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

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Hairpin Polyamide Py-Im 1, Scaffold 1, PDB code: 7rim 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) 82.43 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.22, 221.93, 193.71, 90, 99.63, 90
R / Rfree (%) 21.5 / 25.1

Other elements in 7rim:

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

Zinc binding site 1 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:179.9
occ:1.00
 SG A:CYS167 2.3 172.6 1.0
N A:CYS110 2.5 167.9 1.0
SG A:CYS107 2.6 195.8 1.0
SG A:CYS110 2.7 160.9 1.0
CB A:CYS110 2.9 163.2 1.0
CB A:CYS167 2.9 175.0 1.0
CA A:CYS110 3.2 166.4 1.0
CB A:HIS109 3.5 172.2 1.0
CB A:CYS107 3.5 185.8 1.0
C A:HIS109 3.5 163.7 1.0
SG A:CYS148 3.6 159.8 1.0
CA A:HIS109 3.8 169.4 1.0
N A:HIS109 3.9 170.4 1.0
N A:CYS167 4.0 174.5 1.0
CA A:CYS167 4.0 174.3 1.0
C A:CYS110 4.2 162.8 1.0
O A:CYS110 4.2 159.5 1.0
CB A:CYS148 4.3 161.4 1.0
O A:HIS109 4.7 152.6 1.0
C A:CYS167 4.7 161.3 1.0
CA A:CYS107 4.7 172.5 1.0
CG A:HIS109 4.8 167.1 1.0
C A:CYS107 4.8 167.3 1.0
N A:GLY168 4.8 158.3 1.0
ND2 A:ASN169 4.9 165.2 1.0

Zinc binding site 2 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:95.8
occ:1.00
 NE2 A:HIS80 2.2 154.8 1.0
SG A:CYS67 2.3 144.2 1.0
SG A:CYS77 2.4 96.0 1.0
SG A:CYS70 2.7 157.1 1.0
CB A:CYS70 3.0 157.2 1.0
CE1 A:HIS80 3.1 146.0 1.0
CD2 A:HIS80 3.1 145.8 1.0
CB A:CYS67 3.1 148.0 1.0
CB A:CYS77 3.4 111.1 1.0
ND1 A:HIS80 4.2 142.5 1.0
CG A:HIS80 4.2 139.1 1.0
CA A:CYS77 4.3 118.5 1.0
O A:PRO78 4.3 140.1 1.0
CA A:CYS70 4.5 172.7 1.0
CA A:CYS67 4.6 151.5 1.0
N A:GLN68 4.8 166.3 1.0
O A:LEU58 4.8 143.0 1.0
O A:GLN68 4.9 183.3 1.0
C A:CYS77 4.9 119.0 1.0
CA A:GLY59 5.0 135.2 1.0

Zinc binding site 3 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:134.5
occ:1.00
 SG B:CYS1166 2.1 190.0 1.0
SG B:CYS1163 2.5 113.2 1.0
SG B:CYS1185 2.5 160.8 1.0
SG B:CYS1182 2.6 142.1 1.0
CB B:CYS1163 3.0 110.5 1.0
CB B:CYS1166 3.2 140.3 1.0
CB B:CYS1185 3.3 158.2 1.0
CD1 B:ILE1165 3.3 131.5 1.0
O B:CYS1166 3.6 140.2 1.0
N B:CYS1166 3.6 122.2 1.0
CA B:CYS1166 3.8 122.7 1.0
CB B:CYS1182 3.8 147.7 1.0
CG1 B:ILE1165 4.1 131.0 1.0
C B:CYS1166 4.2 131.2 1.0
CA B:CYS1163 4.5 113.2 1.0
CA B:CYS1185 4.7 156.8 1.0
C B:ILE1165 4.9 122.5 1.0

Zinc binding site 4 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:81.0
occ:1.00
 SG C:CYS88 2.2 60.5 1.0
SG C:CYS95 2.3 79.2 1.0
SG C:CYS92 2.4 81.6 1.0
SG C:CYS86 2.4 63.1 1.0
N C:CYS92 3.1 60.3 1.0
CB C:CYS86 3.2 70.1 1.0
CB C:CYS92 3.2 75.8 1.0
CB C:CYS88 3.3 62.2 1.0
CB C:CYS95 3.5 75.8 1.0
CA C:CYS92 3.7 61.8 1.0
C C:HIS91 3.7 70.0 1.0
CA C:HIS91 3.8 70.9 1.0
N C:CYS95 4.3 93.0 1.0
N C:CYS88 4.4 62.8 1.0
C C:CYS92 4.4 62.0 1.0
CA C:CYS88 4.5 62.7 1.0
CA C:CYS95 4.5 74.6 1.0
CA C:CYS86 4.6 68.1 1.0
N C:HIS91 4.7 75.1 1.0
O C:HIS91 4.7 66.3 1.0
O C:CYS92 4.7 83.3 1.0
CB C:LYS94 4.9 91.9 1.0
C C:CYS86 4.9 64.4 1.0
CB C:HIS91 4.9 60.6 1.0
N C:LYS94 4.9 84.3 1.0
O C:ASP90 5.0 82.4 1.0
C C:LYS94 5.0 103.2 1.0

Zinc binding site 5 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:90.2
occ:1.00
 SG I:CYS7 2.3 86.2 1.0
SG I:CYS10 2.4 95.1 1.0
SG I:CYS29 2.4 95.0 1.0
SG I:CYS32 2.6 98.2 1.0
CB I:CYS7 2.9 95.0 1.0
CB I:CYS29 3.1 98.0 1.0
OG1 I:THR31 3.2 94.3 1.0
CB I:CYS10 3.2 93.4 1.0
CB I:CYS32 3.9 93.8 1.0
N I:CYS10 3.9 95.7 1.0
N I:CYS32 4.0 109.5 1.0
CB I:TYR34 4.2 80.5 1.0
CA I:CYS10 4.2 93.2 1.0
CA I:CYS7 4.4 100.1 1.0
CA I:CYS32 4.5 104.3 1.0
CB I:THR31 4.6 96.3 1.0
CA I:CYS29 4.6 89.9 1.0
CB I:ASP9 4.8 106.4 1.0
C I:CYS32 4.8 117.8 1.0
C I:THR31 4.9 110.3 1.0
N I:THR31 4.9 98.1 1.0
C I:ASP9 4.9 101.1 1.0
N I:TYR34 5.0 107.5 1.0

Zinc binding site 6 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:106.5
occ:1.00
 SG I:CYS106 2.2 94.2 1.0
SG I:CYS103 2.2 123.0 1.0
SG I:CYS78 2.2 44.6 1.0
SG I:CYS75 2.4 72.3 1.0
CB I:CYS103 2.8 99.0 1.0
CB I:CYS75 3.1 68.2 1.0
CB I:CYS106 3.4 77.9 1.0
OG I:SER80 3.5 82.4 1.0
CB I:CYS78 3.6 60.5 1.0
N I:CYS106 3.8 77.4 1.0
N I:CYS78 3.9 58.7 1.0
CA I:CYS106 4.1 76.3 1.0
CA I:CYS103 4.2 71.0 1.0
CA I:CYS78 4.3 52.8 1.0
CB I:HIS108 4.4 85.5 1.0
CA I:CYS75 4.6 75.3 1.0
C I:CYS106 4.6 83.5 1.0
CB I:LYS77 4.7 52.8 1.0
C I:SER105 4.7 72.0 1.0
N I:HIS79 4.7 76.5 1.0
CB I:SER105 4.8 86.5 1.0
C I:CYS78 4.8 63.1 1.0
N I:HIS108 4.9 64.8 1.0
C I:CYS103 4.9 75.7 1.0
CB I:SER80 4.9 74.0 1.0
N I:SER107 5.0 88.1 1.0
N I:SER105 5.0 85.5 1.0
N I:SER80 5.0 73.4 1.0

Zinc binding site 7 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:86.6
occ:1.00
 SG J:CYS7 2.2 87.6 1.0
SG J:CYS46 2.2 50.8 1.0
SG J:CYS45 2.5 103.4 1.0
SG J:CYS10 2.5 65.0 1.0
CB J:CYS7 2.9 73.6 1.0
N J:CYS46 3.1 81.6 1.0
CB J:CYS46 3.3 74.0 1.0
CA J:CYS46 3.3 69.4 1.0
C J:CYS45 3.6 70.4 1.0
CB J:CYS45 3.7 79.8 1.0
CB J:CYS10 3.7 67.4 1.0
N J:CYS10 3.8 63.2 1.0
O J:CYS45 4.1 62.2 1.0
CA J:CYS10 4.3 68.7 1.0
CA J:CYS45 4.3 63.1 1.0
CA J:CYS7 4.4 53.3 1.0
N J:GLY11 4.4 70.8 1.0
CB J:SER9 4.5 65.2 1.0
NH2 J:ARG43 4.7 91.7 1.0
C J:CYS10 4.8 72.0 1.0
N J:SER9 4.8 54.6 1.0
C J:SER9 4.8 67.6 1.0
C J:CYS7 4.8 53.1 1.0
C J:CYS46 4.8 61.0 1.0
O J:ARG43 4.9 69.0 1.0
N J:LYS12 4.9 54.0 1.0
NE J:ARG43 4.9 75.2 1.0
CA J:SER9 4.9 66.9 1.0

Zinc binding site 8 out of 8 in 7rim

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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 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:110.4
occ:1.00
 SG L:CYS34 2.3 123.0 1.0
SG L:CYS48 2.3 125.5 1.0
SG L:CYS31 2.5 101.5 1.0
SG L:CYS51 2.7 123.4 1.0
CB L:CYS34 3.2 123.1 1.0
CB L:CYS48 3.4 124.4 1.0
CB L:CYS31 3.4 90.1 1.0
CB L:CYS51 3.4 134.3 1.0
N L:CYS34 3.9 135.8 1.0
N L:CYS51 4.0 161.8 1.0
CA L:CYS34 4.0 128.7 1.0
CA L:CYS51 4.3 153.3 1.0
OG L:SER36 4.5 116.5 1.0
C L:CYS34 4.6 122.8 1.0
CA L:CYS48 4.7 141.7 1.0
O L:CYS48 4.8 149.7 1.0
N L:SER35 4.8 121.4 1.0
CB L:SER36 4.8 122.1 1.0
CA L:CYS31 4.8 88.8 1.0
CB L:ASP50 4.8 153.1 1.0
C L:CYS48 4.9 152.8 1.0
C L:ASP50 4.9 164.6 1.0
C L:GLU33 5.0 141.3 1.0
N L:GLY52 5.0 126.0 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 10:22:09 2024

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