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Zinc in PDB 8iue: Rna Polymerase III Pre-Initiation Complex Melting Complex 1

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

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

Other elements in 8iue:

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

Zinc binding site 1 out of 8 in 8iue

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Zinc binding site 1 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:168.4
occ:1.00
 NE2 A:HIS82 2.3 114.2 1.0
SG A:CYS79 2.5 128.9 1.0
CD2 A:HIS82 2.5 114.2 1.0
SG A:CYS72 2.6 125.0 1.0
SG A:CYS69 2.6 126.9 1.0
CE1 A:HIS82 3.5 114.2 1.0
CB A:CYS69 3.6 126.9 1.0
CG A:HIS82 3.8 114.2 1.0
CA A:GLY61 3.9 130.1 1.0
N A:GLY81 3.9 113.8 1.0
N A:GLY61 4.0 130.1 1.0
CB A:CYS79 4.1 128.9 1.0
CB A:CYS72 4.1 125.0 1.0
CA A:GLY81 4.1 113.8 1.0
ND1 A:HIS82 4.2 114.2 1.0
N A:CYS72 4.2 125.0 1.0
C A:GLY81 4.3 113.8 1.0
CB A:THR71 4.6 114.2 1.0
O A:GLY81 4.6 113.8 1.0
N A:HIS82 4.7 114.2 1.0
N A:LEU80 4.7 115.6 1.0
CA A:CYS72 4.7 125.0 1.0
CA A:CYS79 4.8 128.9 1.0
O A:CYS72 4.8 125.0 1.0
C A:GLY61 4.9 130.1 1.0
CB A:HIS82 5.0 114.2 1.0

Zinc binding site 2 out of 8 in 8iue

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Zinc binding site 2 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:190.3
occ:1.00
 SG A:CYS109 2.4 135.3 1.0
SG A:CYS112 2.5 134.8 1.0
SG A:CYS159 2.5 149.2 1.0
SG A:CYS156 2.5 154.6 1.0
CB A:CYS109 3.3 135.3 1.0
CB A:CYS156 3.5 154.6 1.0
CB A:CYS112 3.5 134.8 1.0
N A:CYS112 3.6 134.8 1.0
CB A:CYS159 3.7 149.2 1.0
N A:CYS159 4.0 149.2 1.0
CA A:CYS112 4.2 134.8 1.0
CB A:THR111 4.2 126.3 1.0
ND2 A:ASN163 4.3 152.8 1.0
CA A:CYS159 4.4 149.2 1.0
CE A:MET116 4.6 156.0 1.0
C A:THR111 4.6 126.3 1.0
N A:THR111 4.6 126.3 1.0
N A:GLY160 4.6 151.7 1.0
CB A:ALA161 4.7 150.6 1.0
N A:ALA161 4.7 150.6 1.0
CA A:THR111 4.7 126.3 1.0
CA A:CYS109 4.7 135.3 1.0
CB A:HIS158 4.8 151.3 1.0
CA A:CYS156 4.8 154.6 1.0
C A:CYS159 4.9 149.2 1.0
CG2 A:THR111 5.0 126.3 1.0
OD1 A:ASN163 5.0 152.8 1.0

Zinc binding site 3 out of 8 in 8iue

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Zinc binding site 3 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:162.0
occ:1.00
 SG B:CYS1095 2.5 118.7 1.0
SG B:CYS1080 2.5 117.2 1.0
SG B:CYS1083 2.5 117.1 1.0
SG B:CYS1092 2.5 113.0 1.0
CB B:CYS1095 3.1 118.7 1.0
CB B:CYS1080 3.1 117.2 1.0
CB B:CYS1092 3.5 113.0 1.0
CB B:CYS1083 3.6 117.1 1.0
N B:CYS1083 3.9 117.1 1.0
N B:CYS1095 3.9 118.7 1.0
CA B:CYS1095 4.1 118.7 1.0
CA B:CYS1083 4.4 117.1 1.0
CB B:GLN1082 4.5 114.1 1.0
CA B:CYS1080 4.6 117.2 1.0
CD1 B:TYR1094 4.6 116.2 1.0
CB B:TYR1094 4.8 116.2 1.0
OE1 B:GLN1082 4.9 114.1 1.0
C B:GLN1082 5.0 114.1 1.0
CA B:CYS1092 5.0 113.0 1.0

Zinc binding site 4 out of 8 in 8iue

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Zinc binding site 4 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:201.4
occ:1.00
 SG I:CYS8 2.5 159.3 1.0
SG I:CYS28 2.5 152.9 1.0
CB I:CYS5 2.6 157.7 1.0
SG I:CYS5 2.6 157.7 1.0
SG I:CYS25 2.7 160.8 1.0
CB I:CYS25 3.2 160.8 1.0
N I:CYS8 3.7 159.3 1.0
CB I:CYS8 4.0 159.3 1.0
CA I:CYS5 4.0 157.7 1.0
OG1 I:THR27 4.1 156.9 1.0
CB I:CYS28 4.1 152.9 1.0
CA I:CYS8 4.3 159.3 1.0
N I:ASN10 4.4 158.0 1.0
CB I:ASN10 4.4 158.0 1.0
N I:GLY9 4.5 157.8 1.0
C I:CYS5 4.5 157.7 1.0
ND2 I:ASN10 4.6 158.0 1.0
C I:CYS8 4.6 159.3 1.0
N I:CYS5 4.6 157.7 1.0
O I:CYS5 4.6 157.7 1.0
N I:GLY7 4.7 150.2 1.0
C I:GLY7 4.7 150.2 1.0
CA I:CYS25 4.7 160.8 1.0
N I:CYS28 4.7 152.9 1.0
CA I:GLY7 4.7 150.2 1.0
CA I:ASN10 4.9 158.0 1.0
CD2 I:LEU12 4.9 152.7 1.0
CG I:ASN10 4.9 158.0 1.0
O I:ASN10 5.0 158.0 1.0
CA I:CYS28 5.0 152.9 1.0

Zinc binding site 5 out of 8 in 8iue

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Zinc binding site 5 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:329.4
occ:1.00
 N I:HIS74 2.3 284.0 1.0
SG I:CYS69 2.5 274.1 1.0
O I:HIS74 2.7 284.0 1.0
CB I:HIS74 2.7 284.0 1.0
CA I:HIS74 2.7 284.0 1.0
SG I:CYS72 2.8 275.6 1.0
SG I:CYS97 2.8 272.0 1.0
C I:HIS74 3.0 284.0 1.0
C I:GLU73 3.4 266.5 1.0
N I:GLU73 3.5 266.5 1.0
CA I:GLU73 3.8 266.5 1.0
CB I:CYS69 3.8 274.1 1.0
C I:CYS72 4.0 275.6 1.0
O I:ARG76 4.0 275.5 1.0
CG I:HIS74 4.2 284.0 1.0
CB I:CYS72 4.3 275.6 1.0
CB I:CYS97 4.3 272.0 1.0
N I:CYS69 4.3 274.1 1.0
N I:PRO75 4.3 282.4 1.0
O I:GLU73 4.4 266.5 1.0
CA I:CYS72 4.5 275.6 1.0
O I:CYS72 4.5 275.6 1.0
N I:CYS72 4.6 275.6 1.0
CA I:CYS69 4.7 274.1 1.0

Zinc binding site 6 out of 8 in 8iue

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Zinc binding site 6 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:154.4
occ:1.00
 SG J:CYS44 2.5 102.7 1.0
SG J:CYS7 2.5 97.8 1.0
SG J:CYS45 2.5 104.7 1.0
SG J:CYS10 2.5 100.3 1.0
CB J:CYS7 2.7 97.8 1.0
N J:CYS45 3.1 104.7 1.0
CA J:CYS45 3.4 104.7 1.0
CB J:CYS44 3.5 102.7 1.0
C J:CYS44 3.5 102.7 1.0
CB J:CYS45 3.5 104.7 1.0
CB J:CYS10 3.9 100.3 1.0
O J:CYS44 4.1 102.7 1.0
CA J:CYS44 4.1 102.7 1.0
CA J:CYS7 4.2 97.8 1.0
OG1 J:THR9 4.3 96.6 1.0
N J:CYS10 4.4 100.3 1.0
CD J:ARG42 4.6 101.8 1.0
CA J:CYS10 4.7 100.3 1.0
N J:GLY11 4.8 97.3 1.0
CG J:ARG42 4.9 101.8 1.0
N J:CYS44 4.9 102.7 1.0
C J:CYS7 4.9 97.8 1.0
C J:CYS45 4.9 104.7 1.0
N J:CYS7 5.0 97.8 1.0
N J:LYS12 5.0 94.1 1.0

Zinc binding site 7 out of 8 in 8iue

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Zinc binding site 7 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:172.1
occ:1.00
 SG L:CYS36 2.5 139.2 1.0
SG L:CYS39 2.6 138.1 1.0
CB L:CYS39 2.8 138.1 1.0
SG L:CYS19 2.9 121.8 1.0
CB L:CYS19 3.3 121.8 1.0
CB L:CYS36 3.4 139.2 1.0
SG L:CYS22 3.4 133.4 1.0
CB L:CYS22 3.4 133.4 1.0
N L:CYS22 4.0 133.4 1.0
CA L:CYS22 4.3 133.4 1.0
CA L:CYS39 4.3 138.1 1.0
O L:ARG37 4.4 130.8 1.0
OE2 L:GLU21 4.4 127.5 1.0
N L:GLY20 4.6 119.3 1.0
CD L:GLU21 4.6 127.5 1.0
CA L:CYS19 4.7 121.8 1.0
CA L:CYS36 4.8 139.2 1.0
N L:GLU21 4.8 127.5 1.0
CB L:TYR41 4.9 120.4 1.0
OG1 L:THR24 4.9 129.0 1.0
CG L:GLU21 4.9 127.5 1.0
N L:HIS23 4.9 129.5 1.0

Zinc binding site 8 out of 8 in 8iue

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Zinc binding site 8 out of 8 in the Rna Polymerase III Pre-Initiation Complex Melting 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 Melting Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Zn700

b:30.0
occ:1.00
 SG V:CYS7 2.6 178.3 1.0
CB V:CYS31 2.6 175.5 1.0
SG V:CYS31 2.7 175.5 1.0
SG V:CYS33 3.1 164.4 1.0
CA V:CYS31 3.9 175.5 1.0
SG V:CYS10 4.0 181.8 1.0
CB V:CYS7 4.0 178.3 1.0
N V:CYS31 4.2 175.5 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
OG V:SER12 4.8 167.0 1.0
CB V:ASP9 4.9 172.3 1.0
NH1 A:ARG430 5.0 131.5 1.0
SG V:CYS28 5.0 172.1 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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