Atomistry » Zinc » PDB 6hch-6hqx » 6hko
Atomistry »
  Zinc »
    PDB 6hch-6hqx »
      6hko »

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

Go back to Zinc Binding Sites List in 6hko
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

Go back to Zinc Binding Sites List in 6hko
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy