Atomistry » Zinc » PDB 6uob-6v73 » 6uq3
Atomistry »
  Zinc »
    PDB 6uob-6v73 »
      6uq3 »

Zinc in PDB 6uq3: Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5

Enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5

All present enzymatic activity of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5, PDB code: 6uq3 was solved by J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.27 / 3.47
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.189, 222.584, 194.612, 90.00, 101.34, 90.00
R / Rfree (%) 23.4 / 28.6

Other elements in 6uq3:

The structure of Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5 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 with 5-Guanidinohydantoin Lesion in State 5 (pdb code 6uq3). 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 with 5-Guanidinohydantoin Lesion in State 5, PDB code: 6uq3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:1.0
occ:1.00
 SG A:CYS167 2.4 0.5 1.0
SG A:CYS110 2.5 0.2 1.0
SG A:CYS107 2.5 0.6 1.0
CB A:CYS167 2.7 0.6 1.0
CB A:CYS148 3.1 0.1 1.0
CB A:CYS107 3.1 0.0 1.0
O A:MET108 3.3 0.1 1.0
SG A:CYS148 3.5 0.9 1.0
N A:CYS167 3.6 0.8 1.0
CA A:CYS167 3.8 0.1 1.0
CB A:CYS110 3.9 0.3 1.0
O A:CYS148 4.1 0.0 1.0
CA A:CYS148 4.3 0.5 1.0
CA A:CYS107 4.4 0.5 1.0
N A:CYS110 4.4 0.5 1.0
C A:CYS107 4.4 0.3 1.0
C A:MET108 4.5 0.6 1.0
N A:GLY168 4.6 0.2 1.0
O A:CYS110 4.6 0.4 1.0
C A:CYS148 4.7 0.8 1.0
N A:MET108 4.7 0.7 1.0
N A:CYS148 4.7 0.1 1.0
CA A:CYS110 4.7 0.5 1.0
C A:CYS167 4.7 0.3 1.0
O A:CYS107 4.7 0.3 1.0
C A:GLY166 4.9 0.9 1.0

Zinc binding site 2 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.1
occ:1.00
 NE2 A:HIS80 2.2 0.7 1.0
SG A:CYS70 2.5 0.8 1.0
SG A:CYS77 2.5 0.2 1.0
SG A:CYS67 2.5 0.6 1.0
CB A:CYS70 2.6 0.4 1.0
CB A:CYS77 2.8 0.8 1.0
CE1 A:HIS80 2.9 0.5 1.0
CD2 A:HIS80 3.2 0.4 1.0
NE2 A:GLN68 3.5 0.7 1.0
CB A:CYS67 3.7 0.5 1.0
CA A:CYS77 3.8 0.8 1.0
O A:CYS67 3.9 0.6 1.0
CA A:CYS70 4.0 0.7 1.0
ND1 A:HIS80 4.1 0.1 1.0
CG A:HIS80 4.2 0.2 1.0
N A:CYS70 4.6 0.4 1.0
C A:CYS67 4.6 0.7 1.0
CD A:GLN68 4.6 0.7 1.0
C A:CYS77 4.7 0.7 1.0
CA A:CYS67 4.8 0.0 1.0
N A:CYS77 4.8 0.8 1.0
CG A:GLN68 4.9 0.6 1.0

Zinc binding site 3 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1402

b:0.5
occ:1.00
 SG B:CYS1185 2.4 0.7 1.0
SG B:CYS1163 2.4 0.7 1.0
SG B:CYS1166 2.4 0.5 1.0
SG B:CYS1182 2.5 0.9 1.0
N B:CYS1166 2.9 0.6 1.0
CB B:CYS1166 3.0 0.2 1.0
CB B:CYS1185 3.2 0.6 1.0
CB B:CYS1163 3.3 0.4 1.0
CA B:CYS1166 3.4 0.3 1.0
O B:CYS1166 3.7 0.7 1.0
CB B:CYS1182 3.8 0.9 1.0
CB B:ILE1165 4.0 0.5 1.0
C B:CYS1166 4.0 0.5 1.0
C B:ILE1165 4.1 0.0 1.0
CA B:ILE1165 4.4 0.4 1.0
N B:ILE1165 4.4 0.8 1.0
CA B:CYS1185 4.5 0.8 1.0
CA B:CYS1163 4.7 0.2 1.0
CG1 B:ILE1165 4.8 0.1 1.0
N B:CYS1185 4.8 0.7 1.0
CG2 B:ILE1165 4.8 0.5 1.0
C B:CYS1163 5.0 0.0 1.0

Zinc binding site 4 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:94.6
occ:1.00
 SG C:CYS92 2.5 76.3 1.0
SG C:CYS95 2.5 80.1 1.0
SG C:CYS86 2.5 0.1 1.0
SG C:CYS88 2.5 55.0 1.0
CB C:CYS95 2.6 68.3 1.0
CB C:CYS86 2.8 0.2 1.0
N C:CYS95 3.5 70.7 1.0
CB C:CYS92 3.6 80.2 1.0
CA C:CYS95 3.7 55.7 1.0
CB C:CYS88 3.8 35.5 1.0
N C:CYS92 3.8 89.3 1.0
CA C:CYS92 4.2 72.9 1.0
CA C:CYS86 4.2 96.3 1.0
C C:LYS94 4.3 86.0 1.0
N C:CYS88 4.5 57.5 1.0
C C:HIS91 4.5 88.1 1.0
C C:CYS92 4.5 47.9 1.0
CB C:LYS94 4.6 74.4 1.0
O C:CYS92 4.6 62.6 1.0
C C:CYS86 4.7 83.0 1.0
CA C:HIS91 4.7 85.2 1.0
C C:CYS95 4.8 56.9 1.0
CA C:CYS88 4.8 50.4 1.0
N C:PHE87 4.8 58.6 1.0
N C:LYS94 4.8 53.8 1.0
CA C:LYS94 4.8 70.1 1.0
N C:SER96 4.9 64.6 1.0

Zinc binding site 5 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.5
occ:1.00
 SG I:CYS32 2.4 0.3 1.0
SG I:CYS29 2.5 0.9 1.0
SG I:CYS10 2.8 1.0 1.0
SG I:CYS7 2.8 67.5 1.0
CB I:CYS32 2.8 0.0 1.0
CB I:CYS10 3.0 0.6 1.0
N I:CYS32 3.3 94.7 1.0
CB I:CYS29 3.3 0.2 1.0
CB I:CYS7 3.4 82.1 1.0
CA I:CYS32 3.6 0.8 1.0
N I:CYS10 3.7 0.3 1.0
CA I:CYS10 3.9 0.7 1.0
C I:CYS32 4.3 0.5 1.0
C I:THR31 4.4 0.3 1.0
CB I:ASP9 4.6 99.9 1.0
C I:ASP9 4.7 0.4 1.0
CB I:THR31 4.7 0.7 1.0
N I:THR31 4.8 97.9 1.0
O I:CYS32 4.8 0.0 1.0
CA I:CYS29 4.8 94.2 1.0
CA I:THR31 4.9 0.5 1.0
CA I:CYS7 4.9 95.0 1.0
C I:CYS10 4.9 0.5 1.0
N I:SER33 4.9 0.3 1.0
CB I:ASN12 4.9 66.3 1.0

Zinc binding site 6 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:92.9
occ:1.00
 SG I:CYS75 2.4 0.4 1.0
SG I:CYS103 2.5 88.9 1.0
CB I:CYS106 2.5 0.5 1.0
SG I:CYS78 2.5 58.2 1.0
CB I:CYS103 3.0 91.5 1.0
CB I:CYS75 3.1 96.7 1.0
OG I:SER80 3.4 0.4 1.0
CA I:CYS106 3.5 1.0 1.0
N I:CYS106 3.6 0.4 1.0
CB I:CYS78 3.6 77.3 1.0
SG I:CYS106 3.7 0.9 1.0
N I:CYS78 3.9 0.9 1.0
CB I:HIS108 3.9 95.4 1.0
C I:CYS106 4.3 0.5 1.0
CA I:CYS78 4.3 97.3 1.0
N I:HIS108 4.4 67.8 1.0
CA I:CYS103 4.5 81.3 1.0
CB I:LYS77 4.6 63.8 1.0
N I:SER107 4.6 1.0 1.0
CA I:CYS75 4.6 0.8 1.0
C I:SER105 4.6 0.2 1.0
CB I:SER80 4.8 0.9 1.0
CA I:HIS108 4.8 89.3 1.0
C I:CYS78 4.8 89.8 1.0
N I:HIS79 4.9 88.6 1.0
CG I:HIS108 5.0 0.4 1.0
C I:LYS77 5.0 0.2 1.0
ND1 I:HIS108 5.0 0.3 1.0

Zinc binding site 7 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.5
occ:1.00
 SG J:CYS7 2.4 29.8 1.0
SG J:CYS46 2.5 73.8 1.0
SG J:CYS10 2.5 78.2 1.0
SG J:CYS45 2.5 83.5 1.0
N J:CYS46 2.7 0.3 1.0
CA J:CYS46 2.8 1.0 1.0
CB J:CYS7 3.0 56.8 1.0
CB J:CYS46 3.1 98.2 1.0
C J:CYS45 3.2 0.5 1.0
O J:CYS45 3.5 0.3 1.0
CB J:CYS10 3.7 75.8 1.0
CB J:CYS45 3.7 87.8 1.0
CA J:CYS45 4.0 79.0 1.0
N J:CYS10 4.1 64.9 1.0
NH2 J:ARG43 4.2 85.9 1.0
C J:CYS46 4.3 86.8 1.0
CA J:CYS10 4.5 65.5 1.0
CA J:CYS7 4.5 72.2 1.0
NE J:ARG43 4.6 76.5 1.0
CB J:LYS12 4.7 11.9 1.0
CZ J:ARG43 4.8 78.8 1.0
N J:CYS45 4.8 61.9 1.0
N J:GLY11 4.9 54.7 1.0
O J:CYS46 4.9 68.3 1.0
N J:LYS12 5.0 48.6 1.0

Zinc binding site 8 out of 8 in 6uq3

Go back to Zinc Binding Sites List in 6uq3
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with 5-Guanidinohydantoin Lesion in State 5


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 with 5-Guanidinohydantoin Lesion in State 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.6
occ:1.00
 SG L:CYS48 2.4 69.0 1.0
SG L:CYS31 2.4 0.6 1.0
SG L:CYS34 2.4 0.1 1.0
SG L:CYS51 2.4 0.2 1.0
CB L:CYS31 2.9 0.5 1.0
CB L:CYS48 3.2 67.9 1.0
CB L:CYS51 3.3 0.1 1.0
CB L:CYS34 3.7 0.5 1.0
OG L:SER36 4.0 0.9 1.0
N L:CYS51 4.0 0.6 1.0
CA L:CYS51 4.2 0.4 1.0
N L:CYS34 4.3 0.4 1.0
CB L:SER36 4.3 0.5 1.0
CA L:CYS31 4.4 0.8 1.0
CA L:CYS34 4.5 0.2 1.0
CB L:HIS53 4.5 0.0 1.0
CA L:CYS48 4.6 82.9 1.0
C L:CYS51 4.7 0.7 1.0
C L:CYS34 4.9 0.5 1.0
C L:CYS31 4.9 0.2 1.0

Reference:

J.Oh, A.M.Fleming, J.Xu, J.Chong, C.J.Burrows, D.Wang. Rna Polymerase II Stalls on Oxidative Dna Damage Via A Torsion-Latch Mechanism Involving Lone Pair-Pi and Ch-Pi Interactions. Proc.Natl.Acad.Sci.Usa V. 117 9338 2020.
ISSN: ESSN 1091-6490
PubMed: 32284409
DOI: 10.1073/PNAS.1919904117
Page generated: Tue Oct 29 08:44:30 2024

Last articles

Mg in 9MM6
Mg in 9MM2
Mg in 9MHS
Mg in 9MJ5
Mg in 9MHG
Mg in 9MHH
Mg in 9MHF
Mg in 9MHD
Mg in 9MGZ
Mg in 9MGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy