Zinc in PDB 7aea: Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2

Enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2:
2.7.7.6;

Other elements in 7aea:

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

Zinc binding site 1 out of 7 in 7aea

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1401

b:134.8
occ:1.00
SG A:CYS79 2.5 117.5 1.0
SG A:CYS69 2.5 139.0 1.0
CB A:CYS69 3.1 139.0 1.0
SG A:CYS72 3.2 129.5 1.0
O A:CYS72 3.3 129.5 1.0
CE1 A:HIS82 3.4 117.8 1.0
ND1 A:HIS82 3.5 117.8 1.0
CB A:CYS79 3.6 117.5 1.0
N A:CYS72 3.7 129.5 1.0
C A:CYS72 4.2 129.5 1.0
CA A:GLY61 4.3 129.3 1.0
CA A:CYS72 4.3 129.5 1.0
CB A:CYS72 4.3 129.5 1.0
CB A:THR71 4.5 131.2 1.0
CA A:CYS69 4.6 139.0 1.0
N A:THR71 4.6 131.2 1.0
N A:GLY61 4.6 129.3 1.0
NE2 A:HIS82 4.6 117.8 1.0
C A:THR71 4.8 131.2 1.0
CG A:HIS82 4.8 117.8 1.0
CA A:THR71 4.9 131.2 1.0
CA A:CYS79 4.9 117.5 1.0
N A:GLU70 4.9 133.8 1.0
C A:CYS69 4.9 139.0 1.0

Zinc binding site 2 out of 7 in 7aea

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1402

b:167.6
occ:1.00
SG A:CYS159 2.5 154.3 1.0
SG A:CYS112 2.5 145.2 1.0
SG A:CYS109 2.6 139.6 1.0
CB A:CYS109 2.8 139.6 1.0
SG A:CYS156 3.0 155.8 1.0
CB A:CYS156 3.2 155.8 1.0
CB A:CYS112 3.8 145.2 1.0
CB A:CYS159 3.9 154.3 1.0
N A:CYS112 4.0 145.2 1.0
CA A:CYS109 4.3 139.6 1.0
ND2 A:ASN163 4.4 150.5 1.0
CA A:CYS112 4.4 145.2 1.0
N A:CYS159 4.6 154.3 1.0
CA A:CYS156 4.7 155.8 1.0
CB A:ALA161 4.8 149.4 1.0
CA A:CYS159 4.8 154.3 1.0
N A:ALA161 4.8 149.4 1.0
N A:GLY160 4.8 153.2 1.0
CB A:THR111 4.8 140.9 1.0
N A:THR111 4.9 140.9 1.0
C A:THR111 5.0 140.9 1.0

Zinc binding site 3 out of 7 in 7aea

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Zinc binding site 3 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:129.0
occ:1.00
SG B:CYS1092 2.5 118.6 1.0
SG B:CYS1095 2.5 124.1 1.0
SG B:CYS1080 2.5 109.8 1.0
SG B:CYS1083 2.9 111.9 1.0
CB B:CYS1080 3.4 109.8 1.0
CB B:CYS1095 3.4 124.1 1.0
CB B:CYS1092 3.7 118.6 1.0
N B:CYS1095 4.1 124.1 1.0
CB B:CYS1083 4.1 111.9 1.0
CD2 B:TYR1094 4.3 113.1 1.0
N B:CYS1083 4.3 111.9 1.0
CA B:CYS1095 4.4 124.1 1.0
OE1 B:GLN1082 4.5 115.9 1.0
CB B:TYR1094 4.6 113.1 1.0
CB B:GLN1082 4.6 115.9 1.0
CA B:CYS1083 4.8 111.9 1.0
CA B:CYS1080 4.9 109.8 1.0
CG B:TYR1094 5.0 113.1 1.0

Zinc binding site 4 out of 7 in 7aea

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:247.0
occ:1.00
N I:CYS98 2.8 234.5 1.0
C I:CYS97 2.9 231.8 1.0
CB I:CYS97 2.9 231.8 1.0
N I:ASN99 3.0 239.1 1.0
SG I:CYS97 3.1 231.8 1.0
C I:CYS98 3.1 234.5 1.0
CA I:CYS98 3.3 234.5 1.0
CB I:ASN99 3.3 239.1 1.0
CA I:CYS97 3.4 231.8 1.0
O I:CYS97 3.4 231.8 1.0
SG I:CYS72 3.6 227.3 1.0
CA I:ASN99 3.7 239.1 1.0
O I:CYS98 3.8 234.5 1.0
O I:ARG76 4.0 226.8 1.0
O I:CYS102 4.1 237.3 1.0
SG I:CYS102 4.1 237.3 1.0
CG I:ASN99 4.5 239.1 1.0
CB I:CYS102 4.7 237.3 1.0
N I:CYS97 4.7 231.8 1.0
CB I:CYS98 4.8 234.5 1.0
CB I:CYS72 4.8 227.3 1.0
C I:ASN99 4.9 239.1 1.0
ND2 I:ASN99 4.9 239.1 1.0
C I:CYS102 4.9 237.3 1.0

Zinc binding site 5 out of 7 in 7aea

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:124.5
occ:1.00
SG I:CYS8 2.5 106.2 1.0
SG I:CYS28 2.5 121.2 1.0
SG I:CYS5 2.5 108.0 1.0
SG I:CYS25 2.6 119.7 1.0
CB I:CYS5 2.7 108.0 1.0
CB I:CYS25 3.0 119.7 1.0
CB I:CYS28 3.8 121.2 1.0
CB I:CYS8 3.9 106.2 1.0
N I:CYS8 4.0 106.2 1.0
CA I:CYS5 4.2 108.0 1.0
CA I:CYS25 4.4 119.7 1.0
CA I:CYS8 4.5 106.2 1.0
N I:CYS28 4.6 121.2 1.0
OG1 I:THR27 4.6 114.5 1.0
N I:GLY9 4.6 103.4 1.0
CB I:TYR30 4.6 117.7 1.0
N I:ASN10 4.7 101.7 1.0
CA I:CYS28 4.7 121.2 1.0
CB I:ASN10 4.8 101.7 1.0
C I:CYS8 4.9 106.2 1.0
C I:CYS5 4.9 108.0 1.0
CD2 I:LEU12 5.0 115.2 1.0
N I:CYS5 5.0 108.0 1.0

Zinc binding site 6 out of 7 in 7aea

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:77.0
occ:1.00
SG J:CYS7 2.4 56.5 1.0
SG J:CYS45 2.4 59.6 1.0
SG J:CYS10 2.5 57.1 1.0
SG J:CYS44 2.5 57.9 1.0
CB J:CYS7 3.1 56.5 1.0
N J:CYS45 3.3 59.6 1.0
CB J:CYS45 3.6 59.6 1.0
CA J:CYS45 3.6 59.6 1.0
C J:CYS44 3.6 57.9 1.0
CB J:CYS44 3.7 57.9 1.0
CB J:CYS10 3.7 57.1 1.0
N J:CYS10 3.9 57.1 1.0
O J:CYS44 4.1 57.9 1.0
CA J:CYS44 4.3 57.9 1.0
CA J:CYS10 4.3 57.1 1.0
N J:GLY11 4.4 56.1 1.0
NH2 J:ARG42 4.5 58.3 1.0
CA J:CYS7 4.5 56.5 1.0
NE J:ARG42 4.7 58.3 1.0
CB J:THR9 4.8 54.2 1.0
N J:LYS12 4.8 55.1 1.0
CB J:LYS12 4.8 55.1 1.0
C J:CYS7 4.9 56.5 1.0
N J:THR9 4.9 54.2 1.0
C J:CYS10 4.9 57.1 1.0
C J:THR9 4.9 54.2 1.0
N J:CYS44 5.0 57.9 1.0

Zinc binding site 7 out of 7 in 7aea

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:117.6
occ:1.00
SG L:CYS22 2.5 92.6 1.0
SG L:CYS36 2.5 97.4 1.0
SG L:CYS19 2.5 85.4 1.0
CB L:CYS36 3.0 97.4 1.0
CB L:CYS39 3.1 109.1 1.0
CB L:CYS22 3.5 92.6 1.0
CB L:CYS19 3.7 85.4 1.0
SG L:CYS39 3.7 109.1 1.0
N L:CYS39 3.8 109.1 1.0
CA L:CYS39 3.9 109.1 1.0
N L:CYS22 4.0 92.6 1.0
CB L:TYR41 4.1 88.4 1.0
C L:CYS39 4.3 109.1 1.0
CA L:CYS22 4.4 92.6 1.0
OG1 L:THR24 4.5 92.8 1.0
CA L:CYS36 4.5 97.4 1.0
N L:TYR41 4.5 88.4 1.0
O L:CYS39 4.6 109.1 1.0
O L:TYR41 4.8 88.4 1.0
CA L:TYR41 4.9 88.4 1.0
C L:GLU38 4.9 104.5 1.0
CB L:GLU21 5.0 93.4 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 16:16:21 2021

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