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Zinc in PDB 6rwe: Rna Polymerase I Open Complex Conformation 2

Enzymatic activity of Rna Polymerase I Open Complex Conformation 2

All present enzymatic activity of Rna Polymerase I Open Complex Conformation 2:
2.7.7.6;

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase I Open Complex Conformation 2 (pdb code 6rwe). 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 2, PDB code: 6rwe:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6rwe

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1701

b:83.1
occ:1.00
 SG A:CYS65 2.5 74.9 1.0
SG A:CYS62 2.5 86.4 1.0
CB A:CYS65 2.8 74.9 1.0
CB A:CYS62 2.9 86.4 1.0
CB A:CYS72 3.0 84.6 1.0
NE2 A:HIS75 3.5 71.6 1.0
CD2 A:HIS75 3.5 71.6 1.0
N A:CYS65 3.6 74.9 1.0
CA A:CYS65 3.8 74.9 1.0
CA A:GLY55 3.9 82.7 1.0
CA A:CYS72 3.9 84.6 1.0
SG A:CYS72 4.1 84.6 1.0
N A:ALA56 4.3 88.8 1.0
N A:GLY74 4.4 75.8 1.0
N A:GLY55 4.4 82.7 1.0
CA A:CYS62 4.5 86.4 1.0
CD A:PRO73 4.5 77.5 1.0
C A:GLY55 4.5 82.7 1.0
C A:CYS72 4.6 84.6 1.0
N A:PRO73 4.6 77.5 1.0
CE1 A:HIS75 4.7 71.6 1.0
C A:THR64 4.8 76.1 1.0
C A:CYS65 4.8 74.9 1.0
CG A:HIS75 4.8 71.6 1.0
CA A:GLY74 4.9 75.8 1.0
CB A:THR64 4.9 76.1 1.0

Zinc binding site 2 out of 8 in 6rwe

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:0.2
occ:1.00
 SG A:CYS102 2.4 0.5 1.0
SG A:CYS105 2.5 0.4 1.0
SG A:CYS233 2.5 0.3 1.0
SG A:CYS236 2.5 0.2 1.0
CB A:CYS233 2.6 0.3 1.0
CB A:CYS105 3.2 0.4 1.0
CB A:CYS102 3.3 0.5 1.0
O A:MET238 3.7 1.0 1.0
N A:CYS105 3.9 0.4 1.0
CA A:CYS233 4.1 0.3 1.0
CB A:CYS236 4.2 0.2 1.0
CA A:CYS105 4.2 0.4 1.0
N A:CYS236 4.5 0.2 1.0
CA A:CYS102 4.7 0.5 1.0
CA A:CYS236 4.7 0.2 1.0
N A:CYS233 4.8 0.3 1.0
CB A:PHE104 4.8 0.0 1.0
C A:PHE104 4.9 0.0 1.0
C A:CYS236 4.9 0.2 1.0
C A:MET238 4.9 1.0 1.0
C A:CYS233 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 6rwe

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Zinc binding site 3 out of 8 in the Rna Polymerase I Open Complex Conformation 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:74.8
occ:1.00
 SG B:CYS1131 2.4 75.8 1.0
SG B:CYS1107 2.4 66.7 1.0
SG B:CYS1104 2.5 64.6 1.0
SG B:CYS1128 2.5 73.8 1.0
CB B:CYS1104 3.1 64.6 1.0
CB B:CYS1107 3.1 66.7 1.0
CB B:CYS1128 3.3 73.8 1.0
CB B:CYS1131 3.3 75.8 1.0
N B:CYS1107 3.5 66.7 1.0
CA B:CYS1107 3.9 66.7 1.0
N B:CYS1131 4.0 75.8 1.0
CA B:CYS1131 4.2 75.8 1.0
CA B:CYS1104 4.5 64.6 1.0
C B:GLU1106 4.6 70.9 1.0
CB B:GLU1106 4.6 70.9 1.0
OG B:SER1109 4.7 66.7 1.0
CA B:CYS1128 4.8 73.8 1.0
CG B:ARG1130 4.8 71.7 1.0
C B:CYS1107 4.8 66.7 1.0
N B:GLY1108 4.9 66.5 1.0
N B:GLU1106 5.0 70.9 1.0
C B:ARG1130 5.0 71.7 1.0
CA B:GLU1106 5.0 70.9 1.0

Zinc binding site 4 out of 8 in 6rwe

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Zinc binding site 4 out of 8 in the Rna Polymerase I Open Complex Conformation 2


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

b:0.7
occ:1.00
 SG I:CYS13 2.5 89.4 1.0
CB I:CYS30 2.5 0.2 1.0
SG I:CYS10 2.6 88.3 1.0
SG I:CYS30 2.9 0.2 1.0
CB I:CYS33 3.0 0.5 1.0
CB I:CYS10 3.2 88.3 1.0
O I:CYS33 3.2 0.5 1.0
N I:CYS33 3.6 0.5 1.0
CA I:CYS33 3.7 0.5 1.0
C I:CYS33 3.9 0.5 1.0
SG I:CYS33 3.9 0.5 1.0
CB I:CYS13 4.0 89.4 1.0
CA I:CYS30 4.0 0.2 1.0
N I:CYS13 4.3 89.4 1.0
N I:CYS30 4.5 0.2 1.0
CB I:ASP15 4.7 86.3 1.0
CA I:CYS10 4.7 88.3 1.0
CA I:CYS13 4.7 89.4 1.0
C I:CYS30 4.7 0.2 1.0
CB I:ALA35 4.7 0.4 1.0
C I:GLN32 4.9 0.3 1.0

Zinc binding site 5 out of 8 in 6rwe

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Zinc binding site 5 out of 8 in the Rna Polymerase I Open Complex Conformation 2


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

b:0.2
occ:0.75
 SG I:CYS117 2.5 1.0 1.0
SG I:CYS114 2.5 0.2 1.0
SG I:CYS89 2.5 0.7 1.0
SG I:CYS86 2.5 0.3 1.0
CB I:CYS86 3.4 0.3 1.0
CB I:CYS114 3.4 0.2 1.0
CB I:CYS117 3.5 1.0 1.0
CB I:ASN91 4.0 0.0 1.0
CB I:CYS89 4.0 0.7 1.0
N I:CYS117 4.1 1.0 1.0
N I:CYS89 4.4 0.7 1.0
CA I:CYS117 4.4 1.0 1.0
N I:ASN91 4.7 0.0 1.0
CA I:CYS89 4.8 0.7 1.0
CA I:CYS86 4.8 0.3 1.0
ND2 I:ASN91 4.8 0.0 1.0
N I:GLY118 4.9 0.4 1.0
CA I:CYS114 4.9 0.2 1.0
CA I:ASN91 5.0 0.0 1.0
CG I:ASN91 5.0 0.0 1.0

Zinc binding site 6 out of 8 in 6rwe

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Zinc binding site 6 out of 8 in the Rna Polymerase I Open Complex Conformation 2


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

b:55.4
occ:1.00
 SG J:CYS10 2.4 40.8 1.0
SG J:CYS45 2.4 39.9 1.0
SG J:CYS7 2.4 40.0 1.0
N J:CYS46 2.5 39.0 1.0
CB J:CYS46 2.5 39.0 1.0
CA J:CYS46 2.7 39.0 1.0
CB J:CYS7 3.0 40.0 1.0
C J:CYS45 3.3 39.9 1.0
SG J:CYS46 3.4 39.0 1.0
CB J:CYS45 3.5 39.9 1.0
CB J:CYS10 3.5 40.8 1.0
CA J:CYS45 4.0 39.9 1.0
N J:CYS10 4.0 40.8 1.0
O J:CYS45 4.1 39.9 1.0
C J:CYS46 4.2 39.0 1.0
CA J:CYS10 4.3 40.8 1.0
N J:GLY11 4.5 38.0 1.0
CA J:CYS7 4.5 40.0 1.0
NE J:ARG43 4.6 39.2 1.0
N J:CYS45 4.6 39.9 1.0
NH2 J:ARG43 4.8 39.2 1.0
N J:ARG47 4.9 39.4 1.0
N J:LYS12 4.9 37.7 1.0
C J:CYS10 5.0 40.8 1.0

Zinc binding site 7 out of 8 in 6rwe

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Zinc binding site 7 out of 8 in the Rna Polymerase I Open Complex Conformation 2


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

b:66.5
occ:1.00
 SG L:CYS51 2.4 59.2 1.0
SG L:CYS34 2.4 56.7 1.0
SG L:CYS31 2.4 54.2 1.0
SG L:CYS48 2.4 59.3 1.0
CB L:CYS48 2.9 59.3 1.0
CB L:CYS31 3.1 54.2 1.0
CB L:CYS34 3.5 56.7 1.0
N L:CYS34 3.7 56.7 1.0
CB L:CYS51 3.8 59.2 1.0
N L:CYS51 4.0 59.2 1.0
OG L:SER36 4.1 57.2 1.0
CA L:CYS34 4.1 56.7 1.0
CA L:CYS51 4.4 59.2 1.0
CA L:CYS48 4.4 59.3 1.0
CA L:CYS31 4.5 54.2 1.0
CB L:HIS53 4.6 60.0 1.0
CB L:GLU33 4.6 62.2 1.0
C L:CYS51 4.8 59.2 1.0
C L:CYS34 4.8 56.7 1.0
C L:GLU33 4.8 62.2 1.0
N L:SER35 4.9 53.5 1.0
N L:GLU33 4.9 62.2 1.0
O L:CYS51 5.0 59.2 1.0

Zinc binding site 8 out of 8 in 6rwe

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Zn601

b:0.8
occ:1.00
 ND2 Q:ASN14 2.1 0.1 1.0
CD2 Q:HIS33 2.3 90.0 1.0
SG Q:CYS10 2.5 0.3 1.0
CB Q:HIS33 2.5 90.0 1.0
CG Q:HIS33 2.6 90.0 1.0
SG Q:CYS29 2.7 98.8 1.0
CG Q:ASN14 2.9 0.1 1.0
CB Q:ASN14 3.4 0.1 1.0
CB Q:CYS29 3.5 98.8 1.0
NE2 Q:HIS33 3.6 90.0 1.0
CB Q:CYS10 3.6 0.3 1.0
OD1 Q:ASN14 3.7 0.1 1.0
ND1 Q:HIS33 3.8 90.0 1.0
CA Q:HIS33 3.8 90.0 1.0
OG1 Q:THR12 4.0 0.5 1.0
N Q:HIS33 4.1 90.0 1.0
O Q:GLY11 4.2 0.2 1.0
CE1 Q:HIS33 4.2 90.0 1.0
O Q:HIS33 4.3 90.0 1.0
C Q:HIS33 4.5 90.0 1.0
CA Q:ASN14 4.8 0.1 1.0
CA Q:CYS29 4.9 98.8 1.0
CA Q:CYS10 5.0 0.3 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 06:47:54 2024

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