Zinc in PDB 7riq: Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide

Enzymatic activity of Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide

All present enzymatic activity of Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide, PDB code: 7riq 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) 48.15 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.849, 223.467, 193.032, 90, 100.3, 90
R / Rfree (%) 21.3 / 26.4

Other elements in 7riq:

The structure of Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide 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 Scaffold 1 Without Polyamide (pdb code 7riq). 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 Scaffold 1 Without Polyamide, PDB code: 7riq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7riq

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:330.9
occ:1.00
 SG A:CYS107 2.3 175.5 1.0
SG A:CYS148 2.4 208.8 1.0
CB A:CYS110 2.4 182.6 1.0
CB A:CYS167 2.6 268.9 1.0
SG A:CYS110 2.8 189.9 1.0
CB A:CYS107 3.1 182.4 1.0
CB A:CYS148 3.1 208.8 1.0
N A:CYS110 3.1 188.5 1.0
N A:CYS167 3.2 246.3 1.0
CA A:CYS110 3.3 187.4 1.0
CA A:CYS167 3.4 257.2 1.0
SG A:CYS167 4.1 279.4 1.0
C A:CYS167 4.2 252.2 1.0
C A:GLY166 4.3 206.2 1.0
C A:HIS109 4.4 181.9 1.0
C A:CYS110 4.4 193.1 1.0
O A:CYS110 4.5 191.5 1.0
N A:GLY168 4.5 218.3 1.0
OD1 A:ASN169 4.6 176.9 1.0
CA A:CYS107 4.6 184.1 1.0
CA A:CYS148 4.6 210.4 1.0
CA A:GLY166 4.7 177.3 1.0
CB A:HIS109 4.7 185.9 1.0
O A:CYS148 4.8 221.2 1.0
N A:HIS109 4.9 180.3 1.0
CA A:HIS109 4.9 182.6 1.0
O A:CYS167 5.0 261.0 1.0

Zinc binding site 2 out of 8 in 7riq

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:113.5
occ:1.00
 NE2 A:HIS80 2.0 149.6 1.0
SG A:CYS77 2.3 106.3 1.0
SG A:CYS67 2.4 151.9 1.0
CB A:CYS70 2.4 159.1 1.0
SG A:CYS70 2.6 156.6 1.0
CE1 A:HIS80 2.9 142.1 1.0
CD2 A:HIS80 2.9 141.3 1.0
CB A:CYS67 3.1 139.0 1.0
CB A:CYS77 3.5 115.6 1.0
ND1 A:HIS80 3.9 137.4 1.0
CG A:HIS80 3.9 134.1 1.0
CA A:CYS70 3.9 171.2 1.0
O A:LEU58 4.2 133.2 1.0
CA A:CYS77 4.4 117.8 1.0
O A:PRO78 4.6 118.1 1.0
N A:CYS70 4.6 205.3 1.0
CA A:CYS67 4.6 138.4 1.0
N A:GLN68 4.6 160.1 1.0
C A:CYS70 4.6 159.4 1.0
O A:GLN68 4.7 175.3 1.0
N A:GLN71 4.7 145.6 1.0
C A:CYS77 5.0 108.9 1.0
CD A:PRO78 5.0 110.2 1.0

Zinc binding site 3 out of 8 in 7riq

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:155.9
occ:1.00
 SG B:CYS1185 2.4 183.6 1.0
SG B:CYS1166 2.4 125.6 1.0
SG B:CYS1163 2.4 133.5 1.0
SG B:CYS1182 2.5 161.1 1.0
CB B:CYS1185 2.7 180.4 1.0
CB B:CYS1163 3.1 131.8 1.0
CB B:CYS1166 3.1 124.6 1.0
N B:CYS1166 3.4 123.6 1.0
CB B:CYS1182 3.6 163.5 1.0
CA B:CYS1166 3.8 128.2 1.0
CB B:ILE1165 4.2 111.7 1.0
CA B:CYS1185 4.2 178.5 1.0
C B:ILE1165 4.4 115.3 1.0
CG2 B:ILE1165 4.5 116.1 1.0
CA B:CYS1163 4.5 125.3 1.0
CA B:ILE1165 4.7 114.1 1.0
N B:ILE1165 4.7 114.8 1.0
N B:CYS1185 4.7 169.7 1.0
CB B:ASN1187 4.8 152.3 1.0
C B:CYS1166 4.8 133.1 1.0
C B:CYS1163 4.9 125.6 1.0
CA B:CYS1182 5.0 164.3 1.0

Zinc binding site 4 out of 8 in 7riq

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:240.1
occ:1.00
 SG C:CYS95 2.3 174.2 1.0
SG C:CYS86 2.3 98.4 1.0
SG C:CYS92 2.3 113.6 1.0
SG C:CYS88 2.4 78.1 1.0
CB C:CYS86 2.9 93.7 1.0
CB C:CYS95 3.0 124.9 1.0
CB C:CYS92 3.2 94.4 1.0
N C:CYS92 3.3 102.5 1.0
CB C:CYS88 3.6 80.0 1.0
CA C:CYS92 3.8 78.7 1.0
N C:CYS95 4.0 98.9 1.0
CA C:CYS95 4.1 88.7 1.0
C C:HIS91 4.2 96.5 1.0
N C:CYS88 4.3 67.5 1.0
CA C:CYS86 4.3 88.8 1.0
CA C:HIS91 4.4 91.3 1.0
C C:CYS92 4.5 64.8 1.0
C C:LYS94 4.6 94.5 1.0
CA C:CYS88 4.6 69.3 1.0
O C:CYS92 4.7 71.2 1.0
C C:CYS86 4.7 89.1 1.0
N C:PHE87 4.8 80.6 1.0
C C:CYS95 5.0 89.1 1.0
N C:LYS94 5.0 70.6 1.0

Zinc binding site 5 out of 8 in 7riq

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:113.2
occ:1.00
 SG I:CYS7 2.4 103.2 1.0
SG I:CYS29 2.4 89.7 1.0
OG1 I:THR31 2.5 126.1 1.0
SG I:CYS32 2.5 116.3 1.0
CB I:CYS7 2.7 104.3 1.0
SG I:CYS10 2.7 131.2 1.0
CB I:CYS10 3.2 121.6 1.0
CB I:CYS29 3.3 95.6 1.0
N I:CYS32 3.6 111.5 1.0
CB I:CYS32 3.8 101.7 1.0
CB I:THR31 3.9 119.2 1.0
N I:CYS10 4.0 115.0 1.0
CA I:CYS7 4.2 111.2 1.0
CA I:CYS10 4.2 116.0 1.0
CA I:CYS32 4.2 104.2 1.0
CB I:TYR34 4.4 87.0 1.0
CG2 I:THR31 4.6 107.5 1.0
C I:THR31 4.6 123.5 1.0
CA I:THR31 4.6 122.2 1.0
N I:THR31 4.6 121.4 1.0
C I:CYS32 4.8 123.2 1.0
CA I:CYS29 4.8 93.1 1.0
C I:CYS7 4.8 112.4 1.0
O I:CYS32 4.9 120.7 1.0
N I:CYS7 5.0 100.6 1.0
C I:CYS10 5.0 108.3 1.0

Zinc binding site 6 out of 8 in 7riq

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:97.8
occ:1.00
 SG I:CYS78 2.2 140.3 1.0
SG I:CYS106 2.3 84.1 1.0
SG I:CYS75 2.4 84.3 1.0
SG I:CYS103 2.4 109.3 1.0
CB I:CYS75 2.6 70.4 1.0
CB I:CYS103 3.0 78.1 1.0
OG I:SER80 3.5 128.3 1.0
CB I:CYS78 3.5 130.2 1.0
CB I:CYS106 3.6 97.9 1.0
N I:CYS78 3.8 89.5 1.0
N I:CYS106 4.0 101.7 1.0
CA I:CYS78 4.1 106.8 1.0
CA I:CYS75 4.2 75.2 1.0
CA I:CYS106 4.3 103.7 1.0
CA I:CYS103 4.5 74.3 1.0
CB I:HIS108 4.6 80.1 1.0
N I:HIS79 4.6 91.8 1.0
C I:CYS78 4.6 99.1 1.0
CB I:LYS77 4.6 65.5 1.0
CB I:SER80 4.7 97.9 1.0
N I:SER80 4.7 100.3 1.0
CB I:SER105 4.8 91.6 1.0
C I:SER105 4.8 95.8 1.0
C I:CYS75 4.8 99.7 1.0
C I:CYS106 4.9 97.9 1.0
C I:LYS77 4.9 76.7 1.0
N I:CYS75 4.9 91.4 1.0

Zinc binding site 7 out of 8 in 7riq

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:83.9
occ:1.00
 SG J:CYS7 2.3 148.9 1.0
SG J:CYS10 2.4 71.0 1.0
SG J:CYS46 2.4 76.3 1.0
SG J:CYS45 2.4 102.4 1.0
N J:CYS46 2.9 105.8 1.0
CB J:CYS7 2.9 106.5 1.0
CA J:CYS46 3.1 103.1 1.0
CB J:CYS46 3.2 89.5 1.0
C J:CYS45 3.4 87.1 1.0
CB J:CYS45 3.7 94.8 1.0
CB J:CYS10 3.8 72.8 1.0
O J:CYS45 3.9 77.9 1.0
N J:CYS10 3.9 89.6 1.0
CA J:CYS45 4.1 79.0 1.0
CA J:CYS7 4.4 91.5 1.0
NE J:ARG43 4.4 104.3 1.0
CA J:CYS10 4.4 83.8 1.0
CB J:SER9 4.6 95.5 1.0
C J:CYS46 4.7 93.2 1.0
CB J:ARG43 4.8 97.4 1.0
N J:GLY11 4.8 68.5 1.0
N J:CYS45 4.9 76.7 1.0
N J:SER9 4.9 83.2 1.0
CB J:LYS12 4.9 47.5 1.0
C J:CYS7 4.9 95.6 1.0
C J:SER9 4.9 91.2 1.0

Zinc binding site 8 out of 8 in 7riq

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Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex Scaffold 1 Without Polyamide


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 Scaffold 1 Without Polyamide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:388.9
occ:1.00
 SG L:CYS48 2.4 166.1 1.0
SG L:CYS31 2.4 210.9 1.0
SG L:CYS34 2.4 208.1 1.0
SG L:CYS51 2.4 226.9 1.0
CB L:CYS34 2.5 208.0 1.0
N L:CYS34 3.0 221.3 1.0
CA L:CYS34 3.3 208.6 1.0
CB L:CYS48 3.3 165.0 1.0
CB L:CYS31 3.4 181.1 1.0
CB L:CYS51 3.7 226.6 1.0
N L:CYS51 3.9 219.6 1.0
C L:GLU33 4.2 219.0 1.0
CA L:CYS51 4.2 225.9 1.0
N L:GLY52 4.2 170.9 1.0
N L:HIS53 4.3 184.0 1.0
C L:CYS34 4.3 197.4 1.0
CB L:HIS53 4.3 185.3 1.0
ND1 L:HIS53 4.5 205.8 1.0
N L:SER35 4.5 181.1 1.0
CB L:GLU33 4.5 199.6 1.0
C L:CYS51 4.6 223.9 1.0
N L:GLU33 4.6 196.0 1.0
CA L:GLU33 4.7 204.0 1.0
CA L:CYS48 4.7 178.3 1.0
CG L:HIS53 4.8 199.8 1.0
OG L:SER36 4.8 175.0 1.0
CA L:CYS31 4.8 162.7 1.0
CA L:HIS53 4.9 171.7 1.0
CB L:ASP50 4.9 193.8 1.0
C L:ASP50 5.0 209.2 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 10:22:44 2024

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