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: Wed Dec 16 11:57:30 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy