Zinc in PDB 7ked: Rna Polymerase II Elongation Complex with Unnatural Base DTPT3

Enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3

All present enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, PDB code: 7ked was solved by J.Oh, W.Wang, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.60 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.89, 223.01, 194.7, 90, 101.6, 90
R / Rfree (%) 26.6 / 30.5

Other elements in 7ked:

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3 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 Unnatural Base DTPT3 (pdb code 7ked). 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 Unnatural Base DTPT3, PDB code: 7ked:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7ked

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:165.2
occ:1.00
 SG A:CYS107 2.4 164.7 1.0
SG A:CYS110 2.5 162.9 1.0
N A:GLY168 2.6 163.1 1.0
CA A:GLY168 2.9 160.8 1.0
CB A:CYS107 3.0 159.5 1.0
CB A:CYS110 3.3 158.2 1.0
N A:CYS167 3.7 162.8 1.0
C A:CYS167 3.7 161.2 1.0
SG A:CYS167 3.8 160.6 1.0
SG A:CYS148 3.9 148.1 1.0
C A:GLY166 4.1 157.9 1.0
CA A:CYS167 4.2 163.4 1.0
C A:GLY168 4.2 162.6 1.0
N A:CYS110 4.3 156.4 1.0
CA A:GLY166 4.3 161.8 1.0
CA A:CYS107 4.4 153.8 1.0
CA A:CYS110 4.4 156.4 1.0
N A:ASN169 4.5 167.6 1.0
CB A:CYS167 4.5 163.3 1.0
O A:CYS167 4.8 162.8 1.0
O A:GLY166 4.8 159.5 1.0
OE1 A:GLN171 4.8 160.4 1.0
O A:CYS148 4.9 153.9 1.0

Zinc binding site 2 out of 8 in 7ked

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:129.6
occ:1.00
 NE2 A:HIS80 2.0 108.3 1.0
SG A:CYS70 2.5 126.8 1.0
CB A:CYS70 2.5 127.9 1.0
SG A:CYS67 2.6 139.8 1.0
CE1 A:HIS80 2.6 108.7 1.0
SG A:CYS77 2.8 104.5 1.0
CB A:CYS77 3.0 100.3 1.0
CD2 A:HIS80 3.2 108.0 1.0
CB A:CYS67 3.3 135.1 1.0
OE1 A:GLN68 3.4 134.4 1.0
ND1 A:HIS80 3.9 109.1 1.0
CA A:CYS77 3.9 98.9 1.0
CA A:CYS70 4.1 129.3 1.0
NE2 A:GLN68 4.1 133.0 1.0
CG A:HIS80 4.2 109.4 1.0
CD A:GLN68 4.2 134.4 1.0
CA A:CYS67 4.7 136.5 1.0
N A:CYS70 4.7 131.1 1.0
C A:CYS70 4.8 130.5 1.0
N A:CYS77 4.9 101.0 1.0
C A:CYS77 4.9 94.2 1.0
O A:GLU72 5.0 117.9 1.0

Zinc binding site 3 out of 8 in 7ked

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:119.3
occ:1.00
 N B:CYS1166 2.3 99.6 1.0
SG B:CYS1166 2.3 99.5 1.0
SG B:CYS1185 2.4 112.5 1.0
CB B:CYS1166 2.5 99.7 1.0
SG B:CYS1163 2.6 109.8 1.0
CA B:CYS1166 2.8 100.3 1.0
CB B:CYS1185 2.9 113.6 1.0
SG B:CYS1182 3.0 109.9 1.0
C B:ILE1165 3.4 104.4 1.0
CB B:CYS1163 3.5 106.0 1.0
CB B:ILE1165 3.6 104.8 1.0
O B:CYS1166 3.7 105.6 1.0
C B:CYS1166 3.7 102.3 1.0
CA B:ILE1165 3.9 103.9 1.0
N B:ILE1165 4.2 104.6 1.0
CA B:CYS1185 4.3 115.5 1.0
CG1 B:ILE1165 4.4 105.0 1.0
O B:ILE1165 4.5 103.1 1.0
CG2 B:ILE1165 4.5 105.5 1.0
N B:CYS1185 4.6 114.2 1.0
CB B:CYS1182 4.6 110.1 1.0
CA B:CYS1163 4.8 102.4 1.0
O B:LYS1183 4.8 115.5 1.0
C B:CYS1163 5.0 103.0 1.0

Zinc binding site 4 out of 8 in 7ked

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:77.5
occ:1.00
 SG C:CYS92 2.3 66.4 1.0
SG C:CYS86 2.4 77.8 1.0
SG C:CYS88 2.4 67.5 1.0
SG C:CYS95 2.4 59.6 1.0
CB C:CYS95 2.6 62.4 1.0
CB C:CYS86 3.1 75.7 1.0
CB C:CYS88 3.2 68.8 1.0
CB C:CYS92 3.5 64.4 1.0
N C:CYS92 3.6 62.2 1.0
CA C:CYS95 3.9 62.4 1.0
CA C:CYS92 4.1 61.7 1.0
N C:CYS95 4.1 66.5 1.0
N C:CYS88 4.1 72.9 1.0
CA C:CYS88 4.3 70.2 1.0
C C:HIS91 4.4 64.6 1.0
CA C:CYS86 4.5 74.7 1.0
CA C:HIS91 4.6 64.5 1.0
C C:CYS92 4.7 64.1 1.0
CG C:LYS94 4.7 69.0 1.0
C C:CYS95 4.8 60.7 1.0
C C:CYS86 4.9 72.6 1.0
N C:PHE87 4.9 74.8 1.0
O C:CYS92 4.9 64.0 1.0
C C:LYS94 5.0 61.4 1.0

Zinc binding site 5 out of 8 in 7ked

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:78.1
occ:1.00
 SG I:CYS10 2.3 83.5 1.0
SG I:CYS32 2.3 87.0 1.0
SG I:CYS29 2.4 84.7 1.0
SG I:CYS7 2.4 86.1 1.0
CB I:CYS7 2.7 86.1 1.0
CB I:CYS29 2.7 84.6 1.0
CB I:CYS32 3.6 87.1 1.0
N I:CYS32 3.7 92.6 1.0
CB I:TYR34 4.0 81.5 1.0
CB I:CYS10 4.1 82.8 1.0
CA I:CYS32 4.1 89.2 1.0
CA I:CYS7 4.2 86.3 1.0
N I:CYS10 4.2 83.6 1.0
CA I:CYS29 4.3 86.6 1.0
C I:CYS32 4.5 88.8 1.0
N I:TYR34 4.6 83.5 1.0
CA I:CYS10 4.6 82.8 1.0
CB I:THR31 4.7 88.8 1.0
O I:CYS32 4.7 90.6 1.0
N I:ASN11 4.8 82.2 1.0
N I:THR31 4.8 88.4 1.0
C I:THR31 4.8 86.3 1.0
C I:CYS7 4.8 86.3 1.0
N I:ARG8 4.9 84.4 1.0
C I:CYS29 4.9 89.0 1.0
N I:ASP9 4.9 85.7 1.0
N I:CYS7 4.9 85.2 1.0

Zinc binding site 6 out of 8 in 7ked

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:67.2
occ:1.00
 SG I:CYS106 2.3 73.6 1.0
SG I:CYS78 2.3 65.8 1.0
SG I:CYS75 2.3 66.5 1.0
SG I:CYS103 2.4 66.3 1.0
CB I:CYS75 2.8 67.5 1.0
CB I:CYS103 2.9 65.9 1.0
CB I:CYS78 3.4 65.8 1.0
OG I:SER80 3.5 64.3 1.0
CB I:CYS106 3.6 71.4 1.0
N I:CYS78 3.8 68.4 1.0
N I:CYS106 4.0 62.6 1.0
CA I:CYS78 4.1 67.0 1.0
CA I:CYS75 4.3 69.3 1.0
CA I:CYS103 4.4 63.2 1.0
CA I:CYS106 4.4 69.0 1.0
CB I:HIS108 4.4 68.1 1.0
C I:CYS78 4.5 69.7 1.0
N I:HIS79 4.6 65.2 1.0
N I:SER80 4.7 64.4 1.0
CB I:SER80 4.8 65.0 1.0
CB I:LYS77 4.8 72.5 1.0
C I:CYS75 4.9 67.3 1.0
CB I:SER105 4.9 69.6 1.0
C I:CYS103 4.9 62.4 1.0
C I:CYS106 4.9 73.0 1.0
C I:LYS77 4.9 73.6 1.0
O I:CYS75 5.0 66.9 1.0
O I:SER80 5.0 69.0 1.0
C I:SER105 5.0 71.5 1.0
N I:HIS108 5.0 71.3 1.0

Zinc binding site 7 out of 8 in 7ked

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:46.6
occ:1.00
 SG J:CYS45 2.3 53.5 1.0
SG J:CYS10 2.3 49.2 1.0
SG J:CYS7 2.4 51.1 1.0
SG J:CYS46 2.6 53.4 1.0
N J:CYS46 2.8 51.7 1.0
CB J:CYS7 2.9 48.6 1.0
CA J:CYS46 3.0 51.9 1.0
C J:CYS45 3.0 52.5 1.0
CB J:CYS46 3.2 52.3 1.0
O J:CYS45 3.3 52.8 1.0
CB J:CYS10 3.4 50.3 1.0
CB J:CYS45 3.6 52.8 1.0
NH2 J:ARG43 3.7 54.8 1.0
N J:CYS10 3.8 51.1 1.0
CA J:CYS45 3.9 50.7 1.0
CA J:CYS10 4.2 51.8 1.0
CA J:CYS7 4.4 46.9 1.0
C J:CYS46 4.5 50.3 1.0
N J:CYS45 4.7 50.0 1.0
CZ J:ARG43 4.7 55.3 1.0
N J:GLY11 4.7 52.4 1.0
C J:SER9 4.8 49.9 1.0
NE J:ARG43 4.8 55.3 1.0
N J:SER9 4.9 49.4 1.0
C J:CYS7 4.9 48.2 1.0
C J:CYS10 5.0 49.0 1.0
O J:ARG43 5.0 51.7 1.0

Zinc binding site 8 out of 8 in 7ked

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3


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 Unnatural Base DTPT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:122.9
occ:1.00
 SG L:CYS34 2.3 114.3 1.0
SG L:CYS48 2.3 125.6 1.0
SG L:CYS51 2.4 120.2 1.0
CB L:CYS48 2.4 126.4 1.0
SG L:CYS31 2.5 113.4 1.0
CB L:CYS51 3.0 120.2 1.0
CB L:CYS31 3.2 109.1 1.0
OG L:SER36 3.4 113.9 1.0
CB L:CYS34 3.7 116.5 1.0
N L:CYS51 3.8 123.5 1.0
CA L:CYS51 3.9 122.8 1.0
CA L:CYS48 3.9 127.4 1.0
N L:CYS34 4.1 117.3 1.0
N L:GLY52 4.3 118.2 1.0
CA L:CYS34 4.5 117.2 1.0
C L:CYS48 4.5 127.4 1.0
C L:CYS51 4.6 124.5 1.0
CA L:CYS31 4.7 108.8 1.0
N L:CYS48 4.7 128.0 1.0
CB L:SER36 4.7 113.3 1.0
N L:HIS53 4.8 116.4 1.0
C L:ASP50 4.8 116.7 1.0
O L:CYS48 5.0 127.5 1.0
N L:ASP50 5.0 116.7 1.0
N L:LYS49 5.0 115.8 1.0

Reference:

J.Oh, W.Wang, D.Wang. Transcriptional Processing of Unnatural Base Pair By Eukaryotic Rna Polymerase II Nat.Chem.Biol. 2021.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-021-00817-3
Page generated: Mon Jul 12 17:17:14 2021

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