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Zinc in PDB 7du2: Rna Polymerase III Ec Complex in Post-Translocation State

Enzymatic activity of Rna Polymerase III Ec Complex in Post-Translocation State

All present enzymatic activity of Rna Polymerase III Ec Complex in Post-Translocation State:
2.7.7.6;

Other elements in 7du2:

The structure of Rna Polymerase III Ec Complex in Post-Translocation State 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 Ec Complex in Post-Translocation State (pdb code 7du2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rna Polymerase III Ec Complex in Post-Translocation State, PDB code: 7du2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 7du2

Go back to Zinc Binding Sites List in 7du2
Zinc binding site 1 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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 7du2

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Zinc binding site 2 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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 7du2

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Zinc binding site 3 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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 7du2

Go back to Zinc Binding Sites List in 7du2
Zinc binding site 4 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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 5 out of 6 in 7du2

Go back to Zinc Binding Sites List in 7du2
Zinc binding site 5 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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 4.0 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

Zinc binding site 6 out of 6 in 7du2

Go back to Zinc Binding Sites List in 7du2
Zinc binding site 6 out of 6 in the Rna Polymerase III Ec Complex in Post-Translocation State


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 Ec Complex in Post-Translocation State 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

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 19:16:46 2024

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