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Zinc in PDB 7d58: Cryo-Em Structure of Human Rna Polymerase III in Elongating State

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

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

Other elements in 7d58:

The structure of Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State (pdb code 7d58). 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 Elongating State, PDB code: 7d58:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7d58

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Zinc binding site 1 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:102.0
occ:1.00
 NE2 A:HIS82 2.7 87.5 1.0
SG A:CYS69 2.9 115.9 1.0
SG A:CYS72 3.1 103.6 1.0
CE1 A:HIS82 3.4 87.5 1.0
SG A:CYS79 3.5 94.8 1.0
CD2 A:HIS82 3.8 87.5 1.0
CB A:THR71 4.2 103.6 1.0
N A:CYS72 4.2 103.6 1.0
O A:CYS72 4.2 103.6 1.0
CB A:CYS69 4.3 115.9 1.0
ND1 A:HIS82 4.6 87.5 1.0
CB A:CYS72 4.6 103.6 1.0
CB A:CYS79 4.7 94.8 1.0
CG2 A:THR71 4.8 103.6 1.0
CG A:HIS82 4.8 87.5 1.0
OG1 A:THR71 4.8 103.6 1.0
CA A:CYS72 4.8 103.6 1.0
CA A:GLY61 4.9 95.2 1.0
N A:THR71 4.9 103.6 1.0
CA A:THR71 4.9 103.6 1.0

Zinc binding site 2 out of 7 in 7d58

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:129.2
occ:1.00
 CB A:CYS112 2.8 113.1 1.0
SG A:CYS112 2.8 113.1 1.0
SG A:CYS109 3.1 108.4 1.0
SG A:CYS156 3.5 123.2 1.0
CB A:CYS156 3.8 123.2 1.0
CB A:CYS109 3.8 108.4 1.0
CB A:CYS159 3.9 128.9 1.0
CA A:CYS112 4.1 113.1 1.0
SG A:CYS159 4.2 128.9 1.0
N A:CYS159 4.4 128.9 1.0
N A:CYS112 4.5 113.1 1.0
CB A:HIS114 4.5 112.3 1.0
O A:HIS114 4.6 112.3 1.0
CA A:CYS159 4.7 128.9 1.0
C A:CYS112 4.7 113.1 1.0
CD2 A:HIS114 4.9 112.3 1.0
N A:HIS114 4.9 112.3 1.0

Zinc binding site 3 out of 7 in 7d58

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2001

b:110.7
occ:1.00
 SG B:CYS1095 2.8 90.0 1.0
SG B:CYS1092 2.9 92.7 1.0
SG B:CYS1080 2.9 95.8 1.0
CB B:CYS1080 3.0 95.8 1.0
CB B:CYS1092 3.3 92.7 1.0
SG B:CYS1083 3.6 93.0 1.0
CB B:CYS1095 3.8 90.0 1.0
O B:CYS1083 4.1 93.0 1.0
N B:CYS1083 4.5 93.0 1.0
N B:CYS1095 4.5 90.0 1.0
CA B:CYS1080 4.5 95.8 1.0
O B:HIS1100 4.6 104.0 1.0
CB B:GLN1082 4.7 97.7 1.0
CA B:CYS1092 4.8 92.7 1.0
CA B:CYS1095 4.8 90.0 1.0
CB B:CYS1083 4.9 93.0 1.0
C B:CYS1083 5.0 93.0 1.0

Zinc binding site 4 out of 7 in 7d58

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:166.2
occ:1.00
 SG I:CYS8 2.5 148.6 1.0
SG I:CYS5 2.6 149.6 1.0
SG I:CYS25 2.7 157.6 1.0
CB I:CYS5 2.9 149.6 1.0
SG I:CYS28 3.0 155.8 1.0
OG1 I:THR27 3.4 154.2 1.0
CB I:CYS25 3.8 157.6 1.0
CB I:CYS8 3.9 148.6 1.0
CB I:CYS28 4.2 155.8 1.0
O I:CYS28 4.3 155.8 1.0
N I:CYS28 4.3 155.8 1.0
O I:ASN10 4.4 147.2 1.0
CA I:CYS5 4.4 149.6 1.0
N I:ASN10 4.6 147.2 1.0
CB I:ASN10 4.6 147.2 1.0
CA I:CYS28 4.7 155.8 1.0
C I:ASN10 4.7 147.2 1.0
CB I:TYR30 4.8 154.3 1.0
O I:GLY11 4.8 150.6 1.0
CB I:THR27 4.8 154.2 1.0
N I:CYS8 4.8 148.6 1.0
N I:CYS5 4.8 149.6 1.0
C I:CYS28 4.9 155.8 1.0
CA I:ASN10 4.9 147.2 1.0
CA I:CYS8 4.9 148.6 1.0
N I:GLY9 4.9 144.7 1.0
CD2 I:TYR30 5.0 154.3 1.0

Zinc binding site 5 out of 7 in 7d58

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:195.3
occ:0.75
 SG I:CYS102 2.6 189.8 1.0
SG I:CYS98 2.6 194.1 1.0
CB I:CYS98 2.9 194.1 1.0
SG I:CYS72 3.1 203.7 1.0
CB I:LYS71 4.0 198.2 1.0
SG I:CYS69 4.1 200.8 1.0
CG I:LYS71 4.2 198.2 1.0
CB I:CYS72 4.3 203.7 1.0
CB I:CYS102 4.3 189.8 1.0
CA I:CYS98 4.5 194.1 1.0
N I:GLY103 4.6 190.3 1.0
CH2 I:TRP106 4.6 178.3 1.0
N I:CYS72 4.6 203.7 1.0
CB I:CYS69 4.6 200.8 1.0
CD2 I:HIS104 4.6 188.2 1.0
N I:HIS104 4.6 188.2 1.0
CZ2 I:TRP106 4.7 178.3 1.0
C I:LYS71 5.0 198.2 1.0
CB I:HIS104 5.0 188.2 1.0

Zinc binding site 6 out of 7 in 7d58

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn100

b:89.1
occ:1.00
 SG J:CYS7 2.5 62.6 1.0
SG J:CYS10 2.5 65.3 1.0
CB J:CYS45 2.5 73.2 1.0
CB J:CYS7 3.1 62.6 1.0
CA J:CYS45 3.1 73.2 1.0
SG J:CYS44 3.3 72.9 1.0
N J:CYS45 3.3 73.2 1.0
C J:CYS44 3.7 72.9 1.0
CB J:CYS10 3.8 65.3 1.0
O J:CYS44 3.9 72.9 1.0
SG J:CYS45 4.0 73.2 1.0
N J:CYS10 4.1 65.3 1.0
CB J:CYS44 4.4 72.9 1.0
CB J:LYS12 4.4 57.7 1.0
CA J:CYS10 4.5 65.3 1.0
N J:GLY11 4.6 61.2 1.0
CA J:CYS7 4.6 62.6 1.0
N J:LYS12 4.6 57.7 1.0
C J:CYS45 4.6 73.2 1.0
CA J:CYS44 4.7 72.9 1.0

Zinc binding site 7 out of 7 in 7d58

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Zinc binding site 7 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III in Elongating 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 Elongating State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:132.6
occ:1.00
 SG L:CYS19 2.5 101.8 1.0
SG L:CYS39 2.7 118.2 1.0
SG L:CYS36 2.8 116.6 1.0
CB L:CYS19 3.0 101.8 1.0
CB L:CYS22 3.3 112.3 1.0
SG L:CYS22 3.4 112.3 1.0
N L:CYS22 3.5 112.3 1.0
CB L:CYS36 3.5 116.6 1.0
CA L:CYS22 3.9 112.3 1.0
CB L:CYS39 4.1 118.2 1.0
N L:CYS39 4.3 118.2 1.0
N L:HIS23 4.4 107.3 1.0
C L:CYS22 4.5 112.3 1.0
CA L:CYS19 4.5 101.8 1.0
C L:GLU21 4.6 114.0 1.0
N L:GLU21 4.6 114.0 1.0
CB L:GLU21 4.6 114.0 1.0
OG1 L:THR24 4.7 107.8 1.0
CB L:GLU38 4.8 119.7 1.0
CA L:CYS39 4.8 118.2 1.0
CA L:GLU21 4.8 114.0 1.0
N L:THR24 4.9 107.8 1.0
CB L:TYR41 5.0 107.9 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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