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Zinc in PDB 7kee: Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site

Enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site

All present enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site, PDB code: 7kee 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) 49.15 / 3.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.544, 222.739, 194.661, 90, 101.9, 90
R / Rfree (%) 25.9 / 30.2

Other elements in 7kee:

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

Zinc binding site 1 out of 8 in 7kee

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:193.3
occ:1.00
 SG A:CYS110 2.4 162.6 1.0
SG A:CYS148 2.5 203.2 1.0
SG A:CYS167 2.6 175.6 1.0
CB A:CYS148 2.6 187.6 1.0
CB A:CYS107 2.7 166.2 1.0
CB A:CYS110 3.0 153.9 1.0
SG A:CYS107 3.1 169.4 1.0
O A:CYS167 3.6 175.4 1.0
N A:CYS110 3.8 145.3 1.0
CA A:CYS110 3.9 145.3 1.0
C A:CYS167 4.0 171.8 1.0
CB A:CYS167 4.0 176.5 1.0
CA A:CYS107 4.0 150.3 1.0
CA A:CYS148 4.1 169.8 1.0
C A:CYS107 4.4 144.5 1.0
CA A:CYS167 4.4 176.6 1.0
O A:CYS107 4.5 143.0 1.0
O A:CYS148 4.5 165.6 1.0
N A:CYS167 4.5 175.8 1.0
O A:ASN169 4.6 152.7 1.0
N A:GLY168 4.6 183.9 1.0
N A:CYS107 4.6 145.4 1.0
C A:CYS148 4.6 161.3 1.0
C A:HIS109 4.8 148.5 1.0
N A:CYS148 4.9 156.6 1.0
N A:ASN169 4.9 155.5 1.0

Zinc binding site 2 out of 8 in 7kee

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:116.5
occ:1.00
 SG A:CYS67 2.3 124.0 1.0
CE1 A:HIS80 2.4 129.5 1.0
SG A:CYS77 2.4 108.5 1.0
CB A:CYS70 2.5 119.6 1.0
SG A:CYS70 2.6 120.3 1.0
CB A:CYS77 2.8 111.2 1.0
NE2 A:HIS80 3.1 129.6 1.0
CB A:CYS67 3.1 125.8 1.0
CA A:CYS77 3.4 113.2 1.0
ND1 A:HIS80 3.4 129.2 1.0
N A:CYS70 3.5 124.8 1.0
CA A:CYS70 3.6 123.6 1.0
OG1 A:THR69 4.1 136.2 1.0
C A:CYS77 4.1 112.7 1.0
CD2 A:HIS80 4.3 127.8 1.0
CD A:PRO78 4.3 115.0 1.0
N A:PRO78 4.4 114.3 1.0
CG A:HIS80 4.4 128.1 1.0
N A:GLY79 4.5 108.0 1.0
CA A:CYS67 4.6 127.1 1.0
N A:CYS77 4.6 118.9 1.0
C A:CYS70 4.7 131.3 1.0
C A:THR69 4.8 123.0 1.0
O A:CYS77 4.9 111.1 1.0
N A:GLN71 5.0 132.4 1.0
CB A:THR69 5.0 133.9 1.0

Zinc binding site 3 out of 8 in 7kee

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2102

b:121.7
occ:1.00
 CB B:CYS1166 2.4 108.8 1.0
SG B:CYS1163 2.5 126.5 1.0
CB B:CYS1185 2.5 130.8 1.0
SG B:CYS1182 2.5 139.7 1.0
SG B:CYS1185 2.5 129.8 1.0
N B:CYS1166 2.9 118.2 1.0
CA B:CYS1166 3.1 114.0 1.0
CB B:CYS1163 3.3 124.1 1.0
CB B:CYS1182 3.7 136.7 1.0
SG B:CYS1166 3.8 108.8 1.0
CA B:CYS1185 3.9 134.4 1.0
C B:ILE1165 4.1 121.8 1.0
N B:CYS1185 4.3 141.3 1.0
CB B:ILE1165 4.4 120.8 1.0
C B:CYS1166 4.5 117.1 1.0
O B:LYS1183 4.5 144.6 1.0
CA B:ILE1165 4.6 122.6 1.0
C B:CYS1185 4.7 132.2 1.0
CB B:ASN1187 4.8 131.7 1.0
CA B:CYS1163 4.8 123.0 1.0
N B:ILE1165 4.8 125.2 1.0
N B:GLY1167 4.8 117.0 1.0
O B:ILE1165 5.0 125.2 1.0
C B:GLY1184 5.0 136.2 1.0

Zinc binding site 4 out of 8 in 7kee

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:76.9
occ:1.00
 SG C:CYS95 2.3 65.7 1.0
SG C:CYS88 2.3 54.5 1.0
SG C:CYS86 2.5 98.8 1.0
SG C:CYS92 2.7 81.2 1.0
CB C:CYS95 3.0 64.7 1.0
CB C:CYS86 3.1 94.7 1.0
CB C:CYS88 3.4 60.5 1.0
CB C:CYS92 3.7 84.4 1.0
N C:CYS95 3.8 76.8 1.0
CA C:CYS95 4.0 65.0 1.0
N C:CYS92 4.3 89.3 1.0
N C:CYS88 4.3 56.1 1.0
CA C:CYS92 4.4 86.9 1.0
CA C:CYS88 4.5 56.6 1.0
CA C:CYS86 4.5 91.7 1.0
C C:LYS94 4.5 79.0 1.0
CB C:LYS94 4.7 83.1 1.0
C C:CYS86 4.8 88.5 1.0
C C:CYS92 4.8 84.8 1.0
O C:ASP90 4.8 86.5 1.0
O C:CYS88 4.9 92.5 1.0
N C:LYS94 4.9 70.9 1.0
C C:CYS95 4.9 64.0 1.0
CA C:LYS94 4.9 77.0 1.0
O C:CYS92 5.0 86.2 1.0
C C:HIS91 5.0 87.6 1.0

Zinc binding site 5 out of 8 in 7kee

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:71.5
occ:1.00
 SG I:CYS7 2.4 60.8 1.0
CB I:CYS32 2.6 99.5 1.0
OG1 I:THR31 2.7 73.5 1.0
N I:CYS32 2.8 80.3 1.0
SG I:CYS10 3.0 83.3 1.0
CA I:CYS32 3.2 89.1 1.0
SG I:CYS29 3.3 86.2 1.0
CB I:CYS7 3.6 75.0 1.0
CB I:TYR34 3.8 63.4 1.0
C I:THR31 3.9 83.2 1.0
CB I:CYS10 3.9 85.2 1.0
CB I:CYS29 4.0 77.4 1.0
C I:CYS32 4.0 86.7 1.0
CB I:THR31 4.0 77.2 1.0
SG I:CYS32 4.1 104.8 1.0
O I:CYS32 4.2 88.7 1.0
N I:CYS10 4.3 75.0 1.0
CA I:THR31 4.3 77.8 1.0
N I:THR31 4.5 75.1 1.0
CB I:ASP9 4.5 76.5 1.0
N I:TYR34 4.5 64.0 1.0
CG I:TYR34 4.7 63.0 1.0
CA I:CYS10 4.8 81.7 1.0
CA I:TYR34 4.8 63.7 1.0
O I:THR31 4.9 80.0 1.0
N I:SER33 4.9 96.5 1.0
CA I:CYS7 5.0 84.8 1.0

Zinc binding site 6 out of 8 in 7kee

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:76.4
occ:1.00
 CB I:CYS78 2.4 85.1 1.0
SG I:CYS103 2.4 92.6 1.0
CB I:CYS106 2.4 95.1 1.0
SG I:CYS75 2.5 108.7 1.0
CB I:CYS75 2.8 105.3 1.0
CB I:CYS103 3.1 87.3 1.0
SG I:CYS106 3.2 103.3 1.0
SG I:CYS78 3.5 92.5 1.0
CA I:CYS78 3.5 96.5 1.0
N I:CYS78 3.6 103.8 1.0
OG I:SER80 3.6 104.0 1.0
CA I:CYS106 3.7 96.0 1.0
N I:CYS106 3.9 94.8 1.0
CA I:CYS75 4.3 100.4 1.0
C I:CYS78 4.3 95.9 1.0
C I:SER105 4.4 97.2 1.0
CB I:HIS108 4.4 97.5 1.0
CB I:SER80 4.4 101.2 1.0
N I:HIS79 4.5 100.7 1.0
OG I:SER105 4.5 90.7 1.0
CA I:CYS103 4.6 82.6 1.0
N I:SER80 4.6 98.2 1.0
O I:SER105 4.7 103.6 1.0
O I:CYS75 4.7 107.8 1.0
C I:CYS106 4.8 96.6 1.0
C I:LYS77 4.8 93.2 1.0
C I:CYS75 4.8 105.6 1.0
ND1 I:HIS108 4.9 102.4 1.0

Zinc binding site 7 out of 8 in 7kee

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:70.9
occ:1.00
 SG J:CYS7 2.2 107.2 1.0
SG J:CYS46 2.3 145.5 1.0
SG J:CYS45 2.5 95.2 1.0
SG J:CYS10 2.6 116.9 1.0
CB J:CYS10 3.1 95.8 1.0
CB J:CYS7 3.2 85.3 1.0
N J:CYS46 3.2 73.3 1.0
CB J:CYS46 3.4 110.2 1.0
CA J:CYS46 3.4 83.4 1.0
N J:CYS10 3.5 70.2 1.0
CB J:CYS45 3.6 80.4 1.0
CD J:ARG43 3.7 83.7 1.0
C J:CYS45 3.8 75.6 1.0
CA J:CYS10 3.9 75.0 1.0
CA J:CYS45 4.3 67.4 1.0
O J:CYS45 4.4 70.4 1.0
NE J:ARG43 4.4 85.0 1.0
CG J:ARG43 4.5 83.0 1.0
N J:GLY11 4.5 56.9 1.0
OG J:SER9 4.6 89.1 1.0
CA J:CYS7 4.6 66.3 1.0
C J:SER9 4.7 67.3 1.0
CB J:SER9 4.7 82.1 1.0
C J:CYS10 4.8 59.8 1.0
NH1 J:ARG48 4.9 72.1 1.0
C J:CYS46 4.9 60.7 1.0
N J:SER9 5.0 65.4 1.0
CB J:ARG43 5.0 85.1 1.0

Zinc binding site 8 out of 8 in 7kee

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnamtp Bound to E-Site


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, Rnamtp Bound to E-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:120.4
occ:1.00
 SG L:CYS48 2.4 113.5 1.0
SG L:CYS34 2.5 113.1 1.0
CB L:CYS51 2.7 130.5 1.0
CB L:CYS48 3.2 112.4 1.0
CB L:CYS31 3.4 120.2 1.0
O L:CYS34 3.5 117.1 1.0
CB L:CYS34 3.5 118.8 1.0
SG L:CYS51 3.7 128.6 1.0
N L:CYS34 3.7 127.6 1.0
CA L:CYS51 3.9 129.1 1.0
CA L:CYS34 4.0 123.4 1.0
SG L:CYS31 4.0 124.1 1.0
N L:CYS51 4.0 130.7 1.0
C L:CYS34 4.1 116.8 1.0
CA L:CYS48 4.7 112.8 1.0
CA L:CYS31 4.8 112.7 1.0
C L:CYS51 4.8 126.9 1.0
N L:GLY52 4.8 127.9 1.0
C L:GLU33 4.9 128.5 1.0
OG L:SER36 4.9 118.8 1.0
CB L:HIS53 4.9 119.7 1.0
C L:CYS31 5.0 115.1 1.0
N L:GLU33 5.0 122.5 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: Tue Oct 29 22:09:23 2024

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