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Zinc in PDB 5w4u: Pol II Elongation Complex with An N6-Methyladenine-Containing Template

Enzymatic activity of Pol II Elongation Complex with An N6-Methyladenine-Containing Template

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

Protein crystallography data

The structure of Pol II Elongation Complex with An N6-Methyladenine-Containing Template, PDB code: 5w4u 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) 81.02 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.210, 221.990, 192.700, 90.00, 100.58, 90.00
R / Rfree (%) 22.7 / 25.9

Other elements in 5w4u:

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

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template (pdb code 5w4u). 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, PDB code: 5w4u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.5
occ:1.00
 SG A:CYS110 2.8 0.1 1.0
NE2 A:HIS109 2.8 0.5 1.0
SG A:CYS148 2.9 0.1 1.0
CB A:CYS110 2.9 0.0 1.0
CD2 A:HIS109 3.3 0.9 1.0
CE1 A:HIS109 3.5 0.5 1.0
SG A:CYS107 3.5 0.6 1.0
CB A:CYS167 3.7 1.0 1.0
CA A:CYS167 3.7 1.0 1.0
SG A:CYS167 3.9 0.6 1.0
N A:CYS110 3.9 0.7 1.0
CA A:CYS110 4.0 0.0 1.0
CG A:HIS109 4.1 0.8 1.0
CB A:CYS148 4.2 0.6 1.0
ND1 A:HIS109 4.2 0.2 1.0
CB A:CYS107 4.2 0.1 1.0
N A:GLY168 4.2 0.2 1.0
C A:CYS167 4.4 0.2 1.0
N A:ASN169 4.8 0.4 1.0
N A:CYS167 4.9 0.9 1.0
C A:HIS109 4.9 0.6 1.0

Zinc binding site 2 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:91.9
occ:1.00
 NE2 A:HIS80 2.3 0.1 1.0
SG A:CYS77 2.4 92.0 1.0
CD2 A:HIS80 2.8 0.3 1.0
CB A:CYS67 2.9 0.8 1.0
SG A:CYS70 3.2 0.8 1.0
CE1 A:HIS80 3.5 0.5 1.0
SG A:CYS67 3.5 0.1 1.0
CB A:CYS77 3.7 90.4 1.0
CA A:CYS67 3.8 0.4 1.0
N A:GLN68 4.0 0.8 1.0
CG A:HIS80 4.1 0.9 1.0
C A:CYS67 4.1 0.4 1.0
O A:GLN68 4.3 0.6 1.0
ND1 A:HIS80 4.4 0.5 1.0
O A:PRO78 4.6 0.8 1.0
C A:GLN68 4.8 0.5 1.0
O A:CYS67 4.9 0.7 1.0
CB A:CYS70 4.9 0.2 1.0
CA A:GLY59 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.4
occ:1.00
 SG B:CYS1166 2.4 90.0 1.0
SG B:CYS1185 2.5 0.7 1.0
SG B:CYS1163 2.6 0.0 1.0
SG B:CYS1182 2.7 0.5 1.0
CB B:CYS1163 3.1 97.7 1.0
CB B:CYS1185 3.3 0.6 1.0
CB B:CYS1166 3.6 91.4 1.0
N B:CYS1166 4.0 93.0 1.0
CA B:CYS1166 4.4 91.0 1.0
CB B:CYS1182 4.4 0.5 1.0
CA B:CYS1185 4.6 0.5 1.0
CA B:CYS1163 4.6 95.9 1.0
CB B:ILE1165 4.7 0.7 1.0
N B:CYS1185 4.7 0.6 1.0
CB B:THR1170 4.8 0.4 1.0
N B:GLY1167 5.0 0.5 1.0
OG1 B:THR1170 5.0 0.3 1.0

Zinc binding site 4 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:52.8
occ:1.00
 SG C:CYS88 2.3 54.1 1.0
SG C:CYS95 2.4 71.3 1.0
SG C:CYS86 2.5 53.1 1.0
SG C:CYS92 2.5 50.0 1.0
CB C:CYS86 3.0 51.2 1.0
CB C:CYS95 3.1 73.5 1.0
CB C:CYS88 3.4 57.1 1.0
N C:CYS92 3.5 46.1 1.0
CB C:CYS92 3.6 50.1 1.0
N C:CYS95 4.0 76.0 1.0
CA C:CYS92 4.0 48.1 1.0
CA C:CYS95 4.2 74.1 1.0
C C:HIS91 4.3 49.9 1.0
CA C:CYS86 4.4 51.8 1.0
C C:LYS94 4.5 88.5 1.0
CA C:HIS91 4.5 48.0 1.0
N C:CYS88 4.6 57.7 1.0
C C:CYS92 4.6 47.9 1.0
CA C:CYS88 4.6 57.8 1.0
N C:LYS94 4.7 87.2 1.0
C C:CYS86 4.8 52.3 1.0
CB C:LYS94 4.8 91.9 1.0
CA C:LYS94 4.9 89.1 1.0
O C:CYS92 5.0 46.2 1.0

Zinc binding site 5 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:72.0
occ:1.00
 SG I:CYS32 2.5 0.1 1.0
SG I:CYS29 2.5 0.8 1.0
SG I:CYS7 2.6 71.4 1.0
SG I:CYS10 2.9 93.4 1.0
CB I:CYS10 3.0 83.7 1.0
CB I:CYS7 3.2 71.0 1.0
CB I:CYS29 3.4 0.2 1.0
CB I:CYS32 3.6 0.8 1.0
N I:CYS32 3.7 0.8 1.0
N I:CYS10 3.8 82.8 1.0
CB I:THR31 3.9 88.0 1.0
CA I:CYS10 4.0 83.2 1.0
CA I:CYS32 4.3 0.6 1.0
C I:THR31 4.3 89.7 1.0
CB I:TYR34 4.5 73.0 1.0
CA I:THR31 4.5 88.8 1.0
OG1 I:THR31 4.6 88.3 1.0
N I:THR31 4.6 88.3 1.0
CA I:CYS7 4.7 70.6 1.0
CG2 I:THR31 4.7 88.2 1.0
O I:CYS29 4.7 0.7 1.0
CA I:CYS29 4.8 0.6 1.0
C I:ASP9 4.8 84.1 1.0
C I:CYS10 4.8 82.9 1.0
C I:CYS29 4.9 0.4 1.0
CB I:ASP9 4.9 84.5 1.0
N I:SER33 4.9 86.5 1.0
N I:ASN11 5.0 79.5 1.0
N I:TYR34 5.0 75.0 1.0

Zinc binding site 6 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:50.3
occ:1.00
 SG I:CYS78 2.4 67.6 1.0
SG I:CYS106 2.5 68.0 1.0
SG I:CYS103 2.5 62.5 1.0
SG I:CYS75 2.5 58.0 1.0
CB I:CYS103 3.1 60.6 1.0
CB I:CYS75 3.3 56.0 1.0
CB I:CYS78 3.6 70.2 1.0
N I:CYS78 3.7 69.9 1.0
CB I:CYS106 4.0 72.1 1.0
N I:CYS106 4.0 71.8 1.0
CB I:HIS108 4.2 54.1 1.0
CA I:CYS78 4.2 70.4 1.0
CB I:LYS77 4.3 52.5 1.0
CA I:CYS106 4.5 72.4 1.0
CB I:SER105 4.5 84.2 1.0
N I:HIS79 4.6 71.9 1.0
CA I:CYS103 4.6 60.1 1.0
N I:HIS108 4.7 54.4 1.0
C I:CYS78 4.7 71.5 1.0
N I:SER80 4.7 60.7 1.0
CB I:SER80 4.7 60.6 1.0
C I:LYS77 4.8 52.0 1.0
CA I:CYS75 4.8 56.3 1.0
C I:CYS106 4.9 72.7 1.0
N I:SER107 5.0 87.2 1.0
CA I:LYS77 5.0 52.7 1.0

Zinc binding site 7 out of 8 in 5w4u

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:32.3
occ:1.00
 SG J:CYS45 2.4 51.2 1.0
SG J:CYS46 2.4 35.5 1.0
SG J:CYS7 2.5 59.0 1.0
SG J:CYS10 2.5 56.0 1.0
N J:CYS46 3.3 35.3 1.0
CB J:CYS7 3.4 52.4 1.0
CB J:CYS10 3.5 58.3 1.0
N J:CYS10 3.5 55.8 1.0
CB J:CYS45 3.6 48.1 1.0
CB J:CYS46 3.7 35.0 1.0
CA J:CYS46 3.7 34.9 1.0
C J:CYS45 3.9 47.3 1.0
NE J:ARG43 4.0 68.4 1.0
CB J:SER9 4.0 31.1 1.0
NH2 J:ARG43 4.1 69.2 1.0
CA J:CYS10 4.1 58.1 1.0
CA J:CYS45 4.3 47.8 1.0
N J:GLY11 4.5 43.8 1.0
CZ J:ARG43 4.5 68.3 1.0
C J:SER9 4.6 32.1 1.0
O J:CYS45 4.6 48.0 1.0
CA J:SER9 4.7 31.1 1.0
N J:SER9 4.7 31.2 1.0
CA J:CYS7 4.8 52.9 1.0
OG J:SER9 4.8 30.4 1.0
C J:CYS10 4.9 58.7 1.0
N J:LYS12 5.0 27.2 1.0
CB J:ARG43 5.0 67.4 1.0

Zinc binding site 8 out of 8 in 5w4u

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Zinc binding site 8 out of 8 in the Pol II Elongation Complex with An N6-Methyladenine-Containing Template


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.7
occ:1.00
 SG L:CYS48 2.5 0.2 1.0
SG L:CYS34 2.5 0.5 1.0
CB L:CYS51 2.5 0.6 1.0
SG L:CYS51 2.6 1.0 1.0
SG L:CYS31 2.8 0.4 1.0
CB L:CYS48 3.2 0.3 1.0
CB L:CYS31 3.3 0.3 1.0
CA L:CYS51 4.0 0.9 1.0
CB L:CYS34 4.1 0.7 1.0
N L:CYS51 4.6 0.5 1.0
OG L:SER36 4.6 0.8 1.0
CA L:CYS48 4.6 0.1 1.0
O L:LYS49 4.7 1.0 1.0
N L:LYS49 4.7 0.5 1.0
CA L:CYS31 4.8 0.4 1.0
C L:CYS51 4.9 0.8 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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