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Zinc in PDB 8ity: Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1

Enzymatic activity of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1

All present enzymatic activity of Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1:
2.7.7.6;

Other elements in 8ity:

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

Zinc binding site 1 out of 7 in 8ity

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Zinc binding site 1 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:309.0
occ:1.00
 SG A:CYS72 2.3 229.1 1.0
SG A:CYS79 3.1 228.3 1.0
NE2 A:HIS82 3.1 222.4 1.0
CB A:CYS72 3.4 229.1 1.0
N A:GLY81 3.4 227.0 1.0
N A:LEU80 3.5 212.8 1.0
CB A:CYS79 3.5 228.3 1.0
CD2 A:HIS82 3.5 222.4 1.0
SG A:CYS69 3.5 248.7 1.0
CA A:CYS79 3.6 228.3 1.0
C A:CYS79 3.9 228.3 1.0
CE1 A:HIS82 4.0 222.4 1.0
CA A:GLY81 4.1 227.0 1.0
CE A:LYS74 4.1 222.1 1.0
CB A:CYS69 4.1 248.7 1.0
C A:LEU80 4.4 212.8 1.0
C A:GLY81 4.4 227.0 1.0
CA A:LEU80 4.4 212.8 1.0
NZ A:LYS74 4.5 222.1 1.0
CG A:HIS82 4.5 222.4 1.0
O A:GLY81 4.6 227.0 1.0
CA A:CYS72 4.6 229.1 1.0
N A:CYS72 4.7 229.1 1.0
ND1 A:HIS82 4.7 222.4 1.0
CB A:LEU80 4.8 212.8 1.0
O A:CYS79 4.9 228.3 1.0
O A:CYS72 4.9 229.1 1.0
N A:CYS79 5.0 228.3 1.0

Zinc binding site 2 out of 7 in 8ity

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Zinc binding site 2 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:279.4
occ:1.00
 O A:ASN154 1.6 252.3 1.0
N A:ASN163 2.2 251.3 1.0
C A:ASN154 2.3 252.3 1.0
O A:ASN163 2.4 251.3 1.0
CA A:ASN154 2.5 252.3 1.0
CA A:ASN163 2.8 251.3 1.0
CB A:ASN154 2.9 252.3 1.0
CB A:ASN163 2.9 251.3 1.0
C A:ASN163 3.0 251.3 1.0
C A:PHE162 3.3 251.5 1.0
ND2 A:ASN163 3.5 251.3 1.0
CG A:ASN163 3.5 251.3 1.0
N A:ILE155 3.6 248.1 1.0
CA A:PHE162 3.7 251.5 1.0
N A:ASN154 3.9 252.3 1.0
O A:ALA161 3.9 242.3 1.0
CD1 A:PHE162 4.0 251.5 1.0
CG A:ASN154 4.1 252.3 1.0
N A:GLY164 4.3 245.1 1.0
O A:LYS153 4.3 242.9 1.0
O A:PHE162 4.4 251.5 1.0
CA A:ILE155 4.4 248.1 1.0
CG A:PHE162 4.4 251.5 1.0
OD1 A:ASN163 4.5 251.3 1.0
CE1 A:PHE162 4.5 251.5 1.0
C A:LYS153 4.6 242.9 1.0
CB A:PHE162 4.6 251.5 1.0
OD1 A:ASN154 4.7 252.3 1.0
N A:PHE162 4.7 251.5 1.0
C A:ALA161 4.8 242.3 1.0
CE A:MET116 4.8 258.9 1.0
ND2 A:ASN154 4.8 252.3 1.0
CG2 A:ILE155 4.9 248.1 1.0

Zinc binding site 3 out of 7 in 8ity

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Zinc binding site 3 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:252.0
occ:1.00
 SG B:CYS1092 2.3 180.9 1.0
SG B:CYS1083 2.3 179.7 1.0
SG B:CYS1095 2.3 179.3 1.0
SG B:CYS1080 2.3 185.4 1.0
CB B:CYS1080 2.6 185.4 1.0
CB B:CYS1083 2.8 179.7 1.0
CB B:CYS1095 2.9 179.3 1.0
N B:CYS1083 3.4 179.7 1.0
CB B:CYS1092 3.5 180.9 1.0
CA B:CYS1083 3.7 179.7 1.0
N B:CYS1095 3.9 179.3 1.0
CA B:CYS1095 4.0 179.3 1.0
CA B:CYS1080 4.0 185.4 1.0
O B:CYS1080 4.4 185.4 1.0
C B:CYS1080 4.4 185.4 1.0
CB B:GLN1082 4.6 178.1 1.0
C B:GLN1082 4.6 178.1 1.0
C B:CYS1083 4.7 179.7 1.0
N B:GLY1084 4.8 176.0 1.0
CA B:CYS1092 4.9 180.9 1.0
N B:CYS1080 4.9 185.4 1.0
N B:GLN1082 5.0 178.1 1.0
CA B:GLN1082 5.0 178.1 1.0

Zinc binding site 4 out of 7 in 8ity

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Zinc binding site 4 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:164.2
occ:1.00
 SG I:CYS28 2.3 127.0 1.0
SG I:CYS8 2.3 127.7 1.0
SG I:CYS5 2.3 124.7 1.0
SG I:CYS25 2.3 129.6 1.0
CB I:CYS5 3.1 124.7 1.0
CB I:CYS25 3.1 129.6 1.0
CB I:CYS28 3.5 127.0 1.0
CB I:CYS8 3.7 127.7 1.0
OG1 I:THR27 3.7 125.5 1.0
N I:CYS8 3.9 127.7 1.0
N I:CYS28 4.1 127.0 1.0
CA I:CYS28 4.3 127.0 1.0
CA I:CYS8 4.3 127.7 1.0
O I:CYS28 4.4 127.0 1.0
CB I:TYR30 4.5 130.4 1.0
CA I:CYS5 4.6 124.7 1.0
CA I:CYS25 4.6 129.6 1.0
C I:CYS28 4.7 127.0 1.0
C I:GLY7 4.7 125.8 1.0
C I:CYS8 4.9 127.7 1.0
CA I:GLY7 4.9 125.8 1.0
CB I:ASN10 4.9 124.3 1.0
C I:THR27 4.9 125.5 1.0
N I:GLY9 5.0 121.7 1.0
N I:ASN10 5.0 124.3 1.0

Zinc binding site 5 out of 7 in 8ity

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Zinc binding site 5 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:127.9
occ:1.00
 N J:CYS45 2.1 85.6 1.0
SG J:CYS45 2.3 85.6 1.0
SG J:CYS44 2.3 83.1 1.0
SG J:CYS7 2.3 75.7 1.0
CA J:CYS45 2.3 85.6 1.0
C J:CYS44 2.7 83.1 1.0
CB J:CYS45 2.7 85.6 1.0
CB J:CYS7 2.9 75.7 1.0
O J:CYS44 3.2 83.1 1.0
CB J:CYS44 3.4 83.1 1.0
CA J:CYS44 3.6 83.1 1.0
SG J:CYS10 3.6 76.4 1.0
C J:CYS45 3.8 85.6 1.0
CA J:CYS7 4.3 75.7 1.0
N J:CYS44 4.3 83.1 1.0
O J:CYS45 4.5 85.6 1.0
N J:ARG46 4.6 81.4 1.0
OG1 J:THR9 4.7 77.2 1.0
CG J:ARG42 4.7 85.4 1.0
CD J:ARG42 4.8 85.4 1.0
CB J:CYS10 4.8 76.4 1.0

Zinc binding site 6 out of 7 in 8ity

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Zinc binding site 6 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:144.7
occ:1.00
 SG L:CYS36 2.3 120.9 1.0
SG L:CYS22 2.3 119.6 1.0
SG L:CYS19 3.0 106.5 1.0
CB L:CYS22 3.1 119.6 1.0
N L:CYS22 3.1 119.6 1.0
CA L:CYS22 3.5 119.6 1.0
CB L:CYS36 3.6 120.9 1.0
CB L:CYS19 3.7 106.5 1.0
CB L:CYS39 3.9 114.1 1.0
OE2 L:GLU21 4.0 113.8 1.0
CD L:GLU21 4.0 113.8 1.0
OG1 L:THR24 4.0 115.3 1.0
OE1 L:GLU21 4.1 113.8 1.0
SG L:CYS39 4.1 114.1 1.0
C L:CYS22 4.2 119.6 1.0
N L:HIS23 4.2 113.7 1.0
C L:GLU21 4.3 113.8 1.0
N L:GLU21 4.3 113.8 1.0
CG2 L:THR24 4.5 115.3 1.0
CG L:GLU21 4.7 113.8 1.0
CB L:TYR41 4.7 108.0 1.0
CA L:GLU21 4.8 113.8 1.0
N L:GLY20 4.8 109.0 1.0
N L:THR24 4.8 115.3 1.0
CB L:THR24 4.9 115.3 1.0
O L:ARG37 4.9 128.9 1.0
CA L:CYS36 4.9 120.9 1.0

Zinc binding site 7 out of 7 in 8ity

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Zinc binding site 7 out of 7 in the Human Rna Polymerase III Pre-Initiation Complex Closed Dna 1


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 Pre-Initiation Complex Closed Dna 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn700

b:30.0
occ:1.00
 CB V:CYS31 2.1 175.5 1.0
SG V:CYS31 2.4 175.5 1.0
SG V:CYS7 2.5 178.3 1.0
SG V:CYS33 3.2 164.4 1.0
SG V:CYS10 3.3 181.8 1.0
CA V:CYS31 3.5 175.5 1.0
N V:CYS31 3.8 175.5 1.0
CB V:CYS10 3.8 181.8 1.0
SG V:CYS28 4.1 172.1 1.0
CB V:CYS7 4.2 178.3 1.0
C V:CYS31 4.3 175.5 1.0
N V:CYS10 4.4 181.8 1.0
CB V:CYS33 4.5 164.4 1.0
O V:CYS31 4.7 175.5 1.0
OG V:SER12 4.7 167.0 1.0
CB V:CYS28 4.7 172.1 1.0
CA V:CYS10 4.8 181.8 1.0
C V:ASP30 4.8 174.3 1.0

Reference:

H.Hou, Q.Jin, Y.Ren, Z.Chen, Q.Wang, Y.Xu. Structure of the Snapc-Bound Rna Polymerase III Preinitiation Complex. Cell Res. 2023.
ISSN: ISSN 1001-0602
PubMed: 37165065
DOI: 10.1038/S41422-023-00819-X
Page generated: Thu Oct 31 08:00:41 2024

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