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Zinc in PDB 7ae3: Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3

Enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3

All present enzymatic activity of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3:
2.7.7.6;

Other elements in 7ae3:

The structure of Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3 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 3 (pdb code 7ae3). 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 3, PDB code: 7ae3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 7ae3

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


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

b:128.6
occ:1.00
 SG A:CYS79 2.5 114.4 1.0
SG A:CYS69 2.5 123.5 1.0
SG A:CYS72 2.5 119.0 1.0
CE1 A:HIS82 2.6 112.9 1.0
ND1 A:HIS82 3.0 112.9 1.0
CB A:CYS69 3.2 123.5 1.0
O A:CYS72 3.6 119.0 1.0
N A:CYS72 3.6 119.0 1.0
CB A:CYS79 3.7 114.4 1.0
CB A:CYS72 3.8 119.0 1.0
NE2 A:HIS82 3.8 112.9 1.0
CA A:CYS72 4.1 119.0 1.0
C A:CYS72 4.2 119.0 1.0
CG A:HIS82 4.4 112.9 1.0
CB A:THR71 4.4 117.8 1.0
N A:THR71 4.5 117.8 1.0
CA A:GLY61 4.6 121.7 1.0
CA A:CYS69 4.7 123.5 1.0
C A:THR71 4.7 117.8 1.0
CA A:CYS79 4.7 114.4 1.0
CD2 A:HIS82 4.7 112.9 1.0
CA A:THR71 4.8 117.8 1.0
N A:GLY61 4.9 121.7 1.0

Zinc binding site 2 out of 7 in 7ae3

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


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

b:165.8
occ:1.00
 SG A:CYS112 2.5 138.0 1.0
SG A:CYS159 2.5 148.3 1.0
SG A:CYS109 2.5 134.6 1.0
SG A:CYS156 2.5 147.4 1.0
CB A:CYS109 2.7 134.6 1.0
CB A:CYS156 2.9 147.4 1.0
CB A:CYS159 3.6 148.3 1.0
CB A:CYS112 3.9 138.0 1.0
N A:CYS159 4.0 148.3 1.0
CA A:CYS109 4.2 134.6 1.0
N A:CYS112 4.3 138.0 1.0
CA A:CYS159 4.4 148.3 1.0
CA A:CYS156 4.4 147.4 1.0
ND2 A:ASN163 4.6 137.8 1.0
CA A:CYS112 4.7 138.0 1.0
N A:GLY160 4.7 145.5 1.0
O A:HIS114 4.9 132.1 1.0
C A:CYS159 5.0 148.3 1.0

Zinc binding site 3 out of 7 in 7ae3

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


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

b:145.6
occ:1.00
 SG B:CYS1092 2.4 113.9 1.0
SG B:CYS1083 2.4 110.3 1.0
SG B:CYS1080 2.4 112.4 1.0
SG B:CYS1095 2.5 115.2 1.0
CB B:CYS1095 3.1 115.2 1.0
CB B:CYS1080 3.3 112.4 1.0
CB B:CYS1083 3.4 110.3 1.0
CB B:CYS1092 3.5 113.9 1.0
N B:CYS1095 3.7 115.2 1.0
N B:CYS1083 4.0 110.3 1.0
CA B:CYS1095 4.1 115.2 1.0
CD2 B:TYR1094 4.3 111.0 1.0
CA B:CYS1083 4.3 110.3 1.0
CB B:TYR1094 4.4 111.0 1.0
C B:TYR1094 4.7 111.0 1.0
CA B:CYS1080 4.7 112.4 1.0
CG B:TYR1094 4.9 111.0 1.0
CB B:GLN1082 4.9 114.8 1.0
CA B:CYS1092 4.9 113.9 1.0

Zinc binding site 4 out of 7 in 7ae3

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Zinc binding site 4 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3


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

b:130.2
occ:1.00
 SG I:CYS28 2.4 124.3 1.0
SG I:CYS8 2.4 114.9 1.0
SG I:CYS5 2.4 114.5 1.0
SG I:CYS25 2.5 123.0 1.0
CB I:CYS5 2.8 114.5 1.0
CB I:CYS25 3.0 123.0 1.0
CB I:CYS28 3.7 124.3 1.0
CB I:CYS8 3.9 114.9 1.0
N I:CYS8 3.9 114.9 1.0
CA I:CYS5 4.3 114.5 1.0
OG1 I:THR27 4.3 120.3 1.0
N I:CYS28 4.4 124.3 1.0
CA I:CYS8 4.4 114.9 1.0
CA I:CYS25 4.5 123.0 1.0
CA I:CYS28 4.6 124.3 1.0
N I:GLY9 4.6 113.2 1.0
CB I:TYR30 4.7 120.1 1.0
N I:ASN10 4.8 112.7 1.0
C I:CYS8 4.8 114.9 1.0
C I:CYS5 4.9 114.5 1.0
C I:GLY7 4.9 112.7 1.0
O I:CYS28 5.0 124.3 1.0

Zinc binding site 5 out of 7 in 7ae3

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Zinc binding site 5 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3


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

b:209.1
occ:1.00
 CB I:HIS104 2.6 194.9 1.0
CD2 I:HIS104 2.6 194.9 1.0
CG I:HIS104 2.8 194.9 1.0
CB I:CYS97 3.2 198.4 1.0
SG I:CYS72 3.2 197.1 1.0
SG I:CYS69 3.5 198.0 1.0
CE2 I:TYR95 3.7 190.7 1.0
CA I:HIS104 3.7 194.9 1.0
N I:HIS104 3.8 194.9 1.0
NE2 I:HIS104 3.9 194.9 1.0
CB I:LYS71 3.9 195.9 1.0
SG I:CYS97 4.0 198.4 1.0
CB I:CYS69 4.0 198.0 1.0
ND1 I:HIS104 4.1 194.9 1.0
CD2 I:TYR95 4.2 190.7 1.0
C I:HIS104 4.4 194.9 1.0
CA I:CYS97 4.4 198.4 1.0
N I:CYS72 4.4 197.1 1.0
O I:CYS97 4.5 198.4 1.0
O I:HIS104 4.5 194.9 1.0
CG I:LYS71 4.5 195.9 1.0
N I:CYS97 4.5 198.4 1.0
CB I:CYS72 4.5 197.1 1.0
CE1 I:HIS104 4.6 194.9 1.0
CZ I:TYR95 4.8 190.7 1.0
C I:CYS97 4.9 198.4 1.0
CA I:LYS71 4.9 195.9 1.0
OH I:TYR95 4.9 190.7 1.0

Zinc binding site 6 out of 7 in 7ae3

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Zinc binding site 6 out of 7 in the Cryo-Em Structure of Human Rna Polymerase III Elongation Complex 3


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

b:91.8
occ:1.00
 SG J:CYS44 2.4 75.2 1.0
SG J:CYS10 2.4 67.0 1.0
SG J:CYS45 2.4 73.8 1.0
SG J:CYS7 2.5 69.1 1.0
N J:CYS45 3.1 73.8 1.0
CB J:CYS7 3.1 69.1 1.0
CA J:CYS45 3.4 73.8 1.0
C J:CYS44 3.5 75.2 1.0
CB J:CYS45 3.5 73.8 1.0
CB J:CYS44 3.6 75.2 1.0
CB J:CYS10 3.8 67.0 1.0
O J:CYS44 3.9 75.2 1.0
N J:CYS10 3.9 67.0 1.0
CA J:CYS44 4.1 75.2 1.0
CA J:CYS10 4.4 67.0 1.0
NH2 J:ARG42 4.4 73.4 1.0
N J:GLY11 4.5 64.6 1.0
CA J:CYS7 4.6 69.1 1.0
CB J:THR9 4.7 65.1 1.0
NE J:ARG42 4.7 73.4 1.0
CB J:LYS12 4.9 64.2 1.0
N J:CYS44 4.9 75.2 1.0
N J:LYS12 4.9 64.2 1.0
C J:CYS45 4.9 73.8 1.0
N J:THR9 5.0 65.1 1.0
C J:THR9 5.0 65.1 1.0

Zinc binding site 7 out of 7 in 7ae3

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


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

b:127.5
occ:1.00
 SG L:CYS22 2.5 104.2 1.0
SG L:CYS36 2.5 108.0 1.0
SG L:CYS19 2.5 96.0 1.0
CB L:CYS39 2.9 115.1 1.0
CB L:CYS36 3.2 108.0 1.0
SG L:CYS39 3.4 115.1 1.0
CB L:CYS22 3.6 104.2 1.0
CB L:CYS19 3.6 96.0 1.0
N L:CYS39 3.7 115.1 1.0
CA L:CYS39 3.8 115.1 1.0
CB L:TYR41 4.0 100.3 1.0
N L:CYS22 4.1 104.2 1.0
C L:CYS39 4.4 115.1 1.0
CA L:CYS22 4.5 104.2 1.0
OG1 L:THR24 4.5 103.0 1.0
N L:TYR41 4.5 100.3 1.0
CA L:CYS36 4.7 108.0 1.0
CB L:GLU21 4.7 104.6 1.0
O L:CYS39 4.7 115.1 1.0
CA L:TYR41 4.9 100.3 1.0
C L:GLU38 4.9 114.5 1.0
N L:GLY40 5.0 107.6 1.0
N L:GLU21 5.0 104.6 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: Tue Oct 29 16:41:13 2024

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