Zinc in PDB 7rix: Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2

Enzymatic activity of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2

All present enzymatic activity of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2, PDB code: 7rix was solved by J.Oh, P.B.Dervan, D.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.53 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.701, 222.446, 194.157, 90, 100.01, 90
R / Rfree (%) 22.2 / 26.8

Other elements in 7rix:

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2 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 Hairpin Polyamide Py-Im 1, Scaffold 2 (pdb code 7rix). 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 Hairpin Polyamide Py-Im 1, Scaffold 2, PDB code: 7rix:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7rix

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:206.4
occ:1.00
 N A:CYS110 2.2 202.6 1.0
SG A:CYS110 2.3 180.7 1.0
CB A:CYS167 2.3 191.1 1.0
SG A:CYS107 2.4 197.0 1.0
CB A:CYS110 2.5 185.2 1.0
CA A:CYS110 2.7 189.7 1.0
CB A:CYS107 3.0 191.1 1.0
SG A:CYS167 3.2 194.2 1.0
C A:HIS109 3.3 193.9 1.0
O A:CYS110 3.3 175.4 1.0
C A:CYS110 3.5 179.6 1.0
CA A:CYS167 3.7 189.3 1.0
CB A:HIS109 3.8 179.0 1.0
N A:HIS109 3.8 177.9 1.0
CA A:HIS109 3.8 183.2 1.0
SG A:CYS148 3.8 181.0 1.0
N A:CYS167 4.0 187.7 1.0
CA A:CYS107 4.2 183.4 1.0
C A:CYS107 4.2 176.7 1.0
O A:HIS109 4.4 187.1 1.0
O A:CYS107 4.4 172.0 1.0
CB A:CYS148 4.6 177.7 1.0
N A:MET108 4.7 187.6 1.0
C A:CYS167 4.8 185.1 1.0
N A:GLY111 4.8 175.2 1.0
C A:MET108 4.9 177.0 1.0
N A:GLY168 5.0 185.8 1.0

Zinc binding site 2 out of 8 in 7rix

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:132.6
occ:1.00
 NE2 A:HIS80 1.8 144.1 1.0
CE1 A:HIS80 2.2 140.3 1.0
CB A:CYS70 2.3 150.4 1.0
SG A:CYS67 2.3 147.1 1.0
SG A:CYS70 2.5 151.3 1.0
SG A:CYS77 2.6 125.3 1.0
CD2 A:HIS80 3.1 139.0 1.0
CB A:CYS67 3.2 148.8 1.0
ND1 A:HIS80 3.4 139.8 1.0
CB A:CYS77 3.6 127.7 1.0
CA A:CYS70 3.8 151.8 1.0
CG A:HIS80 3.9 137.1 1.0
O A:PRO78 4.3 138.3 1.0
CA A:CYS77 4.3 124.4 1.0
N A:GLN68 4.4 151.4 1.0
N A:CYS70 4.4 158.6 1.0
C A:CYS70 4.5 146.2 1.0
CA A:CYS67 4.6 147.8 1.0
N A:GLN71 4.6 150.2 1.0
O A:GLN68 4.7 157.5 1.0
C A:CYS77 4.9 120.5 1.0
C A:CYS67 4.9 153.3 1.0

Zinc binding site 3 out of 8 in 7rix

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:164.5
occ:1.00
 SG B:CYS1166 2.3 126.8 1.0
SG B:CYS1185 2.3 156.1 1.0
SG B:CYS1182 2.4 143.8 1.0
SG B:CYS1163 2.5 136.0 1.0
CB B:CYS1185 2.6 154.7 1.0
CB B:CYS1166 3.2 122.5 1.0
CB B:CYS1163 3.3 132.3 1.0
N B:CYS1166 3.4 127.0 1.0
CB B:CYS1182 3.6 143.6 1.0
CA B:CYS1166 3.8 124.0 1.0
CA B:CYS1185 4.1 153.2 1.0
O B:CYS1166 4.2 131.6 1.0
CB B:ILE1165 4.4 127.6 1.0
N B:CYS1185 4.4 153.4 1.0
C B:CYS1166 4.5 127.1 1.0
C B:ILE1165 4.5 125.8 1.0
CA B:CYS1163 4.8 132.1 1.0
CA B:ILE1165 4.9 124.3 1.0
O B:CYS1182 4.9 148.7 1.0
CA B:CYS1182 4.9 145.5 1.0
C B:CYS1185 4.9 152.1 1.0
N B:ILE1165 4.9 122.7 1.0
CG2 B:ILE1165 5.0 131.8 1.0

Zinc binding site 4 out of 8 in 7rix

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:81.9
occ:1.00
 SG C:CYS88 2.1 68.2 1.0
SG C:CYS95 2.3 80.9 1.0
CB C:CYS92 2.5 68.6 1.0
SG C:CYS86 2.5 75.9 1.0
SG C:CYS92 2.6 76.6 1.0
N C:CYS92 2.9 79.6 1.0
CB C:CYS88 3.1 65.8 1.0
CA C:CYS92 3.2 71.1 1.0
CB C:CYS86 3.2 68.2 1.0
CB C:CYS95 3.3 76.6 1.0
C C:HIS91 3.5 83.6 1.0
CA C:HIS91 4.0 80.5 1.0
C C:CYS92 4.1 69.2 1.0
N C:CYS88 4.1 78.7 1.0
CA C:CYS88 4.2 67.7 1.0
O C:HIS91 4.3 75.5 1.0
N C:CYS95 4.3 75.7 1.0
CA C:CYS95 4.4 67.0 1.0
CA C:CYS86 4.6 72.5 1.0
O C:CYS92 4.7 64.3 1.0
N C:ASP93 4.8 74.5 1.0
C C:CYS86 4.8 72.0 1.0
N C:HIS91 4.9 78.4 1.0

Zinc binding site 5 out of 8 in 7rix

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:98.0
occ:1.00
 SG I:CYS32 2.2 97.5 1.0
SG I:CYS29 2.3 113.1 1.0
SG I:CYS7 2.5 99.9 1.0
OG1 I:THR31 2.6 108.0 1.0
SG I:CYS10 2.7 99.3 1.0
CB I:CYS7 2.9 86.8 1.0
CB I:CYS29 3.1 104.4 1.0
N I:CYS32 3.4 99.6 1.0
CB I:CYS32 3.4 101.2 1.0
CB I:CYS10 3.5 90.7 1.0
CA I:CYS32 3.9 101.4 1.0
CB I:THR31 4.0 104.9 1.0
N I:CYS10 4.2 99.7 1.0
C I:THR31 4.3 100.8 1.0
CB I:TYR34 4.3 86.8 1.0
CA I:CYS7 4.4 88.0 1.0
CA I:CYS10 4.4 92.7 1.0
CA I:THR31 4.5 103.8 1.0
CA I:CYS29 4.5 97.3 1.0
C I:CYS32 4.5 110.8 1.0
N I:THR31 4.5 103.6 1.0
O I:CYS32 4.7 113.8 1.0
CG2 I:THR31 4.7 100.0 1.0
CB I:ASP9 4.9 95.5 1.0

Zinc binding site 6 out of 8 in 7rix

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:89.3
occ:1.00
 SG I:CYS106 2.2 64.7 1.0
SG I:CYS75 2.2 77.1 1.0
SG I:CYS78 2.3 59.3 1.0
SG I:CYS103 2.5 103.4 1.0
CB I:CYS75 2.8 83.1 1.0
CB I:CYS103 2.9 82.1 1.0
CB I:CYS78 3.3 61.9 1.0
OG I:SER80 3.5 88.3 1.0
CB I:CYS106 3.7 77.7 1.0
N I:CYS78 3.7 82.4 1.0
N I:CYS106 3.9 79.1 1.0
CA I:CYS78 4.0 77.2 1.0
CB I:HIS108 4.2 72.9 1.0
CA I:CYS75 4.3 81.0 1.0
CA I:CYS106 4.3 77.8 1.0
CA I:CYS103 4.4 64.6 1.0
C I:CYS78 4.5 79.6 1.0
N I:HIS79 4.6 77.7 1.0
CB I:SER80 4.7 78.7 1.0
N I:SER80 4.7 80.0 1.0
CB I:LYS77 4.8 63.6 1.0
C I:SER105 4.8 83.1 1.0
C I:CYS106 4.8 72.8 1.0
C I:LYS77 4.8 76.4 1.0
N I:HIS108 4.9 64.8 1.0
CB I:SER105 4.9 76.8 1.0
C I:CYS75 4.9 85.0 1.0

Zinc binding site 7 out of 8 in 7rix

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:62.8
occ:1.00
 SG J:CYS10 2.2 68.1 1.0
SG J:CYS45 2.2 79.7 1.0
SG J:CYS7 2.4 60.1 1.0
SG J:CYS46 2.6 45.5 1.0
N J:CYS46 2.9 73.0 1.0
CB J:CYS7 3.0 50.8 1.0
CA J:CYS46 3.2 63.8 1.0
CB J:CYS46 3.3 58.3 1.0
C J:CYS45 3.3 58.0 1.0
CB J:CYS10 3.3 63.2 1.0
CB J:CYS45 3.6 73.3 1.0
N J:CYS10 3.7 62.4 1.0
O J:CYS45 3.8 54.4 1.0
NH2 J:ARG43 4.0 71.8 1.0
CA J:CYS45 4.0 55.9 1.0
CA J:CYS10 4.1 60.4 1.0
CA J:CYS7 4.5 54.3 1.0
N J:GLY11 4.6 57.2 1.0
CB J:SER9 4.6 63.5 1.0
C J:CYS46 4.7 57.5 1.0
NE J:ARG43 4.7 80.8 1.0
CZ J:ARG43 4.7 74.2 1.0
C J:CYS10 4.8 51.4 1.0
N J:CYS45 4.8 56.2 1.0
C J:SER9 4.8 57.0 1.0
N J:LYS12 4.9 49.4 1.0
C J:CYS7 4.9 52.0 1.0
N J:SER9 5.0 44.8 1.0

Zinc binding site 8 out of 8 in 7rix

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 2


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 Hairpin Polyamide Py-Im 1, Scaffold 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:153.4
occ:1.00
 SG L:CYS34 2.2 162.2 1.0
SG L:CYS48 2.3 151.1 1.0
SG L:CYS51 2.4 160.0 1.0
CB L:CYS34 2.5 164.8 1.0
CB L:CYS51 2.5 157.3 1.0
SG L:CYS31 3.1 152.8 1.0
CB L:CYS48 3.1 151.2 1.0
N L:CYS51 3.5 154.6 1.0
CA L:CYS51 3.5 156.7 1.0
CB L:CYS31 3.7 133.8 1.0
CA L:CYS34 3.7 168.1 1.0
N L:CYS34 3.9 166.3 1.0
OG L:SER36 4.1 157.4 1.0
C L:ASP50 4.4 154.9 1.0
C L:CYS51 4.4 156.7 1.0
CA L:CYS48 4.5 150.2 1.0
N L:GLY52 4.6 148.9 1.0
C L:CYS34 4.6 170.0 1.0
C L:CYS48 4.8 150.3 1.0
N L:SER35 4.9 159.6 1.0
O L:CYS48 4.9 151.4 1.0
N L:ASP50 4.9 151.2 1.0
CB L:ASP50 4.9 152.7 1.0
CA L:ASP50 5.0 153.0 1.0

Reference:

J.Oh, T.Jia, J.Xu, J.Chong, P.B.Dervan, D.Wang. Rna Polymerase II Trapped on A Molecular Treadmill: Structural Basis of Persistent Transcriptional Arrest By A Minor Groove Dna Binder. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35022237
DOI: 10.1073/PNAS.2114065119
Page generated: Wed Oct 30 10:22:50 2024

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