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Zinc in PDB 8iuh: Rna Polymerase III Pre-Initiation Complex Open Complex 1

Enzymatic activity of Rna Polymerase III Pre-Initiation Complex Open Complex 1

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

Other elements in 8iuh:

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

Zinc binding site 1 out of 8 in 8iuh

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Zinc binding site 1 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:122.6
occ:1.00
 NE2 A:HIS82 2.5 95.5 1.0
SG A:CYS79 2.5 104.1 1.0
SG A:CYS69 2.6 103.6 1.0
SG A:CYS72 2.6 106.7 1.0
CD2 A:HIS82 2.7 95.5 1.0
CB A:CYS69 3.4 103.6 1.0
CE1 A:HIS82 3.7 95.5 1.0
CA A:GLY61 3.8 103.1 1.0
CG A:HIS82 4.0 95.5 1.0
CB A:CYS79 4.0 104.1 1.0
CB A:CYS72 4.1 106.7 1.0
N A:GLY61 4.1 103.1 1.0
N A:GLY81 4.2 96.7 1.0
N A:CYS72 4.2 106.7 1.0
CA A:GLY81 4.4 96.7 1.0
ND1 A:HIS82 4.4 95.5 1.0
CA A:CYS79 4.6 104.1 1.0
CB A:THR71 4.6 100.6 1.0
C A:GLY81 4.6 96.7 1.0
O A:CYS72 4.7 106.7 1.0
CA A:CYS72 4.7 106.7 1.0
C A:GLY61 4.8 103.1 1.0
N A:LEU80 4.8 99.8 1.0
CA A:CYS69 4.9 103.6 1.0
N A:HIS82 4.9 95.5 1.0

Zinc binding site 2 out of 8 in 8iuh

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Zinc binding site 2 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:153.5
occ:1.00
 SG A:CYS112 2.4 118.6 1.0
SG A:CYS109 2.4 114.8 1.0
SG A:CYS159 2.4 130.4 1.0
SG A:CYS156 2.5 130.2 1.0
CB A:CYS156 3.2 130.2 1.0
CB A:CYS109 3.2 114.8 1.0
CB A:CYS112 3.5 118.6 1.0
N A:CYS112 3.6 118.6 1.0
CB A:CYS159 3.9 130.4 1.0
CA A:CYS112 4.2 118.6 1.0
CB A:THR111 4.2 111.5 1.0
N A:CYS159 4.3 130.4 1.0
ND2 A:ASN163 4.5 123.8 1.0
C A:THR111 4.6 111.5 1.0
CA A:CYS159 4.6 130.4 1.0
CA A:CYS156 4.7 130.2 1.0
N A:THR111 4.7 111.5 1.0
CA A:CYS109 4.7 114.8 1.0
CA A:THR111 4.7 111.5 1.0
CB A:ALA161 4.8 124.8 1.0
CG2 A:THR111 4.9 111.5 1.0
N A:ALA161 4.9 124.8 1.0
C A:CYS112 4.9 118.6 1.0
N A:GLY160 5.0 131.2 1.0
CB A:HIS158 5.0 126.9 1.0

Zinc binding site 3 out of 8 in 8iuh

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Zinc binding site 3 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:132.4
occ:1.00
 SG B:CYS1095 2.5 100.2 1.0
SG B:CYS1080 2.5 102.1 1.0
SG B:CYS1092 2.5 97.2 1.0
SG B:CYS1083 2.5 102.0 1.0
CB B:CYS1095 3.1 100.2 1.0
CB B:CYS1080 3.3 102.1 1.0
CB B:CYS1092 3.6 97.2 1.0
CB B:CYS1083 3.6 102.0 1.0
N B:CYS1083 3.9 102.0 1.0
N B:CYS1095 3.9 100.2 1.0
CA B:CYS1095 4.1 100.2 1.0
CB B:GLN1082 4.3 101.7 1.0
CA B:CYS1083 4.4 102.0 1.0
CD2 B:TYR1094 4.5 95.6 1.0
CB B:TYR1094 4.6 95.6 1.0
OE1 B:GLN1082 4.7 101.7 1.0
CA B:CYS1080 4.7 102.1 1.0
C B:GLN1082 4.8 101.7 1.0
C B:TYR1094 4.9 95.6 1.0
CA B:GLN1082 5.0 101.7 1.0
N B:GLN1082 5.0 101.7 1.0
CA B:CYS1092 5.0 97.2 1.0
CG B:GLN1082 5.0 101.7 1.0

Zinc binding site 4 out of 8 in 8iuh

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Zinc binding site 4 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:167.8
occ:1.00
 SG I:CYS8 2.5 130.1 1.0
SG I:CYS28 2.5 128.2 1.0
CB I:CYS5 2.6 130.7 1.0
SG I:CYS25 2.6 130.3 1.0
CB I:CYS25 2.6 130.3 1.0
SG I:CYS5 2.8 130.7 1.0
CA I:CYS5 4.1 130.7 1.0
CB I:CYS28 4.1 128.2 1.0
CB I:CYS8 4.1 130.1 1.0
CA I:CYS25 4.2 130.3 1.0
OG1 I:THR27 4.3 128.3 1.0
N I:ASN10 4.4 126.4 1.0
N I:CYS8 4.4 130.1 1.0
CB I:ASN10 4.4 126.4 1.0
ND2 I:ASN10 4.5 126.4 1.0
CD2 I:LEU12 4.5 129.7 1.0
N I:CYS5 4.6 130.7 1.0
O I:ASN10 4.6 126.4 1.0
N I:GLY9 4.7 127.8 1.0
CA I:CYS8 4.7 130.1 1.0
N I:CYS28 4.7 128.2 1.0
CA I:ASN10 4.8 126.4 1.0
C I:CYS5 4.9 130.7 1.0
N I:CYS25 4.9 130.3 1.0
CB I:TYR30 4.9 126.8 1.0
C I:CYS25 5.0 130.3 1.0
CA I:CYS28 5.0 128.2 1.0
C I:ASN10 5.0 126.4 1.0

Zinc binding site 5 out of 8 in 8iuh

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Zinc binding site 5 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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 Pre-Initiation Complex Open Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:262.2
occ:1.00
 N I:HIS74 2.2 231.2 1.0
SG I:CYS72 2.5 234.3 1.0
SG I:CYS69 2.5 228.5 1.0
SG I:CYS97 2.5 227.9 1.0
N I:GLU73 2.8 225.6 1.0
C I:CYS72 2.9 234.3 1.0
CB I:HIS74 3.0 231.2 1.0
CA I:HIS74 3.1 231.2 1.0
C I:GLU73 3.2 225.6 1.0
O I:CYS72 3.3 234.3 1.0
ND1 I:HIS74 3.3 231.2 1.0
CB I:CYS72 3.4 234.3 1.0
CA I:GLU73 3.4 225.6 1.0
CA I:CYS72 3.5 234.3 1.0
CG I:HIS74 3.6 231.2 1.0
O I:HIS74 3.6 231.2 1.0
CB I:CYS97 3.7 227.9 1.0
N I:CYS72 3.7 234.3 1.0
C I:HIS74 3.8 231.2 1.0
CB I:CYS69 4.2 228.5 1.0
O I:GLU73 4.4 225.6 1.0
CE1 I:HIS74 4.6 231.2 1.0
N I:CYS69 4.9 228.5 1.0
CD2 I:HIS74 4.9 231.2 1.0
CB I:GLU73 4.9 225.6 1.0
O I:CYS69 5.0 228.5 1.0

Zinc binding site 6 out of 8 in 8iuh

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Zinc binding site 6 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:121.6
occ:1.00
 SG J:CYS7 2.4 75.4 1.0
SG J:CYS44 2.4 81.3 1.0
SG J:CYS45 2.5 82.4 1.0
SG J:CYS10 2.5 75.8 1.0
CB J:CYS7 3.0 75.4 1.0
N J:CYS45 3.3 82.4 1.0
CB J:CYS44 3.6 81.3 1.0
CA J:CYS45 3.6 82.4 1.0
CB J:CYS45 3.6 82.4 1.0
C J:CYS44 3.8 81.3 1.0
CB J:CYS10 4.0 75.8 1.0
OG1 J:THR9 4.1 74.8 1.0
CA J:CYS44 4.3 81.3 1.0
O J:CYS44 4.4 81.3 1.0
N J:CYS10 4.4 75.8 1.0
CA J:CYS7 4.5 75.4 1.0
CD J:ARG42 4.6 82.4 1.0
CB J:LYS12 4.6 73.3 1.0
N J:GLY11 4.7 72.7 1.0
N J:LYS12 4.7 73.3 1.0
CA J:CYS10 4.7 75.8 1.0
CG J:ARG42 4.8 82.4 1.0

Zinc binding site 7 out of 8 in 8iuh

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Zinc binding site 7 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:152.9
occ:1.00
 SG L:CYS39 2.5 117.3 1.0
SG L:CYS19 2.6 103.5 1.0
SG L:CYS36 2.7 117.1 1.0
CB L:CYS22 3.0 109.3 1.0
CB L:CYS19 3.1 103.5 1.0
SG L:CYS22 3.1 109.3 1.0
CB L:CYS36 3.5 117.1 1.0
N L:CYS22 3.7 109.3 1.0
CB L:CYS39 3.9 117.3 1.0
CA L:CYS22 3.9 109.3 1.0
O L:ARG37 4.1 118.5 1.0
CG L:GLU21 4.3 110.7 1.0
OG1 L:THR24 4.4 103.3 1.0
N L:HIS23 4.6 107.7 1.0
CA L:CYS19 4.6 103.5 1.0
C L:CYS22 4.6 109.3 1.0
C L:GLU21 4.9 110.7 1.0
OE2 L:GLU21 4.9 110.7 1.0
CA L:CYS36 4.9 117.1 1.0
N L:GLU21 4.9 110.7 1.0

Zinc binding site 8 out of 8 in 8iuh

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Zinc binding site 8 out of 8 in the Rna Polymerase III Pre-Initiation Complex Open Complex 1


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

b:30.0
occ:1.00
 CB V:CYS31 2.5 175.5 1.0
SG V:CYS7 2.5 178.3 1.0
SG V:CYS31 2.6 175.5 1.0
SG V:CYS33 3.0 164.4 1.0
CA V:CYS31 3.9 175.5 1.0
CB V:CYS7 4.0 178.3 1.0
SG V:CYS10 4.1 181.8 1.0
N V:CYS31 4.3 175.5 1.0
CB V:CYS10 4.3 181.8 1.0
CB V:CYS33 4.4 164.4 1.0
N V:CYS10 4.5 181.8 1.0
C V:CYS31 4.6 175.5 1.0
NH2 A:ARG430 4.7 104.6 1.0
CB V:ASP9 4.7 172.3 1.0
OG V:SER12 4.8 167.0 1.0
NH1 A:ARG430 4.8 104.6 1.0
O V:CYS31 4.9 175.5 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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