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

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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

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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

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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

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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

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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

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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: Sat Apr 3 18:32:48 2021

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