Zinc in PDB 7ae1: Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1

Enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1:
2.7.7.6;

Other elements in 7ae1:

The structure of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1 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 Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1 (pdb code 7ae1). 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 Elongation Complex 1, PDB code: 7ae1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7ae1

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


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:84.9
occ:1.00
CE1 A:HIS82 2.4 72.7 1.0
SG A:CYS79 2.4 76.3 1.0
SG A:CYS69 2.5 82.0 1.0
SG A:CYS72 2.5 78.1 1.0
ND1 A:HIS82 3.1 72.7 1.0
CB A:CYS69 3.4 82.0 1.0
NE2 A:HIS82 3.5 72.7 1.0
O A:CYS72 3.6 78.1 1.0
N A:CYS72 3.8 78.1 1.0
CB A:CYS79 3.9 76.3 1.0
CB A:CYS72 3.9 78.1 1.0
CA A:CYS72 4.2 78.1 1.0
CG A:HIS82 4.3 72.7 1.0
C A:CYS72 4.4 78.1 1.0
CA A:GLY61 4.5 81.5 1.0
CD2 A:HIS82 4.6 72.7 1.0
CB A:THR71 4.6 78.6 1.0
CA A:CYS79 4.8 76.3 1.0
CA A:CYS69 4.8 82.0 1.0
N A:GLY81 4.8 70.8 1.0
N A:THR71 4.9 78.6 1.0
C A:THR71 4.9 78.6 1.0
N A:GLY61 4.9 81.5 1.0

Zinc binding site 2 out of 7 in 7ae1

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Zinc binding site 2 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:106.9
occ:1.00
SG A:CYS112 2.4 92.8 1.0
SG A:CYS109 2.4 89.2 1.0
SG A:CYS156 2.4 100.0 1.0
SG A:CYS159 2.5 102.8 1.0
CB A:CYS109 2.8 89.2 1.0
CB A:CYS156 3.1 100.0 1.0
CB A:CYS159 3.5 102.8 1.0
N A:CYS159 3.7 102.8 1.0
CB A:CYS112 3.9 92.8 1.0
CA A:CYS159 4.2 102.8 1.0
N A:CYS112 4.2 92.8 1.0
CA A:CYS109 4.3 89.2 1.0
CA A:CYS156 4.6 100.0 1.0
CA A:CYS112 4.6 92.8 1.0
CB A:HIS158 4.6 102.0 1.0
C A:HIS158 4.8 102.0 1.0
N A:GLY160 4.8 101.8 1.0
ND2 A:ASN163 4.8 94.9 1.0
C A:CYS109 4.9 89.2 1.0
CB A:HIS114 4.9 88.1 1.0
C A:CYS159 5.0 102.8 1.0
O A:HIS114 5.0 88.1 1.0

Zinc binding site 3 out of 7 in 7ae1

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:85.7
occ:1.00
SG B:CYS1080 2.4 70.9 1.0
SG B:CYS1092 2.4 74.2 1.0
SG B:CYS1095 2.4 73.5 1.0
SG B:CYS1083 2.4 70.0 1.0
CB B:CYS1080 3.0 70.9 1.0
CB B:CYS1095 3.4 73.5 1.0
CB B:CYS1092 3.5 74.2 1.0
CB B:CYS1083 3.7 70.0 1.0
N B:CYS1083 4.0 70.0 1.0
N B:CYS1095 4.1 73.5 1.0
CA B:CYS1095 4.4 73.5 1.0
CA B:CYS1083 4.5 70.0 1.0
CA B:CYS1080 4.5 70.9 1.0
CB B:GLN1082 4.6 73.5 1.0
CD2 B:TYR1094 4.6 71.4 1.0
CB B:TYR1094 4.7 71.4 1.0
CA B:CYS1092 4.9 74.2 1.0
C B:CYS1080 5.0 70.9 1.0

Zinc binding site 4 out of 7 in 7ae1

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:196.5
occ:1.00
CB I:ASN99 2.8 191.9 1.0
SG I:CYS72 3.1 186.9 1.0
SG I:CYS102 3.2 191.3 1.0
N I:ASN99 3.2 191.9 1.0
SG I:CYS97 3.5 189.3 1.0
CA I:ASN99 3.6 191.9 1.0
C I:CYS98 3.7 190.6 1.0
CB I:CYS97 3.7 189.3 1.0
N I:CYS98 3.8 190.6 1.0
CB I:CYS102 3.9 191.3 1.0
C I:CYS97 3.9 189.3 1.0
O I:CYS102 4.0 191.3 1.0
CG I:ASN99 4.0 191.9 1.0
CA I:CYS98 4.1 190.6 1.0
ND2 I:ASN99 4.2 191.9 1.0
O I:CYS97 4.3 189.3 1.0
CB I:CYS72 4.4 186.9 1.0
CA I:CYS97 4.4 189.3 1.0
O I:CYS98 4.4 190.6 1.0
O I:ARG76 4.5 186.6 1.0
C I:ASN99 4.6 191.9 1.0
C I:CYS102 4.6 191.3 1.0
O I:ASN99 4.9 191.9 1.0
CA I:CYS102 4.9 191.3 1.0

Zinc binding site 5 out of 7 in 7ae1

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:88.2
occ:1.00
SG I:CYS5 2.4 79.0 1.0
SG I:CYS25 2.5 86.2 1.0
SG I:CYS28 2.5 87.3 1.0
SG I:CYS8 2.5 77.8 1.0
CB I:CYS5 2.8 79.0 1.0
CB I:CYS25 3.0 86.2 1.0
CB I:CYS28 3.7 87.3 1.0
CB I:CYS8 4.0 77.8 1.0
N I:CYS8 4.0 77.8 1.0
CA I:CYS5 4.3 79.0 1.0
OG1 I:THR27 4.4 84.5 1.0
CA I:CYS8 4.4 77.8 1.0
CA I:CYS25 4.5 86.2 1.0
N I:CYS28 4.5 87.3 1.0
N I:GLY9 4.6 76.9 1.0
CB I:TYR30 4.6 87.0 1.0
CA I:CYS28 4.6 87.3 1.0
N I:ASN10 4.7 77.4 1.0
C I:CYS8 4.9 77.8 1.0
C I:CYS5 4.9 79.0 1.0
CB I:ASN10 4.9 77.4 1.0

Zinc binding site 6 out of 7 in 7ae1

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 1


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:53.7
occ:1.00
SG J:CYS10 2.4 33.9 1.0
SG J:CYS7 2.4 34.8 1.0
SG J:CYS45 2.5 38.8 1.0
SG J:CYS44 2.5 37.4 1.0
N J:CYS45 3.2 38.8 1.0
CB J:CYS7 3.4 34.8 1.0
CB J:CYS44 3.6 37.4 1.0
CB J:CYS10 3.6 33.9 1.0
C J:CYS44 3.6 37.4 1.0
CB J:CYS45 3.7 38.8 1.0
CA J:CYS45 3.7 38.8 1.0
N J:CYS10 3.9 33.9 1.0
O J:CYS44 4.1 37.4 1.0
CA J:CYS44 4.2 37.4 1.0
CA J:CYS10 4.3 33.9 1.0
CB J:THR9 4.5 32.2 1.0
NH2 J:ARG42 4.5 38.5 1.0
NE J:ARG42 4.5 38.5 1.0
C J:THR9 4.7 32.2 1.0
CA J:CYS7 4.8 34.8 1.0
N J:CYS44 4.8 37.4 1.0
N J:GLY11 4.9 34.0 1.0
N J:THR9 4.9 32.2 1.0
CB J:LYS12 4.9 32.9 1.0
CA J:THR9 4.9 32.2 1.0
C J:CYS10 5.0 33.9 1.0
CZ J:ARG42 5.0 38.5 1.0

Zinc binding site 7 out of 7 in 7ae1

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


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 Elongation Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:84.1
occ:1.00
SG L:CYS22 2.4 69.6 1.0
SG L:CYS36 2.5 73.0 1.0
SG L:CYS19 2.5 64.1 1.0
CB L:CYS36 3.0 73.0 1.0
CB L:CYS39 3.3 80.1 1.0
CB L:CYS19 3.7 64.1 1.0
CB L:TYR41 3.8 67.1 1.0
N L:CYS39 4.0 80.1 1.0
CA L:CYS39 4.1 80.1 1.0
CB L:CYS22 4.1 69.6 1.0
OG1 L:THR24 4.2 70.9 1.0
N L:CYS22 4.3 69.6 1.0
C L:CYS39 4.3 80.1 1.0
O L:CYS39 4.3 80.1 1.0
N L:TYR41 4.4 67.1 1.0
CA L:CYS36 4.5 73.0 1.0
SG L:CYS39 4.5 80.1 1.0
CB L:GLU21 4.6 67.9 1.0
CA L:TYR41 4.7 67.1 1.0
CA L:CYS22 4.8 69.6 1.0
CG L:TYR41 4.9 67.1 1.0
O L:TYR41 5.0 67.1 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 16:16:20 2021

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