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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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

Go back to Zinc Binding Sites List in 7d59
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: Wed Mar 3 16:20:41 2021

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy