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Zinc in PDB 5w51: Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp

Enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp

All present enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp:
2.7.7.6;

Protein crystallography data

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp, PDB code: 5w51 was solved by W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.79 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.700, 224.000, 193.060, 90.00, 101.04, 90.00
R / Rfree (%) 22.7 / 25.4

Other elements in 5w51:

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp (pdb code 5w51). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp, PDB code: 5w51:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5w51

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Zinc binding site 1 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:1.0
occ:1.00
 SG A:CYS110 2.4 0.1 1.0
NE2 A:HIS109 2.6 0.4 1.0
CB A:CYS110 2.8 0.1 1.0
SG A:CYS148 2.9 0.8 1.0
CE1 A:HIS109 3.1 0.2 1.0
CD2 A:HIS109 3.4 0.3 1.0
CA A:CYS167 3.4 0.6 1.0
SG A:CYS107 3.6 0.3 1.0
CB A:CYS167 3.8 0.7 1.0
ND1 A:HIS109 3.9 0.3 1.0
SG A:CYS167 3.9 0.2 1.0
N A:CYS110 4.0 0.3 1.0
CA A:CYS110 4.0 0.0 1.0
CG A:HIS109 4.1 0.3 1.0
CB A:CYS148 4.2 0.7 1.0
C A:CYS167 4.3 0.2 1.0
N A:CYS167 4.3 0.2 1.0
N A:GLY168 4.3 1.0 1.0
CB A:CYS107 4.4 0.3 1.0

Zinc binding site 2 out of 8 in 5w51

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Zinc binding site 2 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:77.2
occ:1.00
 NE2 A:HIS80 2.1 97.5 1.0
SG A:CYS77 2.4 78.9 1.0
SG A:CYS70 2.5 0.1 1.0
CD2 A:HIS80 2.9 97.9 1.0
CB A:CYS67 2.9 0.6 1.0
CE1 A:HIS80 3.2 96.5 1.0
CB A:CYS77 3.6 77.2 1.0
SG A:CYS67 3.8 0.7 1.0
CA A:CYS67 4.0 0.1 1.0
CG A:HIS80 4.1 97.3 1.0
N A:GLN68 4.1 92.5 1.0
C A:CYS67 4.2 0.5 1.0
CB A:CYS70 4.2 0.1 1.0
ND1 A:HIS80 4.2 96.9 1.0
O A:GLN68 4.4 92.9 1.0
N A:CYS70 4.6 0.5 1.0
C A:GLN68 4.6 94.2 1.0
O A:CYS67 4.8 0.0 1.0
N A:GLN71 4.8 0.7 1.0
CA A:CYS70 4.9 0.6 1.0
CA A:CYS77 4.9 74.8 1.0
O A:GLN71 4.9 0.9 1.0

Zinc binding site 3 out of 8 in 5w51

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Zinc binding site 3 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:83.6
occ:1.00
 SG B:CYS1166 2.4 82.1 1.0
SG B:CYS1163 2.5 75.7 1.0
SG B:CYS1185 2.6 0.5 1.0
SG B:CYS1182 2.7 0.5 1.0
CB B:CYS1163 3.1 72.0 1.0
CB B:CYS1185 3.1 0.7 1.0
CB B:CYS1166 3.6 83.4 1.0
N B:CYS1166 3.9 84.9 1.0
CB B:CYS1182 4.3 0.9 1.0
CA B:CYS1166 4.3 83.3 1.0
CA B:CYS1185 4.5 0.4 1.0
CB B:ILE1165 4.5 0.6 1.0
N B:CYS1185 4.6 0.6 1.0
CA B:CYS1163 4.6 70.7 1.0
N B:GLY1167 4.8 0.4 1.0
C B:ILE1165 5.0 98.2 1.0
O B:CYS1182 5.0 0.1 1.0
CB B:THR1170 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 5w51

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Zinc binding site 4 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:51.0
occ:1.00
 SG C:CYS88 2.3 34.7 1.0
SG C:CYS86 2.4 51.5 1.0
SG C:CYS95 2.4 42.9 1.0
SG C:CYS92 2.5 57.4 1.0
CB C:CYS86 3.1 50.0 1.0
CB C:CYS95 3.2 43.9 1.0
N C:CYS92 3.3 53.7 1.0
CB C:CYS92 3.4 56.9 1.0
CB C:CYS88 3.5 36.6 1.0
CA C:CYS92 3.9 55.0 1.0
N C:CYS95 4.1 45.6 1.0
C C:HIS91 4.1 40.2 1.0
CA C:CYS95 4.3 44.2 1.0
CA C:HIS91 4.3 39.0 1.0
C C:CYS92 4.5 54.8 1.0
CA C:CYS86 4.5 50.6 1.0
N C:CYS88 4.6 37.2 1.0
CA C:CYS88 4.6 36.8 1.0
C C:LYS94 4.7 73.4 1.0
N C:LYS94 4.8 73.8 1.0
C C:CYS86 4.9 51.3 1.0
N C:ASP93 5.0 81.9 1.0
CB C:LYS94 5.0 76.5 1.0

Zinc binding site 5 out of 8 in 5w51

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Zinc binding site 5 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:71.2
occ:1.00
 SG I:CYS29 2.4 91.0 1.0
SG I:CYS32 2.4 81.4 1.0
SG I:CYS10 2.5 79.4 1.0
CB I:CYS10 2.7 78.2 1.0
SG I:CYS7 3.0 64.7 1.0
CB I:CYS32 3.2 84.1 1.0
N I:CYS32 3.3 86.8 1.0
CB I:THR31 3.7 79.5 1.0
CB I:CYS29 3.7 90.7 1.0
CB I:CYS7 3.7 63.6 1.0
N I:CYS10 3.8 78.0 1.0
CA I:CYS32 3.8 87.6 1.0
CA I:CYS10 3.8 78.1 1.0
C I:THR31 3.9 84.3 1.0
CA I:THR31 4.2 83.4 1.0
N I:THR31 4.4 83.6 1.0
CG2 I:THR31 4.4 79.7 1.0
OG1 I:THR31 4.5 78.6 1.0
N I:SER33 4.7 88.7 1.0
O I:THR31 4.7 86.2 1.0
C I:CYS32 4.8 89.7 1.0
C I:ASP9 4.8 66.1 1.0
C I:CYS10 4.8 77.6 1.0
CB I:TYR34 4.9 67.7 1.0
CA I:CYS29 5.0 91.9 1.0

Zinc binding site 6 out of 8 in 5w51

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Zinc binding site 6 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:53.3
occ:1.00
 SG I:CYS78 2.3 64.9 1.0
SG I:CYS106 2.4 55.5 1.0
SG I:CYS75 2.4 54.8 1.0
SG I:CYS103 2.5 74.2 1.0
CB I:CYS103 3.2 73.1 1.0
CB I:CYS75 3.2 53.9 1.0
CB I:CYS78 3.6 68.9 1.0
N I:CYS78 3.7 67.4 1.0
CB I:CYS106 3.9 60.0 1.0
N I:CYS106 4.0 57.0 1.0
CB I:HIS108 4.1 48.2 1.0
CA I:CYS78 4.2 69.0 1.0
CB I:LYS77 4.4 64.5 1.0
CA I:CYS106 4.4 59.4 1.0
CB I:SER105 4.6 72.1 1.0
N I:HIS79 4.6 55.0 1.0
CA I:CYS103 4.7 71.7 1.0
CA I:CYS75 4.7 53.4 1.0
N I:HIS108 4.7 48.0 1.0
C I:CYS78 4.7 68.2 1.0
N I:SER80 4.8 51.8 1.0
C I:LYS77 4.8 66.6 1.0
CB I:SER80 4.9 52.3 1.0
C I:CYS106 4.9 58.1 1.0
C I:SER105 5.0 75.1 1.0

Zinc binding site 7 out of 8 in 5w51

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Zinc binding site 7 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:33.3
occ:1.00
 SG J:CYS46 2.4 23.2 1.0
SG J:CYS7 2.4 31.8 1.0
SG J:CYS45 2.4 34.4 1.0
SG J:CYS10 2.5 44.5 1.0
N J:CYS46 3.2 22.4 1.0
CB J:CYS7 3.4 32.0 1.0
CB J:CYS45 3.6 33.9 1.0
CB J:CYS46 3.6 22.9 1.0
CB J:CYS10 3.6 45.7 1.0
CA J:CYS46 3.6 22.6 1.0
N J:CYS10 3.7 44.8 1.0
C J:CYS45 3.9 33.7 1.0
NE J:ARG43 3.9 46.6 1.0
CB J:SER9 4.1 27.4 1.0
NH2 J:ARG43 4.2 45.8 1.0
CA J:CYS10 4.3 45.5 1.0
CA J:CYS45 4.3 33.6 1.0
CZ J:ARG43 4.5 47.5 1.0
O J:CYS45 4.6 33.6 1.0
N J:GLY11 4.7 34.4 1.0
C J:SER9 4.7 27.7 1.0
CA J:SER9 4.8 27.2 1.0
CB J:ARG43 4.8 46.8 1.0
OG J:SER9 4.8 27.1 1.0
N J:SER9 4.8 26.5 1.0
CA J:CYS7 4.8 31.8 1.0
CD J:ARG43 4.9 49.1 1.0
N J:CYS45 4.9 33.6 1.0

Zinc binding site 8 out of 8 in 5w51

Go back to Zinc Binding Sites List in 5w51
Zinc binding site 8 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Pol II Elongation Complex with An N6-Methyladenine-Containing Template and A Matched Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.0
occ:1.00
 CB L:CYS51 2.4 0.7 1.0
SG L:CYS34 2.4 0.1 1.0
SG L:CYS48 2.5 0.8 1.0
SG L:CYS51 2.6 0.4 1.0
SG L:CYS31 3.0 1.0 1.0
CB L:CYS48 3.3 0.2 1.0
CB L:CYS31 3.5 0.4 1.0
CA L:CYS51 3.9 0.3 1.0
CB L:CYS34 4.0 0.6 1.0
O L:LYS49 4.5 0.8 1.0
N L:CYS51 4.5 0.6 1.0
OG L:SER36 4.5 0.8 1.0
CA L:CYS48 4.7 0.6 1.0
N L:LYS49 4.7 0.1 1.0
C L:CYS51 4.9 0.3 1.0
CA L:CYS31 5.0 0.7 1.0

Reference:

W.Wang, L.Xu, L.Hu, J.Chong, C.He, D.Wang. Epigenetic Dna Modification N6-Methyladenine Causes Site-Specific Rna Polymerase II Transcriptional Pausing. J.Am.Chem.Soc. V. 139 14436 2017.
ISSN: ESSN 1520-5126
PubMed: 28933854
DOI: 10.1021/JACS.7B06381
Page generated: Mon Oct 28 13:46:45 2024

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