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Zinc in PDB 6hls: Yeast Apo Rna Polymerase I*

Enzymatic activity of Yeast Apo Rna Polymerase I*

All present enzymatic activity of Yeast Apo Rna Polymerase I*:
2.7.7.6;

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 6hls

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Zinc binding site 1 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

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

b:59.8
occ:1.00
 NE2 A:HIS75 2.2 45.7 1.0
SG A:CYS72 2.4 50.9 1.0
SG A:CYS62 2.5 58.5 1.0
SG A:CYS65 2.5 53.7 1.0
CD2 A:HIS75 2.6 45.7 1.0
CB A:CYS62 3.3 58.5 1.0
CE1 A:HIS75 3.4 45.7 1.0
CB A:CYS65 3.7 53.7 1.0
CG A:HIS75 3.9 45.7 1.0
N A:CYS65 3.9 53.7 1.0
CB A:CYS72 4.0 50.9 1.0
ND1 A:HIS75 4.2 45.7 1.0
CA A:GLY55 4.3 53.0 1.0
CA A:CYS65 4.4 53.7 1.0
CB A:THR64 4.5 57.4 1.0
CD A:PRO73 4.5 49.9 1.0
CA A:CYS72 4.6 50.9 1.0
N A:GLY74 4.6 45.2 1.0
CA A:CYS62 4.8 58.5 1.0
N A:GLY55 4.8 53.0 1.0
N A:PRO73 4.9 49.9 1.0
C A:THR64 4.9 57.4 1.0
C A:CYS72 5.0 50.9 1.0
N A:ALA56 5.0 55.8 1.0

Zinc binding site 2 out of 7 in 6hls

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Zinc binding site 2 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:0.5
occ:1.00
 SG A:CYS102 2.5 74.2 1.0
SG A:CYS233 2.5 81.5 1.0
SG A:CYS236 2.6 89.2 1.0
CB A:CYS233 2.6 81.5 1.0
CB A:CYS102 2.6 74.2 1.0
SG A:CYS105 2.8 73.1 1.0
O A:CYS236 3.9 89.2 1.0
CB A:CYS105 4.0 73.1 1.0
N A:CYS105 4.0 73.1 1.0
CA A:CYS233 4.1 81.5 1.0
CA A:CYS102 4.1 74.2 1.0
CB A:CYS236 4.2 89.2 1.0
N A:CYS236 4.4 89.2 1.0
CA A:CYS105 4.6 73.1 1.0
CA A:CYS236 4.7 89.2 1.0
C A:CYS236 4.7 89.2 1.0
C A:CYS102 4.7 74.2 1.0
CB A:PHE104 4.8 78.2 1.0
N A:CYS233 4.8 81.5 1.0
N A:CYS102 4.9 74.2 1.0
SD A:MET238 4.9 92.8 1.0
C A:CYS233 4.9 81.5 1.0
N A:PHE104 4.9 78.2 1.0
N A:HIS106 5.0 71.9 1.0

Zinc binding site 3 out of 7 in 6hls

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Zinc binding site 3 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:70.2
occ:1.00
 SG B:CYS1107 2.4 44.0 1.0
SG B:CYS1104 2.6 36.6 1.0
SG B:CYS1128 2.8 51.1 1.0
CB B:CYS1131 3.0 55.6 1.0
CG B:GLU1106 3.3 42.2 1.0
OE2 B:GLU1106 3.5 42.2 1.0
CB B:CYS1128 3.7 51.1 1.0
N B:CYS1131 3.7 55.6 1.0
SG B:CYS1131 3.7 55.6 1.0
CB B:CYS1107 3.7 44.0 1.0
N B:CYS1107 3.8 44.0 1.0
CA B:CYS1131 3.8 55.6 1.0
CD B:GLU1106 3.9 42.2 1.0
CB B:CYS1104 3.9 36.6 1.0
CA B:CYS1107 4.3 44.0 1.0
C B:CYS1131 4.5 55.6 1.0
C B:GLU1106 4.6 42.2 1.0
CB B:GLU1106 4.6 42.2 1.0
O B:CYS1131 4.6 55.6 1.0
C B:ARG1130 4.9 49.9 1.0
N B:GLU1106 4.9 42.2 1.0
CA B:GLU1106 4.9 42.2 1.0
CB B:ARG1130 5.0 49.9 1.0

Zinc binding site 4 out of 7 in 6hls

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Zinc binding site 4 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.1
occ:1.00
 SG I:CYS13 2.5 63.1 1.0
SG I:CYS30 2.5 77.3 1.0
CB I:CYS33 2.6 79.5 1.0
N I:CYS33 2.7 79.5 1.0
SG I:CYS33 3.1 79.5 1.0
CA I:CYS33 3.1 79.5 1.0
CB I:CYS30 3.2 77.3 1.0
SG I:CYS10 3.7 62.5 1.0
CB I:CYS13 3.7 63.1 1.0
C I:GLN32 3.9 71.5 1.0
C I:CYS33 4.0 79.5 1.0
N I:LYS34 4.1 79.3 1.0
CB I:GLN32 4.2 71.5 1.0
N I:GLN32 4.3 71.5 1.0
CB I:CYS10 4.3 62.5 1.0
CA I:GLN32 4.3 71.5 1.0
CA I:CYS30 4.6 77.3 1.0
N I:ALA35 4.8 79.4 1.0
C I:CYS30 4.9 77.3 1.0
N I:CYS13 4.9 63.1 1.0
CB I:ALA35 4.9 79.4 1.0
CB I:ASP15 4.9 58.3 1.0
CA I:CYS13 4.9 63.1 1.0
O I:GLN32 4.9 71.5 1.0
O I:CYS33 5.0 79.5 1.0

Zinc binding site 5 out of 7 in 6hls

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Zinc binding site 5 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3002

b:0.6
occ:0.75
 CB I:SER116 2.5 0.4 1.0
SG I:CYS89 2.5 0.5 1.0
N I:CYS117 2.5 0.6 1.0
SG I:CYS114 2.6 0.0 1.0
CA I:SER116 3.1 0.4 1.0
C I:SER116 3.1 0.4 1.0
OG I:SER116 3.2 0.4 1.0
SG I:CYS117 3.2 0.6 1.0
N I:SER116 3.3 0.4 1.0
CB I:CYS117 3.4 0.6 1.0
CA I:CYS117 3.5 0.6 1.0
SG I:CYS86 3.8 0.5 1.0
CB I:CYS89 4.0 0.5 1.0
O I:SER116 4.3 0.4 1.0
CB I:CYS114 4.3 0.0 1.0
CB I:CYS86 4.4 0.5 1.0
N I:GLY118 4.4 0.3 1.0
C I:CYS117 4.5 0.6 1.0
CB I:ASN91 4.5 0.3 1.0
C I:THR115 4.6 0.8 1.0
N I:THR115 4.8 0.8 1.0
ND2 I:ASN91 5.0 0.3 1.0

Zinc binding site 6 out of 7 in 6hls

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Zinc binding site 6 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:37.3
occ:1.00
 SG J:CYS7 2.5 25.3 1.0
SG J:CYS45 2.5 23.5 1.0
SG J:CYS10 2.5 24.8 1.0
SG J:CYS46 2.8 23.3 1.0
N J:CYS46 3.3 23.3 1.0
CB J:CYS45 3.5 23.5 1.0
C J:CYS45 3.6 23.5 1.0
N J:CYS10 3.6 24.8 1.0
CA J:CYS46 3.6 23.3 1.0
CB J:CYS10 3.7 24.8 1.0
CB J:CYS7 3.7 25.3 1.0
CB J:CYS46 3.8 23.3 1.0
O J:CYS45 3.9 23.5 1.0
CA J:CYS45 4.1 23.5 1.0
CA J:CYS10 4.2 24.8 1.0
N J:GLY11 4.3 23.5 1.0
CB J:SER9 4.5 24.5 1.0
N J:SER9 4.5 24.5 1.0
C J:SER9 4.6 24.5 1.0
N J:LYS12 4.7 23.6 1.0
C J:CYS7 4.7 25.3 1.0
O J:CYS7 4.7 25.3 1.0
C J:CYS10 4.8 24.8 1.0
CA J:SER9 4.8 24.5 1.0
CB J:LYS12 4.8 23.6 1.0
CA J:CYS7 4.9 25.3 1.0
NE J:ARG43 4.9 25.1 1.0
N J:CYS45 5.0 23.5 1.0

Zinc binding site 7 out of 7 in 6hls

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Zinc binding site 7 out of 7 in the Yeast Apo Rna Polymerase I*


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Apo Rna Polymerase I* within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:79.2
occ:1.00
 SG L:CYS34 2.5 49.3 1.0
SG L:CYS51 2.5 69.0 1.0
SG L:CYS48 2.5 69.0 1.0
CB L:CYS48 2.6 69.0 1.0
SG L:CYS31 2.6 47.4 1.0
CB L:CYS31 3.5 47.4 1.0
CB L:CYS34 3.9 49.3 1.0
N L:CYS51 3.9 69.0 1.0
O L:CYS51 3.9 69.0 1.0
CB L:CYS51 4.0 69.0 1.0
CA L:CYS48 4.1 69.0 1.0
CB L:HIS53 4.2 58.1 1.0
CA L:CYS51 4.3 69.0 1.0
N L:CYS34 4.3 49.3 1.0
C L:CYS51 4.4 69.0 1.0
OG L:SER36 4.5 49.7 1.0
CB L:ASP50 4.6 69.9 1.0
C L:ASP50 4.6 69.9 1.0
CA L:CYS34 4.7 49.3 1.0
N L:ASP50 4.7 69.9 1.0
C L:CYS48 4.8 69.0 1.0
N L:CYS48 4.8 69.0 1.0
CB L:GLU33 4.9 48.7 1.0
CA L:ASP50 4.9 69.9 1.0
N L:HIS53 4.9 58.1 1.0
CA L:CYS31 4.9 47.4 1.0

Reference:

L.Tafur, Y.Sadian, J.Hanske, R.Wetzel, F.Weis, C.W.Muller. The Cryo-Em Structure of A 12-Subunit Variant of Rna Polymerase I Reveals Dissociation of the A49-A34.5 Heterodimer and Rearrangement of Subunit A12.2. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 30913026
DOI: 10.7554/ELIFE.43204
Page generated: Mon Oct 28 23:07:01 2024

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