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Zinc in PDB 6hko: Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp

All present enzymatic activity of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp:
2.7.7.6;

Other elements in 6hko:

The structure of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (pdb code 6hko). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp, PDB code: 6hko:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6hko

Go back to Zinc Binding Sites List in 6hko
Zinc binding site 1 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1702

b:81.6
occ:1.00
 NE2 A:HIS75 2.2 64.0 1.0
SG A:CYS65 2.4 71.2 1.0
SG A:CYS62 2.4 74.0 1.0
SG A:CYS72 2.4 65.7 1.0
CD2 A:HIS75 2.8 64.0 1.0
CB A:CYS62 3.0 74.0 1.0
N A:CYS65 3.2 71.2 1.0
CE1 A:HIS75 3.3 64.0 1.0
CB A:CYS65 3.4 71.2 1.0
CB A:CYS72 3.7 65.7 1.0
CA A:CYS65 3.8 71.2 1.0
CG A:HIS75 4.1 64.0 1.0
CB A:THR64 4.1 70.6 1.0
N A:GLY66 4.2 73.8 1.0
C A:THR64 4.3 70.6 1.0
ND1 A:HIS75 4.3 64.0 1.0
C A:CYS65 4.4 71.2 1.0
N A:THR64 4.4 70.6 1.0
CA A:GLY55 4.4 67.6 1.0
CA A:THR64 4.5 70.6 1.0
CA A:CYS62 4.5 74.0 1.0
CA A:CYS72 4.6 65.7 1.0
N A:LEU67 4.8 71.2 1.0
CG2 A:THR64 4.9 70.6 1.0
N A:GLY55 4.9 67.6 1.0
C A:CYS62 5.0 74.0 1.0

Zinc binding site 2 out of 6 in 6hko

Go back to Zinc Binding Sites List in 6hko
Zinc binding site 2 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:0.1
occ:1.00
 SG A:CYS105 2.5 85.0 1.0
SG A:CYS102 2.5 86.0 1.0
SG A:CYS233 2.5 90.1 1.0
SG A:CYS236 2.5 96.2 1.0
CB A:CYS102 2.9 86.0 1.0
CB A:CYS233 3.1 90.1 1.0
CB A:CYS105 3.5 85.0 1.0
N A:CYS105 3.7 85.0 1.0
O A:CYS236 3.9 96.2 1.0
CB A:CYS236 4.1 96.2 1.0
N A:CYS236 4.2 96.2 1.0
CA A:CYS105 4.2 85.0 1.0
CA A:CYS102 4.4 86.0 1.0
CA A:CYS236 4.6 96.2 1.0
CA A:CYS233 4.6 90.1 1.0
CB A:PHE104 4.7 87.4 1.0
C A:CYS236 4.7 96.2 1.0
C A:PHE104 4.8 87.4 1.0
C A:CYS105 4.9 85.0 1.0
N A:HIS106 4.9 82.4 1.0
C A:CYS102 4.9 86.0 1.0
SD A:MET238 4.9 0.7 1.0
CB A:ASN235 5.0 88.2 1.0
N A:PHE104 5.0 87.4 1.0

Zinc binding site 3 out of 6 in 6hko

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Zinc binding site 3 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:87.0
occ:1.00
 SG B:CYS1107 2.4 63.9 1.0
SG B:CYS1104 2.5 63.3 1.0
CB B:CYS1131 2.7 76.8 1.0
SG B:CYS1128 2.9 70.4 1.0
SG B:CYS1131 2.9 76.8 1.0
CB B:CYS1107 3.4 63.9 1.0
N B:CYS1131 3.5 76.8 1.0
CG B:GLU1106 3.5 66.5 1.0
N B:CYS1107 3.6 63.9 1.0
CA B:CYS1131 3.7 76.8 1.0
CB B:CYS1128 3.7 70.4 1.0
CB B:CYS1104 3.9 63.3 1.0
OE2 B:GLU1106 4.0 66.5 1.0
CA B:CYS1107 4.0 63.9 1.0
CD B:GLU1106 4.2 66.5 1.0
C B:GLU1106 4.4 66.5 1.0
C B:CYS1131 4.7 76.8 1.0
C B:ARG1130 4.7 69.8 1.0
CB B:GLU1106 4.7 66.5 1.0
CA B:GLU1106 4.9 66.5 1.0
N B:GLU1106 5.0 66.5 1.0
CB B:ARG1130 5.0 69.8 1.0

Zinc binding site 4 out of 6 in 6hko

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Zinc binding site 4 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:0.3
occ:1.00
 SG I:CYS10 2.5 95.5 1.0
SG I:CYS33 2.5 0.1 1.0
SG I:CYS30 2.5 0.4 1.0
SG I:CYS13 2.7 97.8 1.0
CB I:CYS33 2.9 0.1 1.0
CB I:CYS10 3.2 95.5 1.0
CB I:CYS30 3.5 0.4 1.0
N I:CYS33 3.7 0.1 1.0
CB I:CYS13 3.8 97.8 1.0
N I:CYS13 3.8 97.8 1.0
CA I:CYS33 3.8 0.1 1.0
CA I:CYS13 4.3 97.8 1.0
CB I:ASP15 4.5 89.3 1.0
CB I:ASP12 4.5 0.2 1.0
C I:ASP12 4.6 0.2 1.0
CA I:CYS10 4.7 95.5 1.0
N I:ASP15 4.8 89.3 1.0
C I:GLN32 4.8 97.4 1.0
C I:CYS13 4.9 97.8 1.0
N I:ASP12 4.9 0.2 1.0
N I:GLY14 4.9 91.9 1.0
CA I:ASP12 4.9 0.2 1.0
CA I:CYS30 5.0 0.4 1.0
C I:CYS33 5.0 0.1 1.0

Zinc binding site 5 out of 6 in 6hko

Go back to Zinc Binding Sites List in 6hko
Zinc binding site 5 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:56.9
occ:1.00
 SG J:CYS45 2.4 47.1 1.0
SG J:CYS46 2.5 47.1 1.0
SG J:CYS7 2.5 45.9 1.0
SG J:CYS10 2.5 48.7 1.0
N J:CYS46 3.0 47.1 1.0
CA J:CYS46 3.3 47.1 1.0
C J:CYS45 3.3 47.1 1.0
CB J:CYS46 3.4 47.1 1.0
CB J:CYS45 3.6 47.1 1.0
O J:CYS45 3.7 47.1 1.0
CB J:CYS10 3.7 48.7 1.0
CB J:CYS7 4.0 45.9 1.0
N J:CYS10 4.0 48.7 1.0
CA J:CYS45 4.0 47.1 1.0
CA J:CYS10 4.4 48.7 1.0
NE J:ARG43 4.5 48.4 1.0
N J:GLY11 4.6 47.1 1.0
CB J:LYS12 4.7 47.8 1.0
NH2 J:ARG43 4.7 48.4 1.0
C J:CYS46 4.8 47.1 1.0
N J:CYS45 4.8 47.1 1.0
N J:LYS12 4.8 47.8 1.0
CB J:SER9 5.0 46.3 1.0
CB J:ARG43 5.0 48.4 1.0
N J:SER9 5.0 46.3 1.0

Zinc binding site 6 out of 6 in 6hko

Go back to Zinc Binding Sites List in 6hko
Zinc binding site 6 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:90.2
occ:1.00
 SG L:CYS31 2.4 64.8 1.0
SG L:CYS48 2.5 76.5 1.0
SG L:CYS51 2.5 75.7 1.0
SG L:CYS34 2.5 68.5 1.0
CB L:CYS48 2.9 76.5 1.0
CB L:CYS31 3.0 64.8 1.0
CB L:CYS34 3.8 68.5 1.0
O L:CYS51 3.9 75.7 1.0
OG L:SER36 4.0 67.0 1.0
CB L:CYS51 4.0 75.7 1.0
N L:CYS34 4.0 68.5 1.0
N L:CYS51 4.0 75.7 1.0
CA L:CYS51 4.4 75.7 1.0
CB L:HIS53 4.4 72.3 1.0
CA L:CYS48 4.4 76.5 1.0
CA L:CYS34 4.5 68.5 1.0
C L:CYS51 4.5 75.7 1.0
CA L:CYS31 4.5 64.8 1.0
CB L:GLU33 4.6 68.8 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 23:05:12 2024

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