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Zinc in PDB 9bw0: Rna Polymerase II - No Atp

Enzymatic activity of Rna Polymerase II - No Atp

All present enzymatic activity of Rna Polymerase II - No Atp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II - No Atp, PDB code: 9bw0 was solved by G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.08 / 3.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 219.09, 390.92, 281.65, 90, 90, 90
R / Rfree (%) 21.9 / 24.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II - No Atp (pdb code 9bw0). 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 - No Atp, PDB code: 9bw0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9bw0

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Zinc binding site 1 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:190.4
occ:1.00
 SG A:CYS110 2.3 195.2 1.0
SG A:CYS107 2.3 281.4 1.0
SG A:CYS148 2.9 227.3 1.0
CB A:CYS107 2.9 234.7 1.0
SG A:CYS167 3.3 256.0 1.0
CB A:CYS148 3.8 191.4 1.0
N A:CYS167 3.8 228.3 1.0
CB A:CYS110 4.0 220.1 1.0
C A:CYS167 4.0 228.9 1.0
O A:CYS167 4.0 204.4 1.0
N A:CYS110 4.1 228.2 1.0
CA A:CYS107 4.1 208.0 1.0
CA A:CYS167 4.3 226.8 1.0
N A:GLY168 4.4 227.9 1.0
CB A:CYS167 4.4 242.8 1.0
N A:ASN169 4.5 190.6 1.0
CB A:HIS109 4.6 252.0 1.0
CA A:CYS110 4.6 230.1 1.0
NE2 A:GLN171 4.7 203.8 1.0
C A:CYS107 4.8 190.2 1.0
N A:HIS109 4.8 229.8 1.0
CA A:GLY168 4.9 204.3 1.0

Zinc binding site 2 out of 8 in 9bw0

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Zinc binding site 2 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:158.3
occ:1.00
 NE2 A:HIS80 2.1 147.2 1.0
SG A:CYS70 2.3 121.0 1.0
SG A:CYS77 2.3 143.9 1.0
SG A:CYS67 2.3 172.4 1.0
CD2 A:HIS80 2.8 167.4 1.0
CB A:CYS67 3.1 164.4 1.0
CE1 A:HIS80 3.3 159.8 1.0
O A:CYS70 3.6 196.0 1.0
CB A:CYS77 3.7 172.1 1.0
OG1 A:THR69 3.8 165.8 1.0
CB A:CYS70 3.8 176.4 1.0
CG A:HIS80 4.0 142.3 1.0
N A:CYS70 4.1 178.2 1.0
ND1 A:HIS80 4.2 143.4 1.0
CA A:CYS70 4.3 178.1 1.0
C A:CYS70 4.4 187.2 1.0
N A:GLY79 4.4 134.9 1.0
CD A:PRO78 4.4 132.6 1.0
CA A:CYS77 4.4 156.0 1.0
O A:LEU58 4.6 134.0 1.0
CA A:CYS67 4.6 145.6 1.0
CA A:GLY59 4.7 117.9 1.0
CA A:GLY79 4.8 134.2 1.0
C A:CYS77 4.8 142.6 1.0
N A:PRO78 4.8 133.5 1.0

Zinc binding site 3 out of 8 in 9bw0

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Zinc binding site 3 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:170.8
occ:1.00
 SG B:CYS1185 2.3 134.8 1.0
SG B:CYS1166 2.3 189.0 1.0
SG B:CYS1163 2.3 155.1 1.0
CB B:CYS1163 2.8 161.7 1.0
SG B:CYS1182 3.1 113.7 1.0
N B:CYS1166 3.3 128.4 1.0
CB B:CYS1166 3.5 156.2 1.0
CB B:ILE1165 3.7 138.2 1.0
O B:CYS1166 3.7 168.5 1.0
CA B:CYS1166 3.8 117.3 1.0
CB B:CYS1185 3.9 174.3 1.0
OG1 B:THR1170 4.2 178.2 1.0
C B:CYS1166 4.3 151.8 1.0
C B:ILE1165 4.3 154.0 1.0
CA B:CYS1163 4.3 135.8 1.0
CD1 B:ILE1165 4.3 193.2 1.0
CA B:ILE1165 4.4 144.7 1.0
CG2 B:ILE1165 4.5 180.6 1.0
N B:ILE1165 4.5 153.5 1.0
CB B:CYS1182 4.5 165.0 1.0
ND2 B:ASN1187 4.5 182.8 1.0
CG1 B:ILE1165 4.5 125.0 1.0
O B:CYS1185 4.5 188.4 1.0
C B:CYS1163 4.8 126.2 1.0
CA B:CYS1185 5.0 182.4 1.0

Zinc binding site 4 out of 8 in 9bw0

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Zinc binding site 4 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:163.8
occ:1.00
 SG C:CYS92 2.3 133.5 1.0
SG C:CYS86 2.3 159.3 1.0
SG C:CYS88 2.3 91.2 1.0
SG C:CYS95 2.3 132.6 1.0
CB C:CYS86 3.1 134.1 1.0
CB C:CYS95 3.3 138.8 1.0
N C:CYS92 3.5 134.6 1.0
CB C:CYS88 3.5 177.0 1.0
CB C:CYS92 3.6 169.1 1.0
C C:HIS91 3.9 143.7 1.0
N C:CYS95 4.0 144.7 1.0
CA C:CYS92 4.0 133.2 1.0
CA C:HIS91 4.1 130.7 1.0
CA C:CYS95 4.3 139.5 1.0
N C:CYS88 4.4 125.1 1.0
CA C:CYS86 4.5 154.7 1.0
C C:LYS94 4.5 135.4 1.0
C C:CYS92 4.6 140.2 1.0
CA C:CYS88 4.6 161.6 1.0
O C:CYS92 4.7 164.5 1.0
CB C:LYS94 4.7 153.6 1.0
O C:HIS91 4.7 156.2 1.0
C C:CYS86 4.8 130.7 1.0
N C:LYS94 4.9 128.9 1.0
CA C:LYS94 4.9 129.5 1.0
O C:ASP90 4.9 176.5 1.0
N C:HIS91 5.0 130.1 1.0
N C:PHE87 5.0 142.3 1.0

Zinc binding site 5 out of 8 in 9bw0

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Zinc binding site 5 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:169.8
occ:1.00
 SG I:CYS32 2.3 187.8 1.0
SG I:CYS10 2.3 173.2 1.0
SG I:CYS29 2.3 147.8 1.0
SG I:CYS7 2.3 153.9 1.0
CB I:CYS10 2.4 164.8 1.0
CB I:CYS7 3.2 142.7 1.0
CB I:CYS29 3.4 173.0 1.0
CB I:CYS32 3.5 187.4 1.0
CA I:CYS10 3.6 170.9 1.0
N I:CYS10 3.6 167.1 1.0
N I:CYS32 3.8 186.7 1.0
CA I:CYS32 4.2 192.2 1.0
CB I:THR31 4.4 199.1 1.0
CB I:TYR34 4.4 141.8 1.0
CB I:ASN12 4.5 189.1 1.0
C I:THR31 4.6 180.2 1.0
C I:CYS10 4.7 178.2 1.0
CA I:CYS7 4.7 154.4 1.0
C I:ASP9 4.8 171.2 1.0
CA I:THR31 4.9 174.7 1.0
C I:CYS32 4.9 208.7 1.0
CA I:CYS29 4.9 157.2 1.0
N I:THR31 4.9 156.1 1.0
N I:ASN11 5.0 181.4 1.0
N I:ASN12 5.0 179.5 1.0

Zinc binding site 6 out of 8 in 9bw0

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Zinc binding site 6 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:209.3
occ:1.00
 SG I:CYS78 2.3 205.8 1.0
SG I:CYS75 2.3 210.1 1.0
CB I:CYS106 2.8 189.8 1.0
CB I:CYS75 2.9 215.4 1.0
SG I:CYS103 2.9 247.3 1.0
CB I:CYS103 3.1 240.3 1.0
CB I:CYS78 3.4 225.4 1.0
N I:CYS106 3.7 205.8 1.0
N I:CYS78 3.7 242.1 1.0
OG I:SER80 3.7 218.1 1.0
SG I:CYS106 3.8 263.6 1.0
CA I:CYS106 3.8 184.2 1.0
CA I:CYS78 4.0 241.7 1.0
OG I:SER105 4.0 240.2 1.0
CD2 I:HIS108 4.1 211.8 1.0
NE2 I:HIS108 4.3 220.3 1.0
CA I:CYS75 4.4 205.3 1.0
N I:HIS79 4.4 248.3 1.0
C I:CYS78 4.5 238.6 1.0
CA I:CYS103 4.6 228.7 1.0
C I:CYS106 4.6 204.9 1.0
N I:SER107 4.7 221.0 1.0
CB I:SER80 4.7 216.7 1.0
N I:SER80 4.8 222.0 1.0
C I:LYS77 4.8 242.8 1.0
CB I:LYS77 4.8 228.0 1.0
C I:SER105 4.9 247.0 1.0

Zinc binding site 7 out of 8 in 9bw0

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Zinc binding site 7 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:162.7
occ:1.00
 SG J:CYS10 2.3 152.8 1.0
SG J:CYS45 2.3 167.7 1.0
SG J:CYS7 2.3 128.0 1.0
SG J:CYS46 2.6 157.8 1.0
CB J:CYS45 3.1 140.3 1.0
N J:CYS46 3.2 157.5 1.0
CB J:CYS7 3.3 165.6 1.0
N J:CYS10 3.6 165.3 1.0
C J:CYS45 3.6 158.6 1.0
CB J:CYS10 3.6 172.5 1.0
CA J:CYS46 3.8 140.3 1.0
CB J:CYS46 3.8 165.4 1.0
CA J:CYS45 3.9 135.6 1.0
CB J:SER9 4.0 144.3 1.0
CA J:CYS10 4.2 162.8 1.0
NE J:ARG43 4.3 141.8 1.0
O J:CYS45 4.3 155.6 1.0
C J:SER9 4.5 161.9 1.0
N J:SER9 4.5 119.3 1.0
N J:GLY11 4.6 156.1 1.0
NH2 J:ARG43 4.6 162.7 1.0
CA J:SER9 4.6 122.7 1.0
N J:CYS45 4.6 158.2 1.0
OG J:SER9 4.7 178.6 1.0
CA J:CYS7 4.7 152.4 1.0
C J:CYS10 4.8 160.7 1.0
CZ J:ARG43 4.9 158.7 1.0

Zinc binding site 8 out of 8 in 9bw0

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Zinc binding site 8 out of 8 in the Rna Polymerase II - No Atp


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 - No Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:207.1
occ:1.00
 CB L:CYS51 1.9 189.0 1.0
SG L:CYS51 2.3 139.7 1.0
SG L:CYS34 2.3 150.4 1.0
SG L:CYS31 2.3 225.2 1.0
CA L:CYS51 2.9 221.8 1.0
CB L:CYS34 3.6 209.9 1.0
CB L:CYS31 3.6 188.8 1.0
OE1 L:GLU33 3.7 231.6 1.0
N L:CYS34 3.7 231.7 1.0
N L:CYS51 3.8 240.0 1.0
C L:CYS51 4.0 212.6 1.0
OG L:SER36 4.1 195.2 1.0
CA L:CYS34 4.2 217.3 1.0
C L:ASP50 4.5 236.8 1.0
CB L:GLU33 4.6 199.1 1.0
N L:GLY52 4.6 211.1 1.0
O L:ASP50 4.7 267.1 1.0
N L:SER35 4.7 197.7 1.0
O L:CYS51 4.8 188.3 1.0
CD L:GLU33 4.8 215.9 1.0
C L:GLU33 4.8 216.5 1.0
N L:GLU33 4.8 192.0 1.0
C L:CYS34 4.9 204.1 1.0
CA L:CYS31 5.0 171.8 1.0
CA L:GLU33 5.0 191.4 1.0

Reference:

G.Lin, C.O.Barnes, S.Weiss, B.Dutagaci, C.Qiu, M.Feig, J.Song, A.Lyubimov, A.E.Cohen, C.D.Kaplan, G.Calero. Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser. Proc.Natl.Acad.Sci.Usa V. 121 27121 2024.
ISSN: ESSN 1091-6490
PubMed: 39190355
DOI: 10.1073/PNAS.2318527121
Page generated: Fri Aug 22 16:50:22 2025

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