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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

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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

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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

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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

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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

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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

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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

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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

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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: Tue Oct 29 04:07:06 2024

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