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Zinc in PDB 6hlr: Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (Core Focused)

Enzymatic activity of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (Core Focused)

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

Other elements in 6hlr:

The structure of Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (Core Focused) 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 (Core Focused) (pdb code 6hlr). 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 (Core Focused), PDB code: 6hlr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6hlr

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


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

b:57.2
occ:1.00
 NE2 A:HIS75 2.2 46.3 1.0
SG A:CYS72 2.4 48.5 1.0
SG A:CYS62 2.4 50.8 1.0
SG A:CYS65 2.5 50.8 1.0
CD2 A:HIS75 2.6 46.3 1.0
CB A:CYS62 3.0 50.8 1.0
CE1 A:HIS75 3.4 46.3 1.0
CB A:CYS65 3.6 50.8 1.0
CB A:CYS72 3.7 48.5 1.0
N A:CYS65 3.7 50.8 1.0
CG A:HIS75 4.0 46.3 1.0
CA A:CYS65 4.2 50.8 1.0
ND1 A:HIS75 4.3 46.3 1.0
CA A:GLY55 4.4 48.5 1.0
CA A:CYS72 4.4 48.5 1.0
CB A:THR64 4.4 50.5 1.0
CA A:CYS62 4.5 50.8 1.0
CD A:PRO73 4.7 47.6 1.0
C A:THR64 4.7 50.5 1.0
N A:ALA56 4.8 52.0 1.0
N A:GLY66 4.8 52.0 1.0
N A:THR64 4.8 50.5 1.0
C A:CYS65 4.9 50.8 1.0
N A:GLY55 4.9 48.5 1.0
CA A:THR64 4.9 50.5 1.0
C A:GLY55 5.0 48.5 1.0
N A:GLY74 5.0 45.9 1.0

Zinc binding site 2 out of 6 in 6hlr

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


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 (Core Focused) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1703

b:90.0
occ:1.00
 SG A:CYS105 2.4 67.0 1.0
SG A:CYS233 2.5 73.1 1.0
SG A:CYS102 2.5 67.1 1.0
SG A:CYS236 2.7 76.3 1.0
CB A:CYS233 3.0 73.1 1.0
CB A:CYS102 3.3 67.1 1.0
CB A:CYS105 3.4 67.0 1.0
O A:CYS236 3.5 76.3 1.0
N A:CYS105 3.9 67.0 1.0
N A:CYS236 4.0 76.3 1.0
CB A:CYS236 4.2 76.3 1.0
CA A:CYS105 4.3 67.0 1.0
C A:CYS236 4.4 76.3 1.0
CA A:CYS236 4.4 76.3 1.0
CA A:CYS233 4.5 73.1 1.0
SD A:MET238 4.5 83.7 1.0
CA A:CYS102 4.8 67.1 1.0
CB A:PHE104 4.8 70.1 1.0
CB A:ASN235 4.9 71.3 1.0
C A:CYS233 5.0 73.1 1.0
C A:PHE104 5.0 70.1 1.0

Zinc binding site 3 out of 6 in 6hlr

Go back to Zinc Binding Sites List in 6hlr
Zinc binding site 3 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (Core Focused)


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 (Core Focused) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3001

b:68.4
occ:1.00
 SG B:CYS1104 2.4 46.6 1.0
SG B:CYS1107 2.5 47.5 1.0
CB B:CYS1131 2.7 56.8 1.0
SG B:CYS1128 2.8 51.0 1.0
CB B:CYS1128 3.4 51.0 1.0
SG B:CYS1131 3.4 56.8 1.0
N B:CYS1131 3.5 56.8 1.0
CG B:GLU1106 3.6 50.1 1.0
CA B:CYS1131 3.7 56.8 1.0
CB B:CYS1107 3.7 47.5 1.0
CB B:CYS1104 3.8 46.6 1.0
OE2 B:GLU1106 3.9 50.1 1.0
N B:CYS1107 4.0 47.5 1.0
CD B:GLU1106 4.3 50.1 1.0
CA B:CYS1107 4.4 47.5 1.0
C B:CYS1131 4.4 56.8 1.0
C B:GLU1106 4.7 50.1 1.0
C B:ARG1130 4.7 50.3 1.0
O B:CYS1131 4.8 56.8 1.0
CA B:CYS1128 4.9 51.0 1.0
CB B:GLU1106 4.9 50.1 1.0
CB B:ARG1130 4.9 50.3 1.0

Zinc binding site 4 out of 6 in 6hlr

Go back to Zinc Binding Sites List in 6hlr
Zinc binding site 4 out of 6 in the Yeast Rna Polymerase I Elongation Complex Bound to Nucleotide Analog Gmpcpp (Core Focused)


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 (Core Focused) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3001

b:96.5
occ:1.00
 SG I:CYS13 2.5 71.8 1.0
SG I:CYS10 2.5 72.7 1.0
SG I:CYS30 2.5 82.1 1.0
CB I:CYS33 2.8 81.4 1.0
CB I:CYS30 3.2 82.1 1.0
CB I:CYS10 3.2 72.7 1.0
N I:CYS33 3.3 81.4 1.0
SG I:CYS33 3.4 81.4 1.0
CA I:CYS33 3.6 81.4 1.0
CB I:CYS13 3.9 71.8 1.0
N I:CYS13 4.2 71.8 1.0
N I:LYS34 4.3 83.1 1.0
C I:CYS33 4.3 81.4 1.0
C I:GLN32 4.5 77.7 1.0
CA I:CYS13 4.6 71.8 1.0
N I:ALA35 4.6 85.7 1.0
CB I:ALA35 4.7 85.7 1.0
CA I:CYS30 4.7 82.1 1.0
CA I:CYS10 4.7 72.7 1.0
N I:GLN32 4.8 77.7 1.0
CB I:ASP15 4.9 66.6 1.0
CB I:ASP12 4.9 76.5 1.0
C I:ASP12 5.0 76.5 1.0
CB I:GLN32 5.0 77.7 1.0

Zinc binding site 5 out of 6 in 6hlr

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


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 (Core Focused) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:43.5
occ:1.00
 SG J:CYS45 2.5 35.4 1.0
SG J:CYS46 2.5 35.9 1.0
SG J:CYS10 2.5 37.8 1.0
SG J:CYS7 2.5 36.8 1.0
N J:CYS46 3.4 35.9 1.0
CB J:CYS10 3.6 37.8 1.0
N J:CYS10 3.6 37.8 1.0
CB J:CYS46 3.7 35.9 1.0
CA J:CYS46 3.7 35.9 1.0
CB J:CYS45 3.9 35.4 1.0
C J:CYS45 3.9 35.4 1.0
CB J:CYS7 4.0 36.8 1.0
CA J:CYS10 4.2 37.8 1.0
O J:CYS45 4.3 35.4 1.0
N J:GLY11 4.4 36.9 1.0
CB J:SER9 4.4 34.5 1.0
CA J:CYS45 4.5 35.4 1.0
NE J:ARG43 4.5 37.3 1.0
CB J:LYS12 4.6 37.4 1.0
C J:SER9 4.7 34.5 1.0
N J:LYS12 4.7 37.4 1.0
N J:SER9 4.7 34.5 1.0
NH2 J:ARG43 4.8 37.3 1.0
C J:CYS10 4.8 37.8 1.0
CA J:SER9 4.8 34.5 1.0

Zinc binding site 6 out of 6 in 6hlr

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


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 (Core Focused) within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3001

b:74.5
occ:1.00
 SG L:CYS51 2.5 68.6 1.0
SG L:CYS31 2.5 55.2 1.0
SG L:CYS48 2.5 69.9 1.0
SG L:CYS34 2.5 58.4 1.0
CB L:CYS48 2.6 69.9 1.0
CB L:CYS31 3.3 55.2 1.0
O L:CYS51 3.7 68.6 1.0
N L:CYS51 3.8 68.6 1.0
CB L:CYS34 3.8 58.4 1.0
CB L:CYS51 3.9 68.6 1.0
CA L:CYS48 4.1 69.9 1.0
CA L:CYS51 4.2 68.6 1.0
N L:CYS34 4.2 58.4 1.0
OG L:SER36 4.3 58.1 1.0
C L:CYS51 4.3 68.6 1.0
CB L:HIS53 4.5 60.8 1.0
CA L:CYS34 4.6 58.4 1.0
C L:ASP50 4.6 70.8 1.0
C L:CYS48 4.7 69.9 1.0
CA L:CYS31 4.8 55.2 1.0
CB L:ASP50 4.8 70.8 1.0
N L:CYS48 4.8 69.9 1.0
N L:ASP50 4.8 70.8 1.0
CB L:GLU33 4.8 56.0 1.0
CA L:ASP50 5.0 70.8 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 23:06:07 2024

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