Zinc in PDB 6o6c: Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion

Enzymatic activity of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion

All present enzymatic activity of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion:
2.7.7.6;

Other elements in 6o6c:

The structure of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion (pdb code 6o6c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion, PDB code: 6o6c:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.0
occ:1.00
 O A:MET108 2.3 22.4 1.0
O A:CYS107 2.3 5.4 1.0
SG A:CYS167 2.5 99.2 1.0
C A:CYS107 3.0 38.9 1.0
SG A:CYS148 3.0 0.2 1.0
CB A:CYS167 3.1 0.2 1.0
C A:MET108 3.3 39.4 1.0
CB A:CYS148 3.3 0.4 1.0
CB A:CYS110 3.4 17.9 1.0
CB A:CYS107 3.4 16.3 1.0
N A:MET108 3.7 46.2 1.0
CA A:CYS107 3.8 56.2 1.0
CA A:MET108 3.9 48.8 1.0
N A:CYS110 4.0 46.9 1.0
C A:HIS109 4.2 50.7 1.0
CB A:MET108 4.3 63.3 1.0
CA A:CYS110 4.3 45.5 1.0
OD1 A:ASN169 4.3 0.0 1.0
N A:HIS109 4.3 55.0 1.0
CA A:CYS167 4.4 0.4 1.0
N A:CYS167 4.5 0.4 1.0
O A:HIS109 4.6 54.5 1.0
SG A:CYS110 4.6 0.9 1.0
CA A:HIS109 4.7 57.8 1.0
CA A:CYS148 4.8 1.0 1.0
CB A:HIS109 4.9 59.6 1.0
SG A:CYS107 4.9 83.8 1.0

Zinc binding site 2 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.3
occ:1.00
 O A:CYS67 2.2 59.9 1.0
NE2 A:HIS80 2.3 43.2 1.0
SG A:CYS70 2.4 56.9 1.0
SG A:CYS67 2.5 63.8 1.0
C A:CYS67 3.0 68.9 1.0
CB A:CYS67 3.2 62.5 1.0
CD2 A:HIS80 3.3 50.5 1.0
CE1 A:HIS80 3.3 51.3 1.0
SG A:CYS77 3.4 95.7 1.0
CA A:CYS67 3.7 73.6 1.0
CB A:GLN68 3.9 66.2 1.0
CB A:CYS70 3.9 73.6 1.0
N A:GLN68 4.0 67.6 1.0
O A:PRO78 4.2 51.1 1.0
CA A:GLN68 4.4 68.7 1.0
CG A:HIS80 4.5 53.2 1.0
ND1 A:HIS80 4.5 55.8 1.0
CG A:GLN68 4.6 69.8 1.0
O A:LYS66 4.7 84.5 1.0
N A:CYS70 4.7 75.8 1.0
C A:GLN68 4.8 74.1 1.0
CA A:CYS70 4.8 77.5 1.0
O A:GLN71 4.8 73.9 1.0
N A:CYS67 4.9 75.3 1.0

Zinc binding site 3 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:20.3
occ:1.00
 SG B:CYS1182 2.5 47.6 1.0
SG B:CYS1185 2.6 60.9 1.0
SG B:CYS1163 2.7 79.5 1.0
CB B:CYS1166 3.1 39.1 1.0
CB B:CYS1163 3.3 44.4 1.0
O B:CYS1166 3.4 48.8 1.0
N B:CYS1166 3.4 38.2 1.0
CB B:CYS1185 3.5 55.7 1.0
CA B:CYS1166 3.7 37.5 1.0
SG B:CYS1166 3.7 75.3 1.0
CB B:CYS1182 4.0 57.6 1.0
C B:CYS1166 4.0 43.6 1.0
OG1 B:THR1170 4.5 55.7 1.0
CB B:ILE1165 4.6 44.1 1.0
C B:ILE1165 4.6 45.1 1.0
CA B:CYS1163 4.7 46.1 1.0
CA B:CYS1185 4.8 62.5 1.0
CG2 B:ILE1165 4.9 46.2 1.0
N B:CYS1185 4.9 63.3 1.0
CA B:ILE1165 5.0 44.7 1.0

Zinc binding site 4 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:66.0
occ:1.00
 SG C:CYS95 2.6 53.5 1.0
SG C:CYS92 2.7 74.5 1.0
SG C:CYS86 2.7 73.5 1.0
N C:CYS92 2.9 58.6 1.0
C C:HIS91 3.2 64.0 1.0
CB C:CYS88 3.2 79.9 1.0
CA C:HIS91 3.3 66.5 1.0
O C:CYS88 3.3 89.0 1.0
CB C:CYS92 3.3 70.2 1.0
SG C:CYS88 3.5 0.8 1.0
O C:GLU89 3.7 91.6 1.0
CA C:CYS92 3.7 62.8 1.0
C C:CYS88 3.8 87.7 1.0
O C:HIS91 3.9 70.3 1.0
N C:HIS91 4.0 74.7 1.0
CA C:CYS88 4.0 86.4 1.0
CB C:CYS86 4.1 71.0 1.0
CB C:CYS95 4.1 54.2 1.0
CB C:HIS91 4.5 66.8 1.0
N C:CYS88 4.5 87.8 1.0
O C:ASP90 4.5 79.3 1.0
C C:ASP90 4.5 79.9 1.0
C C:CYS92 4.5 64.9 1.0
O C:CYS92 4.6 71.8 1.0
C C:GLU89 4.7 88.8 1.0
N C:GLU89 4.8 92.4 1.0
N C:CYS95 5.0 58.5 1.0

Zinc binding site 5 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:0.0
occ:1.00
 ND2 G:ASN12 2.3 0.4 1.0
OG1 G:THR31 2.3 18.6 1.0
SG G:CYS32 2.5 0.0 1.0
O G:THR31 2.5 14.6 1.0
C G:THR31 3.0 51.8 1.0
CB G:THR31 3.1 37.3 1.0
CG G:ASN12 3.2 0.3 1.0
CA G:THR31 3.6 69.2 1.0
N G:CYS32 3.7 76.1 1.0
CB G:ASN12 3.7 0.1 1.0
CB G:CYS32 3.9 0.7 1.0
SG G:CYS29 4.0 80.0 1.0
CA G:CYS32 4.0 81.6 1.0
OD1 G:ASN12 4.2 0.0 1.0
N G:THR31 4.4 95.0 1.0
CB G:CYS10 4.5 0.3 1.0
CG2 G:THR31 4.5 86.3 1.0
SG G:CYS10 4.9 0.3 1.0
CB G:CYS29 4.9 0.1 1.0

Zinc binding site 6 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:0.0
occ:1.00
 ND1 G:HIS108 2.4 0.5 1.0
SG G:CYS78 2.6 0.8 1.0
CB G:CYS106 3.0 63.0 1.0
CE1 G:HIS108 3.1 65.2 1.0
SG G:CYS106 3.2 85.4 1.0
CG G:HIS108 3.2 79.2 1.0
SG G:CYS103 3.3 0.7 1.0
CB G:CYS75 3.7 1.0 1.0
CB G:HIS108 3.7 85.6 1.0
CB G:CYS78 3.7 96.2 1.0
CB G:CYS103 3.8 95.7 1.0
NE2 G:HIS108 4.0 70.4 1.0
O G:CYS75 4.1 0.2 1.0
CD2 G:HIS108 4.1 78.2 1.0
CA G:CYS106 4.3 82.0 1.0
N G:CYS78 4.3 0.3 1.0
SG G:CYS75 4.5 0.1 1.0
N G:CYS106 4.5 89.6 1.0
N G:HIS108 4.6 88.6 1.0
CA G:CYS78 4.6 0.5 1.0
CE1 G:PHE110 4.8 0.5 1.0
CA G:HIS108 4.8 94.9 1.0
OG G:SER105 4.8 86.6 1.0
C G:CYS106 4.8 88.0 1.0
CA G:CYS75 4.9 0.8 1.0
CB G:LYS77 4.9 0.5 1.0
C G:CYS75 4.9 0.5 1.0
CZ G:PHE110 4.9 0.6 1.0

Zinc binding site 7 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn101

b:46.0
occ:1.00
 SG H:CYS7 2.4 30.0 1.0
SG H:CYS10 2.4 36.5 1.0
SG H:CYS46 2.5 47.3 1.0
SG H:CYS45 2.5 61.7 1.0
O H:CYS45 2.8 28.4 1.0
C H:CYS45 2.9 26.8 1.0
N H:CYS46 3.2 32.4 1.0
CB H:CYS45 3.3 26.1 1.0
CB H:CYS10 3.4 19.4 1.0
CA H:CYS46 3.5 25.3 1.0
CB H:CYS46 3.5 23.0 1.0
CB H:CYS7 3.6 17.4 1.0
CA H:CYS45 3.7 22.8 1.0
N H:CYS10 3.9 24.4 1.0
CB H:SER9 4.1 18.3 1.0
CA H:CYS10 4.3 13.6 1.0
C H:SER9 4.4 21.4 1.0
NE H:ARG43 4.6 25.9 1.0
N H:CYS45 4.6 24.4 1.0
CA H:SER9 4.6 14.6 1.0
N H:SER9 4.7 17.9 1.0
C H:CYS46 5.0 23.2 1.0
CA H:CYS7 5.0 14.8 1.0
CB H:ARG43 5.0 23.4 1.0
OG H:SER9 5.0 25.5 1.0

Zinc binding site 8 out of 8 in 6o6c

Go back to Zinc Binding Sites List in 6o6c
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Elongation Complex Arrested at A Cpd Lesion within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.0
occ:1.00
 OD1 J:ASP50 2.1 32.7 1.0
SG J:CYS51 2.5 53.0 1.0
SG J:CYS31 2.6 60.5 1.0
CG J:ASP50 2.8 13.6 1.0
SG J:CYS34 2.9 64.6 1.0
CB J:CYS34 2.9 50.7 1.0
OD2 J:ASP50 3.0 29.6 1.0
CB J:CYS31 3.3 60.2 1.0
CB J:SER36 3.7 67.2 1.0
CB J:CYS51 3.8 59.6 1.0
C J:ASP50 4.1 64.9 1.0
O J:ASP50 4.2 61.9 1.0
CB J:ASP50 4.2 58.1 1.0
OG J:SER36 4.2 71.2 1.0
CA J:CYS34 4.3 69.2 1.0
N J:CYS51 4.4 66.7 1.0
O J:CYS34 4.4 69.9 1.0
CA J:ASP50 4.6 65.9 1.0
C J:CYS34 4.6 71.3 1.0
O J:SER36 4.7 87.4 1.0
CA J:CYS51 4.7 67.9 1.0
CB J:CYS48 4.7 85.1 1.0
CA J:SER36 4.8 86.1 1.0
N J:ASP50 4.8 72.9 1.0
CA J:CYS31 4.8 81.0 1.0
N J:SER36 4.9 83.8 1.0
N J:CYS34 5.0 78.8 1.0
O J:ALA32 5.0 70.6 1.0

Reference:

I.Lahiri, J.Xu, B.G.Han, J.Oh, D.Wang, F.Dimaio, A.E.Leschziner. 3.1 Angstrom Structure of Yeast Rna Polymerase II Elongation Complex Stalled at A Cyclobutane Pyrimidine Dimer Lesion Solved Using Streptavidin Affinity Grids. J.Struct.Biol. V. 207 270 2019.
ISSN: ESSN 1095-8657
PubMed: 31200019
DOI: 10.1016/J.JSB.2019.06.004
Page generated: Wed Dec 16 12:25:18 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