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Zinc in PDB 6hlq: 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 6hlq:

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 6hlq). 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 Rna Polymerase I* Elongation Complex Bound to Nucleotide Analog Gmpcpp, PDB code: 6hlq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 6hlq

Go back to Zinc Binding Sites List in 6hlq
Zinc binding site 1 out of 7 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:Zn1701

b:27.4
occ:1.00
 NE2 A:HIS75 2.2 14.2 1.0
SG A:CYS72 2.4 18.4 1.0
SG A:CYS62 2.4 19.7 1.0
SG A:CYS65 2.5 17.7 1.0
CD2 A:HIS75 2.7 14.2 1.0
CB A:CYS62 3.1 19.7 1.0
CE1 A:HIS75 3.4 14.2 1.0
CB A:CYS65 3.6 17.7 1.0
N A:CYS65 3.7 17.7 1.0
CB A:CYS72 3.8 18.4 1.0
CG A:HIS75 4.0 14.2 1.0
CA A:CYS65 4.2 17.7 1.0
ND1 A:HIS75 4.3 14.2 1.0
CB A:THR64 4.4 18.3 1.0
CA A:GLY55 4.4 16.4 1.0
CA A:CYS72 4.5 18.4 1.0
CD A:PRO73 4.6 16.5 1.0
CA A:CYS62 4.6 19.7 1.0
C A:THR64 4.6 18.3 1.0
N A:THR64 4.7 18.3 1.0
N A:GLY66 4.7 17.6 1.0
CA A:THR64 4.8 18.3 1.0
N A:ALA56 4.8 20.1 1.0
C A:CYS65 4.8 17.7 1.0
N A:GLY55 4.9 16.4 1.0
N A:GLY74 5.0 14.7 1.0
C A:GLY55 5.0 16.4 1.0

Zinc binding site 2 out of 7 in 6hlq

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Zinc binding site 2 out of 7 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:Zn1702

b:74.0
occ:1.00
 SG A:CYS102 2.5 38.3 1.0
SG A:CYS233 2.5 37.9 1.0
SG A:CYS236 2.5 47.0 1.0
SG A:CYS105 2.5 39.5 1.0
CB A:CYS233 3.2 37.9 1.0
CB A:CYS102 3.4 38.3 1.0
O A:CYS236 3.4 47.0 1.0
CB A:CYS105 3.6 39.5 1.0
N A:CYS236 3.9 47.0 1.0
N A:CYS105 3.9 39.5 1.0
CB A:CYS236 4.0 47.0 1.0
CA A:CYS236 4.2 47.0 1.0
C A:CYS236 4.3 47.0 1.0
CA A:CYS105 4.3 39.5 1.0
SD A:MET238 4.4 49.3 1.0
CA A:CYS233 4.6 37.9 1.0
CB A:PHE104 4.7 40.7 1.0
CB A:ASN235 4.8 41.9 1.0
CA A:CYS102 4.8 38.3 1.0
C A:PHE104 4.9 40.7 1.0
C A:ASN235 5.0 41.9 1.0

Zinc binding site 3 out of 7 in 6hlq

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Zinc binding site 3 out of 7 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:49.2
occ:1.00
 SG B:CYS1107 2.5 13.0 1.0
SG B:CYS1104 2.5 12.2 1.0
SG B:CYS1128 2.6 21.6 1.0
CB B:CYS1131 2.9 24.2 1.0
CB B:CYS1128 3.4 21.6 1.0
SG B:CYS1131 3.4 24.2 1.0
N B:CYS1131 3.5 24.2 1.0
CA B:CYS1131 3.7 24.2 1.0
CB B:CYS1107 3.8 13.0 1.0
CG B:GLU1106 3.8 13.7 1.0
CB B:CYS1104 4.0 12.2 1.0
OE2 B:GLU1106 4.0 13.7 1.0
N B:CYS1107 4.2 13.0 1.0
CD B:GLU1106 4.4 13.7 1.0
CA B:CYS1107 4.5 13.0 1.0
C B:CYS1131 4.5 24.2 1.0
C B:ARG1130 4.6 20.3 1.0
CB B:ARG1130 4.7 20.3 1.0
C B:GLU1106 4.8 13.7 1.0
CA B:CYS1128 4.9 21.6 1.0
O B:CYS1131 4.9 24.2 1.0
N B:ARG1130 4.9 20.3 1.0

Zinc binding site 4 out of 7 in 6hlq

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Zinc binding site 4 out of 7 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:73.9
occ:1.00
 SG I:CYS10 2.5 34.8 1.0
SG I:CYS13 2.5 39.0 1.0
SG I:CYS30 2.5 43.3 1.0
CB I:CYS10 2.9 34.8 1.0
CB I:CYS30 3.3 43.3 1.0
CB I:CYS33 3.3 47.0 1.0
N I:CYS33 3.7 47.0 1.0
SG I:CYS33 3.8 47.0 1.0
CB I:CYS13 4.0 39.0 1.0
CA I:CYS33 4.1 47.0 1.0
N I:CYS13 4.1 39.0 1.0
CB I:ASP15 4.4 31.1 1.0
CA I:CYS10 4.4 34.8 1.0
CA I:CYS13 4.5 39.0 1.0
N I:LYS34 4.6 45.1 1.0
N I:ASP15 4.7 31.1 1.0
CA I:CYS30 4.7 43.3 1.0
C I:CYS33 4.8 47.0 1.0
CB I:ASP12 4.8 42.8 1.0
C I:GLN32 4.9 42.3 1.0
N I:GLY14 4.9 30.8 1.0
N I:GLN32 5.0 42.3 1.0
C I:CYS13 5.0 39.0 1.0

Zinc binding site 5 out of 7 in 6hlq

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Zinc binding site 5 out of 7 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
I:Zn3002

b:78.3
occ:0.75
 SG I:CYS86 2.5 63.7 1.0
CB I:CYS86 2.6 63.7 1.0
SG I:CYS114 2.6 62.3 1.0
SG I:CYS117 3.5 63.6 1.0
SG I:CYS89 3.6 65.5 1.0
CB I:CYS114 3.7 62.3 1.0
CB I:ASN91 3.8 64.9 1.0
CA I:CYS86 4.0 63.7 1.0
O I:CYS86 4.3 63.7 1.0
N I:GLY90 4.3 64.2 1.0
N I:ASN91 4.3 64.9 1.0
C I:CYS86 4.4 63.7 1.0
N I:CYS89 4.4 65.5 1.0
CB I:CYS117 4.6 63.6 1.0
C I:GLY90 4.6 64.2 1.0
CA I:ASN91 4.7 64.9 1.0
N I:CYS117 4.7 63.6 1.0
CB I:SER116 4.7 65.8 1.0
N I:CYS86 4.7 63.7 1.0
ND2 I:ASN91 4.9 64.9 1.0
CB I:GLN88 4.9 64.0 1.0
CG I:ASN91 4.9 64.9 1.0
SD I:MET94 4.9 59.0 1.0
CB I:CYS89 4.9 65.5 1.0
N I:GLN88 4.9 64.0 1.0
CA I:GLY90 5.0 64.2 1.0
CA I:CYS89 5.0 65.5 1.0
C I:CYS89 5.0 65.5 1.0

Zinc binding site 6 out of 7 in 6hlq

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Zinc binding site 6 out of 7 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
J:Zn3001

b:17.6
occ:1.00
 SG J:CYS45 2.5 8.3 1.0
SG J:CYS46 2.5 7.0 1.0
SG J:CYS10 2.6 7.1 1.0
SG J:CYS7 2.7 6.2 1.0
N J:CYS46 3.3 7.0 1.0
CA J:CYS46 3.6 7.0 1.0
CB J:CYS46 3.6 7.0 1.0
CB J:CYS10 3.6 7.1 1.0
CB J:CYS45 3.7 8.3 1.0
C J:CYS45 3.7 8.3 1.0
N J:CYS10 3.8 7.1 1.0
CB J:CYS7 4.0 6.2 1.0
O J:CYS45 4.1 8.3 1.0
CA J:CYS45 4.3 8.3 1.0
CA J:CYS10 4.3 7.1 1.0
NH2 J:ARG43 4.3 8.6 1.0
NE J:ARG43 4.4 8.6 1.0
N J:GLY11 4.6 7.9 1.0
CB J:SER9 4.7 6.6 1.0
CB J:LYS12 4.7 7.9 1.0
C J:SER9 4.7 6.6 1.0
N J:SER9 4.8 6.6 1.0
N J:LYS12 4.8 7.9 1.0
CZ J:ARG43 4.9 8.6 1.0
C J:CYS10 5.0 7.1 1.0
CA J:SER9 5.0 6.6 1.0

Zinc binding site 7 out of 7 in 6hlq

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Zinc binding site 7 out of 7 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 7 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:49.8
occ:1.00
 SG L:CYS34 2.5 26.6 1.0
SG L:CYS31 2.5 22.9 1.0
SG L:CYS51 2.5 40.0 1.0
SG L:CYS48 2.5 36.0 1.0
CB L:CYS48 2.7 36.0 1.0
CB L:CYS31 3.3 22.9 1.0
O L:CYS51 3.5 40.0 1.0
CB L:CYS34 3.8 26.6 1.0
N L:CYS51 3.8 40.0 1.0
CB L:CYS51 3.9 40.0 1.0
CA L:CYS48 4.1 36.0 1.0
C L:CYS51 4.2 40.0 1.0
CA L:CYS51 4.2 40.0 1.0
N L:CYS34 4.2 26.6 1.0
OG L:SER36 4.2 25.9 1.0
CB L:HIS53 4.4 29.2 1.0
CA L:CYS34 4.6 26.6 1.0
C L:CYS48 4.7 36.0 1.0
C L:ASP50 4.7 43.5 1.0
N L:ASP50 4.8 43.5 1.0
CB L:ASP50 4.8 43.5 1.0
CA L:CYS31 4.8 22.9 1.0
N L:HIS53 4.9 29.2 1.0
N L:CYS48 4.9 36.0 1.0
CB L:GLU33 4.9 24.9 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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