Zinc in PDB 6eu2: Apo Rna Polymerase III - Open Conformation (OPOL3)

Enzymatic activity of Apo Rna Polymerase III - Open Conformation (OPOL3)

All present enzymatic activity of Apo Rna Polymerase III - Open Conformation (OPOL3):
2.7.7.6;

Other elements in 6eu2:

The structure of Apo Rna Polymerase III - Open Conformation (OPOL3) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Apo Rna Polymerase III - Open Conformation (OPOL3) (pdb code 6eu2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Apo Rna Polymerase III - Open Conformation (OPOL3), PDB code: 6eu2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6eu2

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Zinc binding site 1 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:82.1
occ:1.00
CE1 A:HIS80 2.4 45.2 1.0
SG A:CYS70 2.5 66.9 1.0
ND1 A:HIS80 2.9 45.2 1.0
SG A:CYS67 3.1 67.2 1.0
NE2 A:HIS80 3.6 45.2 1.0
SG A:CYS77 3.6 66.2 1.0
CB A:CYS77 3.6 66.2 1.0
OG1 A:THR69 3.7 64.4 1.0
CB A:CYS67 3.9 67.2 1.0
CB A:CYS70 4.2 66.9 1.0
CG A:HIS80 4.3 45.2 1.0
CA A:CYS77 4.3 66.2 1.0
O A:CYS70 4.3 66.9 1.0
N A:CYS70 4.4 66.9 1.0
CD2 A:HIS80 4.6 45.2 1.0
N A:GLY79 4.6 45.4 1.0
CA A:GLY59 4.6 56.5 1.0
N A:HIS78 4.7 46.8 1.0
CA A:CYS70 4.7 66.9 1.0
C A:CYS77 4.8 66.2 1.0
O A:MET58 5.0 57.0 1.0
C A:CYS70 5.0 66.9 1.0

Zinc binding site 2 out of 6 in 6eu2

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Zinc binding site 2 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:82.4
occ:1.00
SG A:CYS154 2.5 68.3 1.0
SG A:CYS157 2.5 70.2 1.0
SG A:CYS107 2.5 48.5 1.0
CB A:CYS110 2.6 53.6 1.0
N A:CYS110 3.1 53.6 1.0
CB A:CYS107 3.2 48.5 1.0
CB A:CYS154 3.3 68.3 1.0
CA A:CYS110 3.4 53.6 1.0
CB A:CYS157 3.9 70.2 1.0
SG A:CYS110 4.1 53.6 1.0
C A:ASN109 4.2 54.5 1.0
N A:CYS157 4.2 70.2 1.0
CB A:ASN109 4.3 54.5 1.0
C A:CYS110 4.3 53.6 1.0
N A:SER111 4.5 44.2 1.0
N A:ASN109 4.6 54.5 1.0
CA A:ASN109 4.6 54.5 1.0
CA A:CYS157 4.6 70.2 1.0
CA A:CYS107 4.6 48.5 1.0
CA A:CYS154 4.8 68.3 1.0
CB A:HIS156 4.9 67.0 1.0
C A:HIS156 4.9 67.0 1.0
C A:CYS107 5.0 48.5 1.0

Zinc binding site 3 out of 6 in 6eu2

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Zinc binding site 3 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:97.5
occ:1.00
O B:LYS1097 2.5 36.6 1.0
SG B:CYS1107 2.5 46.2 1.0
SG B:CYS1095 2.5 37.6 1.0
SG B:CYS1098 3.3 39.3 1.0
CB B:CYS1095 3.3 37.6 1.0
O B:CYS1098 3.6 39.3 1.0
C B:LYS1097 3.7 36.6 1.0
CB B:CYS1110 4.1 55.5 1.0
CB B:CYS1107 4.1 46.2 1.0
C B:CYS1098 4.2 39.3 1.0
CB B:CYS1098 4.5 39.3 1.0
N B:CYS1098 4.5 39.3 1.0
CA B:CYS1098 4.6 39.3 1.0
N B:CYS1110 4.7 55.5 1.0
CA B:LYS1097 4.7 36.6 1.0
CA B:CYS1095 4.7 37.6 1.0
N B:LYS1097 4.8 36.6 1.0
CB B:LYS1097 4.8 36.6 1.0

Zinc binding site 4 out of 6 in 6eu2

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Zinc binding site 4 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.3
occ:1.00
SG I:CYS29 2.5 90.9 1.0
SG I:CYS8 2.5 81.5 1.0
CB I:CYS5 2.5 84.8 1.0
N I:CYS8 3.1 81.5 1.0
SG I:CYS5 3.1 84.8 1.0
CB I:CYS8 3.5 81.5 1.0
CA I:CYS8 3.8 81.5 1.0
CB I:SER7 3.8 81.1 1.0
CA I:CYS5 3.8 84.8 1.0
N I:SER7 3.9 81.1 1.0
C I:SER7 3.9 81.1 1.0
CB I:CYS29 3.9 90.9 1.0
CA I:SER7 4.0 81.1 1.0
C I:CYS5 4.2 84.8 1.0
SG I:CYS26 4.3 88.2 1.0
N I:ASN9 4.3 70.7 1.0
C I:CYS8 4.4 81.5 1.0
OG I:SER7 4.6 81.1 1.0
O I:CYS5 4.6 84.8 1.0
N I:PRO6 4.7 77.0 1.0
CB I:TYR31 4.8 87.8 1.0
N I:ASN10 4.9 70.6 1.0
CB I:SER28 4.9 90.2 1.0
N I:CYS5 5.0 84.8 1.0
O I:SER7 5.0 81.1 1.0

Zinc binding site 5 out of 6 in 6eu2

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Zinc binding site 5 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:53.0
occ:1.00
SG J:CYS45 2.5 29.1 1.0
SG J:CYS10 2.5 24.1 1.0
SG J:CYS46 2.5 23.9 1.0
CB J:CYS10 3.3 24.1 1.0
N J:CYS10 3.3 24.1 1.0
NH2 J:ARG43 3.6 27.1 1.0
SG J:CYS7 3.7 27.5 1.0
CB J:CYS45 3.7 29.1 1.0
CA J:CYS10 3.9 24.1 1.0
NH1 J:ARG43 3.9 27.1 1.0
CZ J:ARG43 3.9 27.1 1.0
CB J:CYS46 4.1 23.9 1.0
CB J:SER9 4.1 23.1 1.0
N J:CYS46 4.1 23.9 1.0
C J:CYS45 4.2 29.1 1.0
CB J:CYS7 4.2 27.5 1.0
N J:GLY11 4.4 24.3 1.0
C J:SER9 4.4 23.1 1.0
CA J:CYS45 4.6 29.1 1.0
CA J:CYS46 4.6 23.9 1.0
O J:CYS45 4.6 29.1 1.0
CA J:SER9 4.6 23.1 1.0
N J:SER9 4.6 23.1 1.0
C J:CYS10 4.6 24.1 1.0
NE J:ARG43 4.8 27.1 1.0

Zinc binding site 6 out of 6 in 6eu2

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Zinc binding site 6 out of 6 in the Apo Rna Polymerase III - Open Conformation (OPOL3)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Apo Rna Polymerase III - Open Conformation (OPOL3) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.6
occ:1.00
SG L:CYS51 2.5 62.4 1.0
SG L:CYS34 2.5 58.4 1.0
SG L:CYS31 2.5 46.9 1.0
CB L:CYS31 2.9 46.9 1.0
SG L:CYS48 3.0 64.0 1.0
CB L:CYS48 3.1 64.0 1.0
CB L:CYS51 3.8 62.4 1.0
N L:CYS51 4.0 62.4 1.0
CB L:CYS34 4.0 58.4 1.0
OG L:SER36 4.0 53.5 1.0
N L:CYS34 4.4 58.4 1.0
CA L:CYS31 4.4 46.9 1.0
CA L:CYS51 4.4 62.4 1.0
CA L:CYS48 4.5 64.0 1.0
N L:GLY52 4.6 50.6 1.0
CB L:ASP50 4.7 69.3 1.0
CB L:HIS53 4.7 45.1 1.0
CA L:CYS34 4.7 58.4 1.0
N L:HIS53 4.8 45.1 1.0
CD2 L:LEU38 4.8 57.3 1.0
N L:ASP50 5.0 69.3 1.0

Reference:

G.Abascal-Palacios, E.P.Ramsay, F.Beuron, E.Morris, A.Vannini. Structural Basis of Rna Polymerase III Transcription Initiation. Nature V. 553 301 2018.
ISSN: ESSN 1476-4687
PubMed: 29345637
DOI: 10.1038/NATURE25441
Page generated: Wed Dec 16 11:44:36 2020

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