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Zinc in PDB 7kef: Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State

Enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State

All present enzymatic activity of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Unnatural Base DTPT3, Rnam in Swing State, PDB code: 7kef 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) 48.70 / 3.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.713, 221.711, 193.255, 90, 101.78, 90
R / Rfree (%) 26.8 / 32.6

Other elements in 7kef:

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

Zinc binding site 1 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:207.0
occ:1.00
 SG A:CYS148 2.4 186.8 1.0
CB A:CYS110 2.4 170.6 1.0
SG A:CYS110 2.5 168.3 1.0
SG A:CYS167 2.5 201.9 1.0
CB A:CYS148 2.8 187.1 1.0
CB A:CYS167 3.2 202.8 1.0
CA A:CYS110 3.7 172.6 1.0
O A:CYS167 3.7 192.4 1.0
C A:CYS167 3.8 194.5 1.0
CB A:CYS107 3.9 180.4 1.0
CA A:CYS167 4.1 200.8 1.0
SG A:CYS107 4.2 188.1 1.0
N A:GLY168 4.3 194.9 1.0
O A:ASN169 4.3 183.2 1.0
CA A:CYS148 4.3 191.4 1.0
N A:CYS110 4.4 173.5 1.0
N A:ASN169 4.4 194.1 1.0
NH2 A:ARG164 4.4 189.6 1.0
C A:CYS148 4.7 195.8 1.0
CA A:GLY168 4.7 197.1 1.0
C A:CYS110 4.8 169.8 1.0
C A:GLY168 4.8 199.4 1.0
N A:CYS167 4.9 206.7 1.0

Zinc binding site 2 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:134.2
occ:1.00
 NE2 A:HIS80 2.2 167.3 1.0
CE1 A:HIS80 2.2 168.9 1.0
SG A:CYS70 2.3 173.2 1.0
SG A:CYS67 2.4 162.3 1.0
SG A:CYS77 2.4 115.5 1.0
CB A:CYS67 3.2 156.6 1.0
CD2 A:HIS80 3.4 150.8 1.0
ND1 A:HIS80 3.4 167.9 1.0
O A:GLN68 3.4 153.2 1.0
CB A:CYS70 3.4 177.6 1.0
N A:GLN68 3.7 161.6 1.0
CB A:CYS77 3.8 114.4 1.0
CG A:HIS80 4.0 155.2 1.0
C A:CYS67 4.1 155.4 1.0
CA A:CYS67 4.1 153.0 1.0
OE1 A:GLN68 4.2 169.8 1.0
C A:GLN68 4.3 164.2 1.0
N A:CYS70 4.6 193.7 1.0
CA A:GLN68 4.6 165.7 1.0
CA A:CYS70 4.6 188.4 1.0
O A:CYS67 4.9 157.1 1.0

Zinc binding site 3 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:179.8
occ:1.00
 SG B:CYS1182 2.3 168.2 1.0
CB B:CYS1166 2.4 147.3 1.0
SG B:CYS1185 2.4 158.6 1.0
SG B:CYS1166 2.4 137.0 1.0
SG B:CYS1163 2.5 169.5 1.0
N B:CYS1166 2.7 164.6 1.0
CA B:CYS1166 3.0 157.6 1.0
CB B:CYS1185 3.0 166.5 1.0
CB B:CYS1163 3.2 158.2 1.0
CB B:CYS1182 3.7 166.6 1.0
C B:ILE1165 3.9 160.3 1.0
CB B:ILE1165 4.2 164.5 1.0
CA B:CYS1185 4.3 165.2 1.0
C B:CYS1166 4.4 155.6 1.0
CA B:ILE1165 4.4 165.0 1.0
N B:CYS1185 4.4 165.3 1.0
N B:ILE1165 4.5 167.8 1.0
CA B:CYS1163 4.7 159.0 1.0
N B:GLY1167 4.8 152.7 1.0
O B:ILE1165 4.8 159.7 1.0
O B:LYS1183 4.9 169.7 1.0
CG2 B:THR1170 4.9 152.9 1.0
CG1 B:ILE1165 5.0 166.3 1.0

Zinc binding site 4 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:92.0
occ:1.00
 CB C:CYS95 2.2 109.7 1.0
SG C:CYS88 2.2 137.6 1.0
SG C:CYS95 2.3 117.5 1.0
N C:CYS95 2.3 104.3 1.0
CB C:CYS88 2.5 89.0 1.0
CA C:CYS95 2.6 99.6 1.0
SG C:CYS86 3.0 130.4 1.0
N C:CYS92 3.3 111.6 1.0
C C:LYS94 3.3 107.9 1.0
O C:CYS92 3.7 104.9 1.0
CA C:CYS88 3.7 82.0 1.0
N C:CYS88 3.8 88.7 1.0
CB C:LYS94 3.9 104.4 1.0
CA C:LYS94 4.0 102.6 1.0
CB C:CYS86 4.0 111.3 1.0
C C:CYS92 4.0 103.5 1.0
CA C:CYS92 4.0 111.2 1.0
C C:CYS95 4.1 94.5 1.0
N C:LYS94 4.1 93.7 1.0
O C:LYS94 4.1 112.0 1.0
C C:HIS91 4.2 111.4 1.0
CB C:CYS92 4.2 110.0 1.0
CA C:HIS91 4.4 108.6 1.0
N C:SER96 4.5 87.4 1.0
C C:CYS88 4.6 83.9 1.0
O C:CYS88 4.8 98.5 1.0
N C:PHE87 4.9 106.5 1.0
N C:ASP93 4.9 104.4 1.0

Zinc binding site 5 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:98.7
occ:1.00
 SG I:CYS32 2.3 106.7 1.0
SG I:CYS7 2.4 96.2 1.0
SG I:CYS10 2.5 99.7 1.0
CB I:CYS7 2.6 98.7 1.0
SG I:CYS29 3.2 125.2 1.0
CB I:CYS29 3.4 111.9 1.0
CB I:CYS32 3.7 102.8 1.0
CA I:CYS7 4.1 102.7 1.0
CB I:CYS10 4.2 108.0 1.0
CB I:ASN12 4.3 103.0 1.0
N I:CYS10 4.3 102.5 1.0
CB I:TYR34 4.3 105.7 1.0
N I:CYS32 4.4 103.3 1.0
C I:CYS7 4.6 103.2 1.0
N I:ASN12 4.6 103.0 1.0
CA I:CYS32 4.6 107.1 1.0
CA I:CYS10 4.7 114.3 1.0
N I:CYS7 4.7 110.4 1.0
CA I:ASN12 4.9 101.8 1.0
O I:CYS7 5.0 109.9 1.0
CA I:CYS29 5.0 108.5 1.0

Zinc binding site 6 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:131.7
occ:1.00
 SG I:CYS78 2.1 114.7 1.0
CB I:CYS106 2.3 119.2 1.0
SG I:CYS75 2.3 136.4 1.0
SG I:CYS103 2.5 130.0 1.0
CB I:CYS103 3.0 124.7 1.0
CB I:CYS75 3.0 137.4 1.0
OG I:SER80 3.2 134.8 1.0
SG I:CYS106 3.3 137.5 1.0
CB I:CYS78 3.3 131.3 1.0
CA I:CYS106 3.5 119.9 1.0
N I:CYS106 3.6 127.3 1.0
N I:CYS78 3.9 146.7 1.0
CA I:CYS78 4.0 142.2 1.0
OG I:SER105 4.2 140.2 1.0
N I:HIS79 4.2 136.2 1.0
C I:CYS78 4.2 139.5 1.0
N I:SER80 4.3 131.1 1.0
CA I:CYS75 4.4 141.8 1.0
CA I:CYS103 4.5 118.2 1.0
O I:CYS75 4.5 143.2 1.0
CB I:SER80 4.5 132.9 1.0
O I:SER80 4.6 124.2 1.0
C I:CYS106 4.6 116.3 1.0
CB I:HIS108 4.7 124.8 1.0
C I:CYS75 4.7 145.4 1.0
C I:SER105 4.9 132.8 1.0
CA I:SER80 4.9 128.9 1.0
C I:CYS103 5.0 118.6 1.0
O I:CYS78 5.0 138.6 1.0

Zinc binding site 7 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:107.5
occ:1.00
 SG J:CYS10 2.3 81.5 1.0
SG J:CYS7 2.3 97.1 1.0
N J:CYS46 2.4 106.2 1.0
CB J:CYS7 2.4 99.5 1.0
CA J:CYS46 2.5 110.4 1.0
SG J:CYS45 2.7 92.4 1.0
C J:CYS45 2.8 105.2 1.0
O J:CYS45 3.0 107.2 1.0
CB J:CYS46 3.1 113.3 1.0
N J:CYS10 3.6 78.4 1.0
CB J:CYS45 3.7 99.2 1.0
CB J:CYS10 3.7 79.0 1.0
CA J:CYS7 3.8 101.2 1.0
CA J:CYS45 3.8 98.9 1.0
C J:CYS46 3.9 108.7 1.0
NH1 J:ARG48 4.0 96.0 1.0
CA J:CYS10 4.1 81.4 1.0
C J:CYS7 4.2 100.7 1.0
SG J:CYS46 4.3 124.9 1.0
N J:GLY11 4.4 88.0 1.0
C J:CYS10 4.4 86.1 1.0
O J:CYS46 4.5 102.5 1.0
OG J:SER9 4.5 93.6 1.0
O J:CYS7 4.6 103.6 1.0
N J:SER9 4.7 82.8 1.0
N J:PHE8 4.7 91.5 1.0
N J:CYS45 4.7 104.6 1.0
N J:CYS7 4.7 104.5 1.0
C J:SER9 4.8 89.0 1.0
N J:ARG47 4.8 100.6 1.0

Zinc binding site 8 out of 8 in 7kef

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


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, Rnam in Swing State within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:179.0
occ:1.00
 O L:CYS34 2.1 166.8 1.0
SG L:CYS51 2.3 134.0 1.0
CB L:CYS34 2.8 169.8 1.0
C L:CYS34 2.8 166.6 1.0
OG L:SER36 3.0 161.3 1.0
CA L:CYS34 3.1 166.1 1.0
CB L:SER36 3.3 161.1 1.0
N L:CYS34 3.4 161.4 1.0
N L:SER36 3.7 160.5 1.0
SG L:CYS48 3.7 131.8 1.0
CB L:CYS51 3.8 139.6 1.0
N L:SER35 4.0 172.8 1.0
SG L:CYS34 4.1 170.7 1.0
CA L:SER36 4.1 160.6 1.0
CB L:CYS31 4.1 154.5 1.0
N L:CYS51 4.3 153.3 1.0
CA L:CYS51 4.4 149.2 1.0
C L:SER35 4.5 174.7 1.0
CA L:SER35 4.7 172.2 1.0
C L:GLU33 4.7 163.0 1.0
O L:CYS31 4.7 159.5 1.0
C L:CYS31 4.8 157.9 1.0
CA L:CYS31 4.9 154.0 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 22:10:53 2024

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