Zinc in PDB 7a6h: Cryo-Em Structure of Human Apo Rna Polymerase III

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

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

Other elements in 7a6h:

The structure of Cryo-Em Structure of Human Apo Rna Polymerase III 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 Cryo-Em Structure of Human Apo Rna Polymerase III (pdb code 7a6h). 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 Apo Rna Polymerase III, PDB code: 7a6h:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:137.4
occ:1.00
N A:GLY61 2.5 95.3 1.0
ND1 A:HIS82 2.5 85.0 1.0
CB G:PRO165 2.6 101.9 1.0
SG A:CYS69 2.7 110.8 1.0
O A:ARG59 2.8 95.0 1.0
C A:ARG59 3.0 95.0 1.0
CE1 A:HIS82 3.2 85.0 1.0
CA A:GLY61 3.3 95.3 1.0
C A:MET60 3.4 90.6 1.0
CG A:HIS82 3.4 85.0 1.0
N A:MET60 3.5 90.6 1.0
CG G:PRO165 3.5 101.9 1.0
CA A:MET60 3.6 90.6 1.0
CA A:ARG59 3.7 95.0 1.0
CA G:PRO165 3.8 101.9 1.0
CB A:HIS82 3.9 85.0 1.0
NE2 A:HIS82 4.2 85.0 1.0
O A:HIS58 4.2 97.4 1.0
CB A:CYS69 4.3 110.8 1.0
C G:PRO165 4.3 101.9 1.0
CD2 A:HIS82 4.3 85.0 1.0
C A:GLY61 4.5 95.3 1.0
SG A:CYS79 4.5 91.4 1.0
O A:MET60 4.5 90.6 1.0
C A:HIS58 4.6 97.4 1.0
N A:ARG59 4.6 95.0 1.0
N A:HIS82 4.7 85.0 1.0
O A:GLY61 4.7 95.3 1.0
O G:PRO165 4.7 101.9 1.0
N G:SER166 4.7 104.8 1.0
CD G:PRO165 4.8 101.9 1.0
CB A:ARG59 4.8 95.0 1.0
N G:PRO165 4.9 101.9 1.0
CA A:HIS82 4.9 85.0 1.0
CA A:CYS69 5.0 110.8 1.0

Zinc binding site 2 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:153.7
occ:1.00
N A:HIS157 2.2 128.3 1.0
SG A:CYS156 2.5 130.7 1.0
CA A:CYS156 2.7 130.7 1.0
C A:CYS156 2.8 130.7 1.0
CB A:CYS156 3.1 130.7 1.0
CA A:HIS157 3.2 128.3 1.0
N A:HIS158 3.3 123.8 1.0
C A:HIS157 3.6 128.3 1.0
CB A:HIS157 3.7 128.3 1.0
O A:CYS156 3.9 130.7 1.0
CA A:MET116 4.0 117.3 1.0
N A:CYS156 4.1 130.7 1.0
CG A:MET116 4.2 117.3 1.0
O A:ILE155 4.3 127.6 1.0
CB A:HIS158 4.3 123.8 1.0
CG A:HIS157 4.3 128.3 1.0
CB A:MET116 4.3 117.3 1.0
CD2 A:HIS157 4.3 128.3 1.0
CA A:HIS158 4.4 123.8 1.0
O A:ILE115 4.6 108.5 1.0
C A:ILE155 4.6 127.6 1.0
C A:MET116 4.7 117.3 1.0
O A:HIS157 4.7 128.3 1.0
N A:LEU117 4.8 118.5 1.0
N A:MET116 4.9 117.3 1.0

Zinc binding site 3 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:90.1
occ:1.00
SG B:CYS1083 2.4 75.5 1.0
SG B:CYS1092 2.4 81.4 1.0
SG B:CYS1080 2.5 75.8 1.0
SG B:CYS1095 2.5 84.0 1.0
CB B:CYS1095 3.2 84.0 1.0
CB B:CYS1083 3.3 75.5 1.0
CB B:CYS1080 3.3 75.8 1.0
CB B:CYS1092 3.4 81.4 1.0
N B:CYS1095 3.7 84.0 1.0
N B:CYS1083 4.0 75.5 1.0
CA B:CYS1095 4.1 84.0 1.0
CA B:CYS1083 4.2 75.5 1.0
CB B:TYR1094 4.4 79.6 1.0
CD2 B:TYR1094 4.4 79.6 1.0
C B:TYR1094 4.8 79.6 1.0
CA B:CYS1080 4.8 75.8 1.0
CA B:CYS1092 4.8 81.4 1.0
CG B:TYR1094 4.9 79.6 1.0

Zinc binding site 4 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:219.5
occ:1.00
CB I:ASN99 2.6 216.8 1.0
N I:ASN99 2.7 216.8 1.0
C I:CYS98 2.8 218.2 1.0
O I:ARG76 3.1 211.8 1.0
N I:CYS98 3.1 218.2 1.0
CA I:ASN99 3.1 216.8 1.0
O I:CYS98 3.2 218.2 1.0
CA I:CYS98 3.5 218.2 1.0
C I:CYS97 3.6 217.0 1.0
CG I:ASN99 3.6 216.8 1.0
CB I:CYS97 3.7 217.0 1.0
ND2 I:ASN99 4.0 216.8 1.0
CA I:CYS97 4.0 217.0 1.0
SG I:CYS97 4.1 217.0 1.0
C I:ARG76 4.2 211.8 1.0
CG I:ARG76 4.3 211.8 1.0
SG I:CYS72 4.3 208.4 1.0
O I:CYS97 4.3 217.0 1.0
CB I:ARG76 4.4 211.8 1.0
OD1 I:ASN99 4.4 216.8 1.0
C I:ASN99 4.5 216.8 1.0
SG I:CYS102 4.6 214.3 1.0
O I:CYS102 4.7 214.3 1.0
CB I:CYS98 4.9 218.2 1.0
CA I:ARG76 4.9 211.8 1.0
CB I:CYS102 5.0 214.3 1.0
O I:ASN99 5.0 216.8 1.0

Zinc binding site 5 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:130.5
occ:1.00
SG I:CYS28 2.4 124.0 1.0
SG I:CYS5 2.5 113.4 1.0
SG I:CYS25 2.5 123.4 1.0
SG I:CYS8 2.5 116.3 1.0
CB I:CYS5 2.6 113.4 1.0
CB I:CYS25 3.0 123.4 1.0
CB I:CYS28 3.8 124.0 1.0
CB I:CYS8 4.0 116.3 1.0
N I:CYS8 4.0 116.3 1.0
CA I:CYS5 4.1 113.4 1.0
CA I:CYS25 4.4 123.4 1.0
CA I:CYS8 4.5 116.3 1.0
N I:CYS28 4.5 124.0 1.0
CB I:TYR30 4.5 124.9 1.0
N I:GLY9 4.5 112.9 1.0
N I:ASN10 4.7 112.8 1.0
OG1 I:THR27 4.7 120.0 1.0
CA I:CYS28 4.7 124.0 1.0
C I:CYS5 4.8 113.4 1.0
N I:CYS5 4.8 113.4 1.0
C I:CYS8 4.8 116.3 1.0
CB I:ASN10 4.9 112.8 1.0
O I:CYS28 5.0 124.0 1.0

Zinc binding site 6 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:83.3
occ:1.00
SG J:CYS44 2.4 62.0 1.0
SG J:CYS45 2.4 62.8 1.0
SG J:CYS7 2.4 57.2 1.0
SG J:CYS10 2.5 56.8 1.0
N J:CYS45 2.6 62.8 1.0
CA J:CYS45 3.0 62.8 1.0
C J:CYS44 3.0 62.0 1.0
CB J:CYS7 3.2 57.2 1.0
CB J:CYS45 3.3 62.8 1.0
CB J:CYS44 3.4 62.0 1.0
O J:CYS44 3.5 62.0 1.0
CB J:CYS10 3.7 56.8 1.0
CA J:CYS44 3.8 62.0 1.0
N J:CYS10 4.2 56.8 1.0
N J:CYS44 4.5 62.0 1.0
C J:CYS45 4.5 62.8 1.0
CA J:CYS10 4.5 56.8 1.0
CA J:CYS7 4.7 57.2 1.0
NE J:ARG42 4.7 65.4 1.0
N J:GLY11 4.8 57.2 1.0
CB J:LYS12 4.9 56.9 1.0
CB J:ARG42 4.9 65.4 1.0

Zinc binding site 7 out of 7 in 7a6h

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


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 Apo Rna Polymerase III within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:119.1
occ:1.00
SG L:CYS22 2.4 93.1 1.0
SG L:CYS36 2.5 100.3 1.0
SG L:CYS19 2.5 85.8 1.0
CB L:CYS39 2.9 105.5 1.0
SG L:CYS39 3.1 105.5 1.0
CB L:CYS36 3.3 100.3 1.0
CB L:CYS22 3.3 93.1 1.0
CB L:CYS19 3.7 85.8 1.0
N L:CYS39 3.8 105.5 1.0
CA L:CYS39 3.9 105.5 1.0
N L:CYS22 3.9 93.1 1.0
CB L:TYR41 4.2 90.0 1.0
CA L:CYS22 4.2 93.1 1.0
C L:CYS39 4.5 105.5 1.0
OG1 L:THR24 4.6 92.1 1.0
N L:TYR41 4.7 90.0 1.0
CA L:CYS36 4.8 100.3 1.0
CB L:GLU21 4.8 90.0 1.0
N L:GLU21 4.8 90.0 1.0
O L:CYS39 4.9 105.5 1.0
C L:GLU21 4.9 90.0 1.0
C L:GLU38 5.0 106.6 1.0

Reference:

M.Girbig, A.D.Misiaszek, M.K.Vorlaender, A.Lafita, H.Groetsch, F.Baudin, A.Bateman, C.W.Mueller. Cryo-Em Structures of Human Rna Polymerase III in Its Unbound and Transcribing States To Be Published.
DOI: 10.1038/S41594-020-00555-5
Page generated: Wed Mar 3 16:16:19 2021

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