Atomistry » Zinc » PDB 7dd9-7doi » 7dn3
Atomistry »
  Zinc »
    PDB 7dd9-7doi »
      7dn3 »

Zinc in PDB 7dn3: Structure of Human Rna Polymerase III Elongation Complex

Enzymatic activity of Structure of Human Rna Polymerase III Elongation Complex

All present enzymatic activity of Structure of Human Rna Polymerase III Elongation Complex:
2.7.7.6;

Other elements in 7dn3:

The structure of Structure of Human Rna Polymerase III Elongation Complex 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 Structure of Human Rna Polymerase III Elongation Complex (pdb code 7dn3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Human Rna Polymerase III Elongation Complex, PDB code: 7dn3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 1 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1902

b:109.9
occ:1.00
 NE2 A:HIS82 2.1 84.0 1.0
SG A:CYS69 2.4 96.0 1.0
SG A:CYS79 2.4 88.7 1.0
CB A:CYS72 2.4 94.5 1.0
SG A:CYS72 2.5 94.5 1.0
CE1 A:HIS82 2.9 84.0 1.0
CD2 A:HIS82 3.1 84.0 1.0
N A:CYS72 3.2 94.5 1.0
CA A:CYS72 3.4 94.5 1.0
CB A:CYS69 4.0 96.0 1.0
ND1 A:HIS82 4.0 84.0 1.0
CB A:CYS79 4.0 88.7 1.0
CG2 A:THR71 4.1 92.6 1.0
CG A:HIS82 4.2 84.0 1.0
C A:THR71 4.2 92.6 1.0
C A:CYS72 4.3 94.5 1.0
O A:CYS72 4.8 94.5 1.0
O A:LEU80 4.8 84.7 1.0
O A:THR71 4.9 92.6 1.0
N A:THR71 4.9 92.6 1.0

Zinc binding site 2 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 2 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1903

b:140.3
occ:1.00
 O A:ALA161 2.1 117.2 1.0
C A:ALA161 2.4 117.2 1.0
N A:ALA161 2.4 117.2 1.0
CA A:ALA161 2.5 117.2 1.0
SG A:CYS159 2.6 121.4 1.0
CB A:ALA161 2.7 117.2 1.0
SG A:CYS156 2.7 118.4 1.0
C A:GLY160 3.5 118.5 1.0
N A:PHE162 3.5 113.6 1.0
SG A:CYS109 3.5 104.6 1.0
OG1 A:THR111 3.5 104.6 1.0
CB A:CYS156 3.8 118.4 1.0
OD1 A:ASN163 4.0 112.6 1.0
N A:GLY160 4.0 118.5 1.0
ND2 A:ASN163 4.1 112.6 1.0
N A:CYS156 4.1 118.4 1.0
CA A:GLY160 4.2 118.5 1.0
O A:GLY160 4.3 118.5 1.0
CB A:CYS159 4.3 121.4 1.0
CG A:ASN163 4.3 112.6 1.0
CA A:PHE162 4.4 113.6 1.0
C A:CYS159 4.4 121.4 1.0
CA A:CYS156 4.6 118.4 1.0
C A:PHE162 4.6 113.6 1.0
CB A:CYS109 4.7 104.6 1.0
CB A:THR111 4.9 104.6 1.0
CA A:CYS159 4.9 121.4 1.0
O A:CYS159 4.9 121.4 1.0
N A:ASN163 5.0 112.6 1.0

Zinc binding site 3 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 3 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:95.5
occ:1.00
 SG B:CYS1083 2.5 81.5 1.0
SG B:CYS1080 2.5 81.6 1.0
O B:TYR1094 2.9 85.8 1.0
SG B:CYS1092 2.9 86.5 1.0
SG B:CYS1095 3.0 88.1 1.0
CB B:CYS1092 3.5 86.5 1.0
CB B:CYS1080 3.7 81.6 1.0
C B:TYR1094 3.9 85.8 1.0
O B:GLN1082 4.1 83.6 1.0
CB B:CYS1095 4.2 88.1 1.0
CB B:CYS1083 4.3 81.5 1.0
CD2 B:TYR1094 4.3 85.8 1.0
O B:CYS1095 4.3 88.1 1.0
CB B:TYR1094 4.5 85.8 1.0
N B:CYS1095 4.7 88.1 1.0
CA B:CYS1095 4.8 88.1 1.0
O B:CYS1092 4.8 86.5 1.0
CA B:TYR1094 4.8 85.8 1.0
CA B:CYS1092 4.8 86.5 1.0
O B:CYS1083 4.8 81.5 1.0
C B:CYS1095 4.9 88.1 1.0
C B:CYS1092 4.9 86.5 1.0
C B:GLN1082 4.9 83.6 1.0
CG B:TYR1094 4.9 85.8 1.0
CG B:GLN1082 5.0 83.6 1.0
N B:TYR1094 5.0 85.8 1.0

Zinc binding site 4 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 4 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2000

b:30.0
occ:1.00
 CD1 I:PHE23 2.5 130.2 1.0
SG I:CYS5 2.7 122.0 1.0
SG I:CYS25 2.9 125.3 1.0
O I:ASN26 3.0 125.5 1.0
CE1 I:PHE23 3.2 130.2 1.0
SG I:CYS8 3.4 117.7 1.0
CG I:PHE23 3.4 130.2 1.0
CB I:CYS5 3.6 122.0 1.0
CB I:PHE23 3.8 130.2 1.0
CB I:CYS28 4.0 130.3 1.0
C I:ASN26 4.2 125.5 1.0
CZ I:PHE23 4.4 130.2 1.0
CB I:CYS8 4.4 117.7 1.0
N I:CYS28 4.5 130.3 1.0
N I:ASN26 4.5 125.5 1.0
CD2 I:PHE23 4.6 130.2 1.0
CB I:CYS25 4.7 125.3 1.0
N I:CYS8 4.8 117.7 1.0
CA I:CYS28 4.8 130.3 1.0
CA I:ASN26 4.9 125.5 1.0
C I:CYS25 4.9 125.3 1.0
CA I:CYS5 4.9 122.0 1.0
CE2 I:PHE23 4.9 130.2 1.0
C I:THR27 4.9 127.2 1.0
CA I:PHE23 5.0 130.2 1.0

Zinc binding site 5 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 5 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:98.6
occ:1.00
 CB L:CYS22 2.5 85.9 1.0
CB L:CYS39 2.7 98.0 1.0
SG L:CYS39 2.8 98.0 1.0
SG L:CYS19 2.9 81.3 1.0
CB L:CYS19 3.0 81.3 1.0
SG L:CYS22 3.3 85.9 1.0
CB L:CYS36 3.5 93.2 1.0
CA L:CYS22 3.8 85.9 1.0
O L:ARG37 3.8 95.1 1.0
N L:CYS22 3.9 85.9 1.0
SG L:CYS36 3.9 93.2 1.0
CA L:CYS39 4.0 98.0 1.0
OG1 L:THR24 4.2 83.6 1.0
N L:CYS39 4.2 98.0 1.0
CA L:CYS19 4.4 81.3 1.0
C L:GLU38 4.6 97.9 1.0
O L:GLU38 4.6 97.9 1.0
C L:CYS22 4.6 85.9 1.0
N L:GLY20 4.7 79.8 1.0
N L:HIS23 4.8 83.8 1.0
CA L:CYS36 4.9 93.2 1.0
C L:ARG37 4.9 95.1 1.0
C L:CYS39 5.0 98.0 1.0

Zinc binding site 6 out of 6 in 7dn3

Go back to Zinc Binding Sites List in 7dn3
Zinc binding site 6 out of 6 in the Structure of Human Rna Polymerase III Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Rna Polymerase III Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2000

b:30.0
occ:1.00
 SG J:CYS45 2.2 54.9 1.0
CB J:CYS10 2.6 57.9 1.0
SG J:CYS7 2.6 54.0 1.0
SG J:CYS44 2.7 57.1 1.0
SG J:CYS10 2.9 57.9 1.0
N J:CYS10 3.0 57.9 1.0
OG1 J:THR9 3.1 55.0 1.0
CB J:CYS7 3.2 54.0 1.0
CA J:CYS10 3.3 57.9 1.0
CB J:CYS45 3.7 54.9 1.0
N J:CYS45 3.8 54.9 1.0
N J:GLY11 3.8 55.5 1.0
C J:CYS10 4.0 57.9 1.0
CA J:CYS45 4.1 54.9 1.0
C J:THR9 4.2 55.0 1.0
CB J:CYS44 4.2 57.1 1.0
C J:CYS44 4.3 57.1 1.0
CD J:ARG42 4.3 58.8 1.0
NH1 J:ARG42 4.4 58.8 1.0
CB J:THR9 4.4 55.0 1.0
N J:LYS12 4.5 54.1 1.0
CA J:CYS7 4.6 54.0 1.0
CG J:ARG42 4.6 58.8 1.0
CA J:THR9 4.6 55.0 1.0
N J:THR9 4.7 55.0 1.0
O J:CYS44 4.7 57.1 1.0
CA J:CYS44 4.9 57.1 1.0
CB J:LYS12 4.9 54.1 1.0
C J:CYS7 5.0 54.0 1.0

Reference:

L.Li, Z.Yu, D.Zhao, Y.Ren, H.Hou, Y.Xu. Structure of Human Rna Polymerase III Elongation Complex. Cell Res. 2021.
ISSN: ISSN 1001-0602
PubMed: 33674783
DOI: 10.1038/S41422-021-00472-2
Page generated: Tue Oct 29 19:06:25 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy