1.0
CD2 W:LEU344 4.8 80.4 1.0
C Z:CYS383 4.9 88.2 1.0
C Z:CYS380 4.9 85.7 1.0
CG W:LEU344 4.9 80.4 1.0
CA Z:CYS380 5.0 85.7 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

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