Atomistry » Zinc » PDB 8ihr-8j54 » 8ity
Atomistry »
  Zinc »
    PDB 8ihr-8j54 »
      8ity »

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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Go back to Zinc Binding Sites List in 8ity
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy