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Zinc in PDB 6ruo: Rna Polymerase I Open Complex Conformation 1

Enzymatic activity of Rna Polymerase I Open Complex Conformation 1

All present enzymatic activity of Rna Polymerase I Open Complex Conformation 1:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I Open Complex Conformation 1 (pdb code 6ruo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase I Open Complex Conformation 1, PDB code: 6ruo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6ruo

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Zinc binding site 1 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn601

b:0.4
occ:1.00
 O Q:THR12 2.2 0.5 1.0
O Q:ASP13 2.2 0.3 1.0
C Q:ASP13 2.5 0.3 1.0
CB Q:ASP13 2.6 0.3 1.0
CA Q:ASP13 2.8 0.3 1.0
C Q:THR12 3.0 0.5 1.0
N Q:ASP13 3.3 0.3 1.0
NH1 D:ARG6 3.4 1.0 1.0
N Q:ASN14 3.5 0.4 1.0
CG Q:ASP13 4.0 0.3 1.0
CA Q:ASN14 4.3 0.4 1.0
CA Q:THR12 4.5 0.5 1.0
OD2 Q:ASP13 4.5 0.3 1.0
CZ D:ARG6 4.7 1.0 1.0
OD1 Q:ASP13 4.9 0.3 1.0

Zinc binding site 2 out of 8 in 6ruo

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Zinc binding site 2 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:0.5
occ:1.00
 NE2 A:HIS75 2.2 0.7 1.0
CD2 A:HIS75 2.3 0.7 1.0
SG A:CYS62 2.4 0.3 1.0
SG A:CYS65 2.5 0.7 1.0
N A:CYS65 2.5 0.7 1.0
CB A:CYS65 3.1 0.7 1.0
CA A:CYS65 3.3 0.7 1.0
C A:THR64 3.4 0.1 1.0
CE1 A:HIS75 3.5 0.7 1.0
CB A:THR64 3.6 0.1 1.0
CG A:HIS75 3.7 0.7 1.0
CA A:THR64 3.7 0.1 1.0
N A:THR64 3.7 0.1 1.0
CB A:CYS62 3.9 0.3 1.0
N A:GLY55 3.9 0.5 1.0
CA A:GLY55 4.2 0.5 1.0
ND1 A:HIS75 4.2 0.7 1.0
O A:THR64 4.4 0.1 1.0
OG1 A:THR64 4.5 0.1 1.0
CG2 A:THR64 4.5 0.1 1.0
C A:CYS65 4.6 0.7 1.0
O A:ALA53 4.7 0.6 1.0
CB A:HIS75 4.9 0.7 1.0
C A:SER63 4.9 0.5 1.0
N A:GLY66 4.9 0.4 1.0
N A:SER63 4.9 0.5 1.0
CB A:CYS72 4.9 0.8 1.0

Zinc binding site 3 out of 8 in 6ruo

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Zinc binding site 3 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:0.1
occ:1.00
 SG A:CYS105 2.5 0.3 1.0
SG A:CYS236 2.5 0.3 1.0
SG A:CYS233 2.5 0.1 1.0
CB A:CYS105 2.6 0.3 1.0
N A:CYS236 2.9 0.3 1.0
CB A:CYS236 3.0 0.3 1.0
CB A:CYS233 3.4 0.1 1.0
C A:ASN235 3.4 0.6 1.0
CA A:CYS236 3.4 0.3 1.0
O A:ASN235 4.0 0.6 1.0
CA A:CYS105 4.1 0.3 1.0
CA A:ASN235 4.1 0.6 1.0
N A:ASN235 4.1 0.6 1.0
CB A:ASN235 4.2 0.6 1.0
C A:CYS236 4.2 0.3 1.0
O A:CYS236 4.3 0.3 1.0
N A:CYS105 4.6 0.3 1.0
O A:PHE108 4.7 0.3 1.0
SG A:CYS102 4.7 0.8 1.0
O A:MET238 4.8 0.9 1.0
CA A:CYS233 4.8 0.1 1.0
N A:ASP234 4.8 0.6 1.0
C A:CYS105 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 6ruo

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Zinc binding site 4 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.3
occ:1.00
 NH1 B:ARG1130 2.3 0.4 1.0
CZ B:ARG1130 2.3 0.4 1.0
SG B:CYS1107 2.5 0.7 1.0
OG B:SER1109 2.6 0.1 1.0
NE B:ARG1130 2.7 0.4 1.0
CG B:ARG1130 2.7 0.4 1.0
OG1 B:THR1112 2.8 0.4 1.0
CD B:ARG1130 3.0 0.4 1.0
NH2 B:ARG1130 3.1 0.4 1.0
CB B:SER1109 3.2 0.1 1.0
CB B:CYS1107 3.5 0.7 1.0
SG B:CYS1128 3.8 0.7 1.0
CB B:THR1112 4.0 0.4 1.0
CB B:ARG1130 4.0 0.4 1.0
CG2 B:THR1112 4.3 0.4 1.0
CA B:SER1109 4.4 0.1 1.0
N B:SER1109 4.4 0.1 1.0
N B:ARG1130 4.5 0.4 1.0
C B:CYS1107 4.6 0.7 1.0
CA B:CYS1107 4.7 0.7 1.0
O B:CYS1107 4.7 0.7 1.0
CA B:ARG1130 4.8 0.4 1.0
C B:GLY1108 4.9 1.0 1.0
N B:GLY1108 5.0 1.0 1.0

Zinc binding site 5 out of 8 in 6ruo

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Zinc binding site 5 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.6
occ:1.00
 CB I:CYS33 2.5 0.4 1.0
SG I:CYS13 2.5 0.7 1.0
CB I:CYS30 2.5 0.4 1.0
SG I:CYS30 2.7 0.4 1.0
SG I:CYS10 3.1 0.6 1.0
CA I:CYS33 3.4 0.4 1.0
N I:CYS33 3.5 0.4 1.0
SG I:CYS33 3.6 0.4 1.0
O I:CYS33 3.6 0.4 1.0
CB I:CYS10 3.7 0.6 1.0
CB I:CYS13 3.9 0.7 1.0
C I:CYS33 3.9 0.4 1.0
CA I:CYS30 4.0 0.4 1.0
CB I:ALA35 4.6 0.0 1.0
N I:CYS30 4.6 0.4 1.0
N I:CYS13 4.6 0.7 1.0
CB I:ASP15 4.7 0.2 1.0
C I:CYS30 4.7 0.4 1.0
C I:GLN32 4.8 0.1 1.0
CA I:CYS13 4.8 0.7 1.0

Zinc binding site 6 out of 8 in 6ruo

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Zinc binding site 6 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.4
occ:0.75
 SG I:CYS117 2.5 0.1 1.0
SG I:CYS89 2.5 0.9 1.0
SG I:CYS86 2.5 0.4 1.0
CB I:CYS117 3.0 0.1 1.0
SG I:CYS114 3.6 0.5 1.0
CB I:ASN91 3.6 0.5 1.0
CB I:CYS86 3.7 0.4 1.0
CB I:CYS89 3.9 0.9 1.0
N I:CYS117 4.1 0.1 1.0
CB I:CYS114 4.1 0.5 1.0
CA I:CYS117 4.1 0.1 1.0
N I:CYS89 4.1 0.9 1.0
ND2 I:ASN91 4.3 0.5 1.0
CG I:ASN91 4.5 0.5 1.0
CA I:CYS89 4.6 0.9 1.0
CE I:MET94 4.6 0.2 1.0
N I:ASN91 4.6 0.5 1.0
CB I:GLN88 4.7 0.8 1.0
CA I:ASN91 4.8 0.5 1.0
OE1 I:GLN88 4.9 0.8 1.0
C I:GLN88 4.9 0.8 1.0
O I:TYR119 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 6ruo

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Zinc binding site 7 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:81.4
occ:1.00
 SG J:CYS10 2.4 66.6 1.0
SG J:CYS45 2.5 69.1 1.0
SG J:CYS7 2.5 70.9 1.0
CB J:CYS46 2.5 72.1 1.0
N J:CYS46 2.9 72.1 1.0
SG J:CYS46 3.0 72.1 1.0
CB J:CYS7 3.0 70.9 1.0
CB J:CYS10 3.1 66.6 1.0
CA J:CYS46 3.2 72.1 1.0
C J:CYS45 3.6 69.1 1.0
CB J:CYS45 3.8 69.1 1.0
N J:CYS10 3.8 66.6 1.0
CA J:CYS10 4.1 66.6 1.0
CA J:CYS45 4.3 69.1 1.0
O J:CYS45 4.3 69.1 1.0
CA J:CYS7 4.5 70.9 1.0
C J:CYS46 4.6 72.1 1.0
NE J:ARG43 4.6 67.1 1.0
N J:GLY11 4.7 60.0 1.0
NH2 J:ARG43 4.7 67.1 1.0
O J:ARG43 4.8 67.1 1.0
N J:CYS45 4.8 69.1 1.0
CB J:ARG43 4.9 67.1 1.0
C J:SER9 5.0 69.6 1.0
C J:CYS10 5.0 66.6 1.0

Zinc binding site 8 out of 8 in 6ruo

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Zinc binding site 8 out of 8 in the Rna Polymerase I Open Complex Conformation 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase I Open Complex Conformation 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:80.9
occ:1.00
 SG L:CYS51 2.4 71.9 1.0
SG L:CYS31 2.5 76.7 1.0
SG L:CYS34 2.5 80.8 1.0
SG L:CYS48 2.6 77.7 1.0
CB L:CYS48 3.0 77.7 1.0
OG L:SER36 3.4 74.4 1.0
CB L:CYS31 3.4 76.7 1.0
N L:CYS51 3.4 71.9 1.0
O L:CYS51 3.6 71.9 1.0
CB L:CYS51 3.7 71.9 1.0
CB L:CYS34 4.0 80.8 1.0
CA L:CYS51 4.0 71.9 1.0
C L:CYS51 4.2 71.9 1.0
CB L:SER36 4.4 74.4 1.0
CA L:CYS48 4.4 77.7 1.0
N L:CYS34 4.4 80.8 1.0
C L:ASP50 4.4 84.7 1.0
N L:ASP50 4.4 84.7 1.0
CB L:ASP50 4.4 84.7 1.0
C L:CYS48 4.7 77.7 1.0
CA L:ASP50 4.7 84.7 1.0
CA L:CYS34 4.7 80.8 1.0
CA L:CYS31 4.8 76.7 1.0
CB L:HIS53 4.8 74.7 1.0
N L:LYS49 4.9 82.0 1.0
N L:SER36 5.0 74.4 1.0

Reference:

Y.Sadian, F.Baudin, L.Tafur, B.Murciano, R.Wetzel, F.Weis, C.W.Muller. Molecular Insight Into Rna Polymerase I Promoter Recognition and Promoter Melting. Nat Commun V. 10 5543 2019.
ISSN: ESSN 2041-1723
PubMed: 31804486
DOI: 10.1038/S41467-019-13510-W
Page generated: Tue Oct 29 06:46:49 2024

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