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Zinc in PDB 7d59: Cryo-Em Structure of Human Rna Polymerase III in Apo State

Enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III in Apo State

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III in Apo State:
2.7.7.6;

Other elements in 7d59:

The structure of Cryo-Em Structure of Human Rna Polymerase III in Apo State also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Human Rna Polymerase III in Apo State (pdb code 7d59). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Cryo-Em Structure of Human Rna Polymerase III in Apo State, PDB code: 7d59:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7d59

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:148.5
occ:1.00
 NE2 A:HIS82 2.7 134.6 1.0
SG A:CYS69 2.8 155.9 1.0
SG A:CYS79 2.9 133.6 1.0
SG A:CYS72 3.2 151.2 1.0
CE1 A:HIS82 3.5 134.6 1.0
CD2 A:HIS82 3.7 134.6 1.0
CB A:CYS69 4.1 155.9 1.0
CB A:THR71 4.2 147.9 1.0
N A:CYS72 4.3 151.2 1.0
O A:CYS72 4.3 151.2 1.0
CB A:CYS79 4.5 133.6 1.0
ND1 A:HIS82 4.6 134.6 1.0
CB A:CYS72 4.7 151.2 1.0
CG A:HIS82 4.8 134.6 1.0
OG1 A:THR71 4.8 147.9 1.0
CG2 A:THR71 4.9 147.9 1.0
CA A:CYS72 4.9 151.2 1.0
CA A:CYS79 5.0 133.6 1.0
N A:THR71 5.0 147.9 1.0

Zinc binding site 2 out of 7 in 7d59

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:177.2
occ:1.00
 CB A:CYS112 2.8 158.0 1.0
SG A:CYS112 2.9 158.0 1.0
SG A:CYS156 3.0 177.0 1.0
SG A:CYS109 3.0 161.4 1.0
SG A:CYS159 3.7 175.1 1.0
CB A:CYS156 3.9 177.0 1.0
CB A:CYS109 4.0 161.4 1.0
CB A:CYS159 4.0 175.1 1.0
CA A:CYS112 4.3 158.0 1.0
N A:CYS159 4.5 175.1 1.0
CB A:HIS114 4.6 159.6 1.0
N A:CYS112 4.8 158.0 1.0
CA A:CYS159 4.8 175.1 1.0
C A:CYS112 4.9 158.0 1.0
O A:HIS114 5.0 159.6 1.0

Zinc binding site 3 out of 7 in 7d59

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:139.9
occ:1.00
 SG B:CYS1080 2.5 124.0 1.0
SG B:CYS1083 2.6 126.2 1.0
SG B:CYS1092 2.9 127.5 1.0
CB B:CYS1080 3.0 124.0 1.0
CB B:CYS1092 3.5 127.5 1.0
O B:CYS1083 3.7 126.2 1.0
CB B:CYS1095 3.7 128.4 1.0
N B:CYS1083 4.1 126.2 1.0
CB B:CYS1083 4.2 126.2 1.0
N B:CYS1095 4.5 128.4 1.0
CA B:CYS1083 4.5 126.2 1.0
C B:CYS1083 4.5 126.2 1.0
CA B:CYS1080 4.5 124.0 1.0
CA B:CYS1095 4.7 128.4 1.0
SG B:CYS1095 4.9 128.4 1.0
CB B:GLN1082 4.9 127.8 1.0
NE2 B:GLN1082 5.0 127.8 1.0

Zinc binding site 4 out of 7 in 7d59

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:180.8
occ:1.00
 SG I:CYS5 2.7 162.5 1.0
SG I:CYS8 2.7 162.6 1.0
SG I:CYS28 2.8 164.8 1.0
CB I:CYS5 2.8 162.5 1.0
SG I:CYS25 2.8 167.4 1.0
OG1 I:THR27 3.4 165.6 1.0
CB I:CYS25 4.1 167.4 1.0
CB I:CYS8 4.2 162.6 1.0
O I:CYS28 4.2 164.8 1.0
CB I:CYS28 4.2 164.8 1.0
CA I:CYS5 4.3 162.5 1.0
N I:CYS28 4.4 164.8 1.0
CB I:TYR30 4.5 166.3 1.0
N I:CYS8 4.6 162.6 1.0
CA I:CYS28 4.7 164.8 1.0
C I:CYS28 4.8 164.8 1.0
O I:ASN10 4.8 159.5 1.0
CB I:THR27 4.8 165.6 1.0
N I:ASN10 4.9 159.5 1.0
CD2 I:TYR30 4.9 166.3 1.0
CG I:TYR30 5.0 166.3 1.0
CA I:CYS8 5.0 162.6 1.0

Zinc binding site 5 out of 7 in 7d59

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:234.2
occ:0.75
 SG I:CYS98 2.5 231.7 1.0
CB I:CYS98 3.4 231.7 1.0
CB I:LYS71 3.4 232.1 1.0
CG I:LYS71 3.5 232.1 1.0
CD2 I:HIS104 3.8 222.2 1.0
SG I:CYS69 3.8 236.0 1.0
SG I:CYS72 3.8 235.9 1.0
CB I:CYS102 4.0 225.0 1.0
N I:GLY103 4.5 224.5 1.0
N I:CYS72 4.5 235.9 1.0
CG I:HIS104 4.6 222.2 1.0
N I:HIS104 4.6 222.2 1.0
CA I:LYS71 4.6 232.1 1.0
CB I:HIS104 4.7 222.2 1.0
CB I:CYS72 4.7 235.9 1.0
C I:LYS71 4.8 232.1 1.0
NE2 I:HIS104 4.8 222.2 1.0
SG I:CYS102 4.8 225.0 1.0
CH2 I:TRP106 4.8 212.8 1.0
CA I:CYS98 4.8 231.7 1.0
CZ2 I:TRP106 4.9 212.8 1.0
CD I:LYS71 5.0 232.1 1.0

Zinc binding site 6 out of 7 in 7d59

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn100

b:100.2
occ:1.00
 SG J:CYS10 2.5 80.3 1.0
SG J:CYS7 2.6 76.2 1.0
CB J:CYS45 2.6 81.8 1.0
N J:CYS45 3.0 81.8 1.0
CA J:CYS45 3.1 81.8 1.0
CB J:CYS7 3.1 76.2 1.0
SG J:CYS44 3.1 84.3 1.0
C J:CYS44 3.2 84.3 1.0
O J:CYS44 3.3 84.3 1.0
SG J:CYS45 3.5 81.8 1.0
CB J:CYS44 3.7 84.3 1.0
CB J:CYS10 3.8 80.3 1.0
CA J:CYS44 4.1 84.3 1.0
N J:CYS10 4.3 80.3 1.0
CB J:LYS12 4.3 70.3 1.0
N J:LYS12 4.5 70.3 1.0
N J:GLY11 4.5 78.2 1.0
C J:CYS45 4.6 81.8 1.0
CA J:CYS7 4.6 76.2 1.0
CA J:CYS10 4.6 80.3 1.0
NH2 J:ARG42 4.8 82.7 1.0
CA J:LYS12 5.0 70.3 1.0

Zinc binding site 7 out of 7 in 7d59

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Apo State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cryo-Em Structure of Human Rna Polymerase III in Apo State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:136.1
occ:1.00
 SG L:CYS19 2.4 113.2 1.0
SG L:CYS36 2.4 126.0 1.0
SG L:CYS22 2.4 119.0 1.0
SG L:CYS39 2.5 130.1 1.0
CB L:CYS19 2.7 113.2 1.0
CB L:CYS36 3.2 126.0 1.0
CB L:CYS22 3.8 119.0 1.0
CB L:CYS39 4.0 130.1 1.0
N L:CYS22 4.0 119.0 1.0
N L:CYS39 4.2 130.1 1.0
CA L:CYS19 4.2 113.2 1.0
OG1 L:THR24 4.3 121.6 1.0
CA L:CYS22 4.4 119.0 1.0
N L:HIS23 4.6 116.8 1.0
CA L:CYS39 4.6 130.1 1.0
CA L:CYS36 4.7 126.0 1.0
CB L:TYR41 4.7 115.2 1.0
CB L:THR24 4.9 121.6 1.0
C L:CYS22 4.9 119.0 1.0
N L:GLU21 4.9 120.8 1.0
N L:THR24 4.9 121.6 1.0
C L:CYS19 5.0 113.2 1.0

Reference:

Q.Wang, S.Li, F.Wan, Y.Xu, Z.Wu, M.Cao, P.Lan, M.Lei, J.Wu. Structural Insights Into Transcriptional Regulation of Human Rna Polymerase III. Nat.Struct.Mol.Biol. 2021.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-021-00557-X
Page generated: Tue Oct 29 18:40:20 2024

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