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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Go back to Zinc Binding Sites List in 8iue
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy