Zinc in PDB 8ukt: Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added

Enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added

All present enzymatic activity of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added, PDB code: 8ukt was solved by P.Hou, J.Oh, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.75 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.681, 221.393, 190.539, 90, 97.67, 90
R / Rfree (%) 25.1 / 29

Other elements in 8ukt:

The structure of Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added 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 Fapy-Dg Lesion with Amp Added (pdb code 8ukt). 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 Fapy-Dg Lesion with Amp Added, PDB code: 8ukt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8ukt

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:358.2
occ:1.00
 OD1 A:ASN169 2.2 315.8 1.0
SG A:CYS110 2.3 218.5 1.0
SG A:CYS167 2.3 337.2 1.0
SG A:CYS107 2.3 293.1 1.0
CB A:CYS167 2.9 319.6 1.0
CB A:CYS110 3.0 199.2 1.0
CG A:ASN169 3.1 294.7 1.0
N A:CYS110 3.3 245.9 1.0
CB A:ASN169 3.4 278.4 1.0
O A:CYS167 3.4 343.9 1.0
CB A:CYS107 3.5 255.0 1.0
CA A:CYS167 3.6 325.0 1.0
C A:CYS167 3.6 324.9 1.0
CB A:HIS109 3.7 308.6 1.0
CA A:CYS110 3.7 219.6 1.0
C A:HIS109 4.0 288.6 1.0
N A:ASN169 4.2 261.8 1.0
ND1 A:HIS109 4.3 311.2 1.0
CA A:HIS109 4.3 298.9 1.0
CG A:HIS109 4.3 317.5 1.0
ND2 A:ASN169 4.4 293.2 1.0
CA A:ASN169 4.4 263.9 1.0
N A:GLY168 4.5 232.4 1.0
O A:CYS110 4.6 223.6 1.0
N A:HIS109 4.6 295.3 1.0
NE2 A:GLN171 4.6 253.8 1.0
C A:CYS110 4.7 229.7 1.0
CA A:CYS107 4.9 238.2 1.0
C A:GLY168 4.9 220.7 1.0
O A:HIS109 4.9 288.7 1.0
N A:CYS167 5.0 319.0 1.0

Zinc binding site 2 out of 8 in 8ukt

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:185.5
occ:1.00
 NE2 A:HIS80 2.1 186.7 1.0
SG A:CYS77 2.3 170.7 1.0
SG A:CYS70 2.3 149.5 1.0
SG A:CYS67 2.3 153.3 1.0
CE1 A:HIS80 2.6 176.5 1.0
CD2 A:HIS80 2.9 176.8 1.0
CB A:CYS70 3.3 126.0 1.0
CB A:CYS67 3.3 146.9 1.0
CB A:CYS77 3.4 157.0 1.0
ND1 A:HIS80 3.5 157.2 1.0
CG A:HIS80 3.7 161.0 1.0
N A:GLY79 3.9 127.7 1.0
CA A:CYS77 4.2 154.0 1.0
CA A:GLY79 4.3 127.5 1.0
CD A:PRO78 4.4 155.6 1.0
C A:CYS77 4.5 159.7 1.0
N A:PRO78 4.5 157.8 1.0
C A:GLY79 4.6 130.4 1.0
CA A:CYS70 4.7 150.3 1.0
CA A:CYS67 4.7 158.0 1.0
N A:HIS80 4.8 142.7 1.0
N A:GLY59 4.9 171.7 1.0
CG A:PRO78 4.9 130.8 1.0
O A:LEU58 4.9 181.1 1.0
CA A:GLY59 4.9 159.6 1.0
C A:LEU58 5.0 165.0 1.0
CB A:HIS80 5.0 149.5 1.0

Zinc binding site 3 out of 8 in 8ukt

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:172.1
occ:1.00
 SG B:CYS1185 2.3 164.9 1.0
SG B:CYS1166 2.3 174.2 1.0
SG B:CYS1163 2.3 176.8 1.0
SG B:CYS1182 2.3 185.5 1.0
CB B:CYS1166 3.1 140.1 1.0
CB B:CYS1185 3.1 164.2 1.0
CB B:CYS1163 3.3 148.1 1.0
N B:CYS1166 3.4 177.4 1.0
CA B:CYS1166 3.7 152.4 1.0
CB B:CYS1182 3.8 174.7 1.0
O B:CYS1166 3.8 166.4 1.0
OG1 B:THR1170 4.0 156.2 1.0
C B:CYS1166 4.2 152.4 1.0
O B:LYS1183 4.3 168.2 1.0
CA B:CYS1185 4.4 181.5 1.0
C B:ILE1165 4.4 170.3 1.0
ND2 B:ASN1187 4.5 182.5 1.0
CB B:ILE1165 4.5 168.1 1.0
N B:CYS1185 4.5 182.4 1.0
CA B:CYS1163 4.7 145.1 1.0
CA B:ILE1165 4.8 163.0 1.0
N B:ILE1165 4.9 145.0 1.0
O B:LEU1168 4.9 136.0 1.0
C B:CYS1163 5.0 162.5 1.0

Zinc binding site 4 out of 8 in 8ukt

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:100.7
occ:1.00
 CB C:CYS92 1.1 105.8 1.0
SG C:CYS86 2.3 88.0 1.0
SG C:CYS88 2.3 69.1 1.0
SG C:CYS92 2.3 132.2 1.0
CA C:CYS92 2.4 98.3 1.0
CB C:CYS95 2.7 64.5 1.0
N C:CYS92 2.8 106.2 1.0
C C:CYS92 3.2 76.5 1.0
CB C:CYS88 3.3 68.9 1.0
CB C:CYS86 3.6 89.8 1.0
N C:CYS95 3.6 101.6 1.0
O C:CYS92 3.7 97.0 1.0
CA C:CYS95 3.8 83.2 1.0
C C:HIS91 3.8 109.0 1.0
SG C:CYS95 4.0 123.6 1.0
N C:ASP93 4.1 68.1 1.0
O C:HIS91 4.4 114.2 1.0
N C:CYS88 4.4 96.2 1.0
CA C:CYS88 4.5 75.6 1.0
C C:LYS94 4.7 98.7 1.0
N C:LYS94 4.8 77.4 1.0
CA C:HIS91 4.8 85.7 1.0
C C:CYS95 4.9 98.2 1.0
N C:SER96 5.0 108.2 1.0
CA C:CYS86 5.0 104.8 1.0

Zinc binding site 5 out of 8 in 8ukt

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:126.5
occ:1.00
 SG I:CYS7 2.3 113.9 1.0
SG I:CYS29 2.3 140.7 1.0
SG I:CYS10 2.3 163.8 1.0
SG I:CYS32 2.3 181.0 1.0
CB I:CYS7 3.2 113.4 1.0
CB I:CYS29 3.4 116.8 1.0
N I:CYS32 3.4 125.8 1.0
CB I:CYS32 3.6 174.4 1.0
CB I:CYS10 3.8 126.2 1.0
CA I:CYS32 4.0 149.9 1.0
CB I:THR31 4.0 134.7 1.0
O I:CYS32 4.2 140.1 1.0
N I:CYS10 4.2 123.6 1.0
C I:THR31 4.3 122.5 1.0
C I:CYS32 4.5 137.9 1.0
CA I:THR31 4.5 133.7 1.0
N I:THR31 4.5 147.7 1.0
CA I:CYS7 4.6 112.9 1.0
CA I:CYS10 4.6 129.0 1.0
OG1 I:THR31 4.6 149.7 1.0
CB I:ASP9 4.7 156.6 1.0
CA I:CYS29 4.8 125.4 1.0
C I:CYS7 4.9 122.6 1.0
CG2 I:THR31 5.0 124.4 1.0
C I:ASP9 5.0 132.2 1.0
N I:ASP9 5.0 112.9 1.0

Zinc binding site 6 out of 8 in 8ukt

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:277.3
occ:1.00
 SG I:CYS78 2.3 152.4 1.0
SG I:CYS106 2.3 159.2 1.0
SG I:CYS75 2.3 207.6 1.0
SG I:CYS103 2.3 231.1 1.0
CB I:CYS103 2.7 153.9 1.0
CB I:CYS75 2.9 172.3 1.0
CB I:CYS78 3.1 130.3 1.0
CB I:CYS106 3.5 131.3 1.0
CE1 I:PHE110 3.6 133.4 1.0
N I:CYS75 3.8 145.9 1.0
CA I:CYS75 3.9 161.6 1.0
CD1 I:PHE110 3.9 108.9 1.0
CA I:CYS103 4.0 126.9 1.0
N I:CYS78 4.2 197.6 1.0
CA I:CYS78 4.2 134.3 1.0
O I:HIS108 4.3 117.2 1.0
N I:CYS106 4.3 155.0 1.0
N I:CYS103 4.3 114.7 1.0
CZ I:PHE110 4.4 150.2 1.0
OG I:SER80 4.4 174.4 1.0
O I:CYS75 4.4 170.8 1.0
CA I:CYS106 4.5 135.7 1.0
C I:CYS103 4.5 135.0 1.0
C I:CYS75 4.5 162.5 1.0
O I:CYS103 4.6 146.2 1.0
O I:SER80 4.7 162.6 1.0
CG I:PHE110 5.0 107.4 1.0

Zinc binding site 7 out of 8 in 8ukt

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:165.2
occ:1.00
 SG J:CYS46 2.3 47.5 1.0
SG J:CYS10 2.3 76.5 1.0
SG J:CYS45 2.3 110.0 1.0
SG J:CYS7 2.3 48.5 1.0
N J:CYS46 3.1 94.9 1.0
CB J:CYS10 3.4 69.4 1.0
CB J:CYS45 3.4 89.3 1.0
CB J:CYS46 3.5 95.1 1.0
C J:CYS45 3.5 81.2 1.0
CB J:CYS7 3.5 72.6 1.0
CA J:CYS46 3.6 94.2 1.0
NH2 J:ARG43 3.8 107.7 1.0
N J:CYS10 3.8 73.8 1.0
CA J:CYS45 4.0 73.1 1.0
NE J:ARG43 4.1 105.0 1.0
O J:CYS45 4.1 61.8 1.0
CA J:CYS10 4.1 70.4 1.0
CZ J:ARG43 4.4 97.5 1.0
N J:GLY11 4.5 65.5 1.0
N J:CYS45 4.7 71.9 1.0
CB J:SER9 4.7 66.2 1.0
C J:CYS10 4.8 56.7 1.0
CB J:ARG43 4.9 92.0 1.0
N J:LYS12 4.9 59.1 1.0
CA J:CYS7 4.9 88.6 1.0
C J:SER9 4.9 69.4 1.0
CB J:LYS12 5.0 52.9 1.0

Zinc binding site 8 out of 8 in 8ukt

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Fapy-Dg Lesion with Amp Added


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 Fapy-Dg Lesion with Amp Added within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:364.5
occ:1.00
 SG L:CYS51 2.3 257.3 1.0
SG L:CYS48 2.3 326.6 1.0
SG L:CYS31 2.3 306.7 1.0
SG L:CYS34 2.3 402.4 1.0
CD1 L:LEU38 2.7 274.4 1.0
CB L:CYS31 2.9 245.5 1.0
CB L:CYS48 3.1 295.6 1.0
CB L:CYS51 3.3 248.2 1.0
CB L:CYS34 3.3 408.5 1.0
CG L:LEU38 3.9 258.1 1.0
CA L:CYS31 4.1 234.3 1.0
N L:CYS51 4.2 256.3 1.0
CA L:CYS48 4.2 280.8 1.0
N L:CYS48 4.3 267.6 1.0
N L:CYS34 4.3 415.0 1.0
CD2 L:LEU38 4.3 272.7 1.0
CA L:CYS51 4.4 240.0 1.0
N L:CYS31 4.4 219.6 1.0
CA L:CYS34 4.4 413.3 1.0
O L:CYS31 4.5 284.5 1.0
C L:CYS31 4.5 277.9 1.0
O L:CYS48 4.8 290.5 1.0
C L:CYS48 4.8 289.8 1.0
O L:SER36 4.9 226.3 1.0
CD2 L:LEU56 4.9 171.7 1.0

Reference:

S.Gao, P.Hou, J.Oh, D.Wang, M.M.Greenberg. Molecular Mechanism of Rna Polymerase II Transcriptional Mutagenesis By the Epimerizable Dna Lesion, Fapy·Dg. J.Am.Chem.Soc. V. 146 6274 2024.
ISSN: ESSN 1520-5126
PubMed: 38393762
DOI: 10.1021/JACS.3C14476
Page generated: Thu Oct 31 12:21:03 2024

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