Zinc in PDB 8u9r: Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser

Enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser

All present enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser:
2.7.7.6;

Protein crystallography data

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser, PDB code: 8u9r was solved by P.Arjunan, G.Calero, C.D.Kaplan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 3.34
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 217.195, 387.44, 276.955, 90, 90, 90
R / Rfree (%) 25.5 / 26.1

Other elements in 8u9r:

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser (pdb code 8u9r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser, PDB code: 8u9r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8u9r

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Zinc binding site 1 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:213.8
occ:1.00
 O A:CYS167 2.4 144.2 1.0
O A:GLU149 3.2 168.0 1.0
C A:CYS167 3.5 139.0 1.0
O A:ARG164 3.6 141.2 1.0
CB A:CYS148 3.8 136.8 1.0
O A:CYS148 3.9 148.9 1.0
CA A:GLY165 3.9 146.7 1.0
SG A:CYS148 3.9 129.1 1.0
SG A:CYS110 4.0 99.7 1.0
CA A:CYS167 4.1 140.1 1.0
C A:CYS148 4.2 147.7 1.0
C A:GLU149 4.3 168.6 1.0
C A:ARG164 4.5 141.2 1.0
CA A:CYS148 4.6 137.1 1.0
N A:GLY168 4.7 135.0 1.0
N A:GLY165 4.7 148.0 1.0
CB A:CYS110 4.8 108.6 1.0
N A:GLU149 4.9 161.6 1.0
C A:GLY165 4.9 152.9 1.0
CA A:THR150 5.0 154.7 1.0
CA A:GLY168 5.0 129.0 1.0
O A:GLY165 5.0 157.4 1.0

Zinc binding site 2 out of 8 in 8u9r

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Zinc binding site 2 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:56.7
occ:1.00
 NE2 A:HIS80 2.1 81.9 1.0
SG A:CYS67 2.2 83.0 1.0
SG A:CYS70 2.3 100.8 1.0
SG A:CYS77 2.3 75.4 1.0
CD2 A:HIS80 2.7 85.0 1.0
CE1 A:HIS80 3.3 82.8 1.0
CB A:CYS77 3.4 75.7 1.0
O A:CYS70 3.4 108.2 1.0
CB A:CYS67 3.4 91.9 1.0
OG1 A:THR69 3.5 90.2 1.0
CB A:CYS70 3.5 99.5 1.0
N A:CYS70 3.5 100.1 1.0
CA A:CYS70 3.9 100.4 1.0
CG A:HIS80 4.0 80.8 1.0
CA A:CYS77 4.0 77.4 1.0
C A:CYS70 4.1 101.9 1.0
ND1 A:HIS80 4.2 81.7 1.0
C A:THR69 4.5 96.1 1.0
CB A:THR69 4.6 90.6 1.0
CD A:PRO78 4.6 73.6 1.0
C A:CYS77 4.7 72.3 1.0
N A:GLY79 4.7 68.1 1.0
CA A:GLY59 4.8 92.5 1.0
O A:LEU58 4.8 92.3 1.0
CA A:CYS67 4.8 90.1 1.0
N A:THR69 4.8 88.9 1.0
CA A:THR69 4.9 94.1 1.0
N A:PRO78 4.9 69.3 1.0

Zinc binding site 3 out of 8 in 8u9r

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Zinc binding site 3 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:61.4
occ:1.00
 SG B:CYS1166 2.2 74.2 1.0
SG B:CYS1185 2.3 76.5 1.0
SG B:CYS1182 2.3 91.9 1.0
SG B:CYS1163 2.3 68.3 1.0
CB B:CYS1185 2.7 88.6 1.0
CB B:CYS1166 2.9 65.8 1.0
CB B:CYS1163 3.2 65.2 1.0
CB B:CYS1182 3.2 89.8 1.0
N B:CYS1166 3.5 67.3 1.0
CA B:CYS1166 3.8 63.3 1.0
O B:CYS1182 4.0 96.2 1.0
CA B:CYS1185 4.1 94.3 1.0
N B:CYS1185 4.4 93.9 1.0
CA B:CYS1182 4.6 91.0 1.0
C B:ILE1165 4.6 67.4 1.0
CA B:CYS1163 4.6 61.7 1.0
C B:CYS1182 4.8 95.5 1.0
N B:GLY1167 4.8 68.8 1.0
C B:CYS1166 4.9 62.2 1.0
N B:ILE1165 4.9 69.2 1.0
CB B:ILE1165 4.9 73.5 1.0
C B:CYS1185 5.0 95.6 1.0
CB B:ASN1187 5.0 77.5 1.0

Zinc binding site 4 out of 8 in 8u9r

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Zinc binding site 4 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:69.2
occ:1.00
 SG C:CYS88 2.3 74.9 1.0
SG C:CYS92 2.3 96.3 1.0
SG C:CYS95 2.3 87.3 1.0
SG C:CYS86 2.3 78.3 1.0
CB C:CYS86 3.2 83.9 1.0
CB C:CYS92 3.4 99.4 1.0
CB C:CYS88 3.5 79.1 1.0
CB C:CYS95 3.7 95.6 1.0
N C:CYS92 3.7 93.2 1.0
C C:HIS91 4.0 93.8 1.0
CA C:CYS92 4.1 96.1 1.0
N C:CYS88 4.2 71.0 1.0
N C:CYS95 4.3 99.4 1.0
CA C:CYS88 4.5 75.8 1.0
CA C:HIS91 4.5 100.3 1.0
O C:HIS91 4.5 91.0 1.0
C C:LYS94 4.6 101.4 1.0
CA C:CYS86 4.6 84.1 1.0
CA C:CYS95 4.6 95.1 1.0
C C:CYS92 4.7 96.8 1.0
N C:PHE87 4.7 70.9 1.0
N C:LYS94 4.8 92.7 1.0
C C:CYS86 4.9 82.3 1.0
O C:LYS94 5.0 106.5 1.0

Zinc binding site 5 out of 8 in 8u9r

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Zinc binding site 5 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:103.7
occ:1.00
 SG I:CYS7 2.3 100.3 1.0
SG I:CYS29 2.3 117.8 1.0
CB I:CYS32 2.7 103.5 1.0
SG I:CYS10 2.8 118.1 1.0
CB I:CYS10 2.8 113.1 1.0
CB I:CYS7 3.2 112.2 1.0
CB I:CYS29 3.3 110.9 1.0
N I:CYS10 3.4 119.3 1.0
N I:CYS32 3.7 117.6 1.0
CA I:CYS10 3.7 115.3 1.0
CA I:CYS32 3.8 111.7 1.0
SG I:CYS32 3.9 116.6 1.0
CB I:TYR34 4.3 101.9 1.0
C I:THR31 4.5 116.1 1.0
CB I:ASP9 4.5 105.9 1.0
CB I:THR31 4.5 120.7 1.0
C I:ASP9 4.5 112.6 1.0
C I:CYS10 4.6 113.9 1.0
CA I:CYS7 4.7 114.0 1.0
CA I:CYS29 4.7 109.5 1.0
N I:ASN11 4.7 109.0 1.0
C I:CYS32 4.8 119.5 1.0
CA I:ASP9 4.9 104.7 1.0
CA I:THR31 4.9 118.6 1.0
N I:ASP9 5.0 101.5 1.0

Zinc binding site 6 out of 8 in 8u9r

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Zinc binding site 6 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:181.6
occ:1.00
 SG I:CYS75 2.3 198.6 1.0
NE2 I:HIS108 2.3 162.4 1.0
SG I:CYS106 2.3 158.7 1.0
CB I:CYS103 2.7 185.5 1.0
CB I:CYS75 3.0 196.4 1.0
CE1 I:HIS108 3.1 166.3 1.0
CD2 I:HIS108 3.1 150.5 1.0
SG I:CYS103 3.4 189.3 1.0
SG I:CYS78 3.7 192.2 1.0
CB I:CYS106 3.8 155.0 1.0
OG I:SER80 3.9 209.7 1.0
ND1 I:HIS108 4.1 159.3 1.0
CA I:CYS103 4.1 179.1 1.0
CG I:HIS108 4.1 150.5 1.0
N I:CYS78 4.2 197.4 1.0
CB I:LYS77 4.3 188.5 1.0
OG I:SER105 4.3 194.8 1.0
CA I:CYS75 4.4 199.4 1.0
N I:CYS106 4.5 174.4 1.0
CB I:CYS78 4.7 192.3 1.0
C I:CYS75 4.7 194.7 1.0
CA I:CYS106 4.7 161.1 1.0
N I:LYS77 4.8 195.8 1.0
N I:HIS79 4.8 213.0 1.0
CA I:CYS78 4.9 198.1 1.0
N I:CYS103 4.9 175.5 1.0
CA I:LYS77 4.9 199.8 1.0
N I:SER80 5.0 225.8 1.0

Zinc binding site 7 out of 8 in 8u9r

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Zinc binding site 7 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:79.3
occ:1.00
 SG J:CYS10 2.3 99.2 1.0
SG J:CYS46 2.3 73.7 1.0
SG J:CYS45 2.3 68.3 1.0
SG J:CYS7 2.3 71.3 1.0
CB J:CYS10 2.8 79.0 1.0
N J:CYS46 3.0 86.1 1.0
CB J:CYS46 3.5 83.3 1.0
CA J:CYS46 3.5 85.7 1.0
CB J:CYS7 3.5 88.2 1.0
C J:CYS45 3.6 83.4 1.0
CB J:CYS45 3.6 76.2 1.0
N J:CYS10 3.8 88.4 1.0
CA J:CYS10 3.9 82.2 1.0
CA J:CYS45 4.1 80.5 1.0
O J:CYS45 4.2 80.8 1.0
NH2 J:ARG43 4.2 80.8 1.0
OG J:SER9 4.5 92.2 1.0
NE J:ARG43 4.5 87.0 1.0
C J:SER9 4.6 95.2 1.0
CB J:LYS12 4.7 99.7 1.0
N J:CYS45 4.7 84.7 1.0
CZ J:ARG43 4.8 86.2 1.0
O J:ARG43 4.9 86.8 1.0
CA J:CYS7 4.9 94.4 1.0
CB J:ARG43 5.0 92.3 1.0
N J:SER9 5.0 93.2 1.0

Zinc binding site 8 out of 8 in 8u9r

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Zinc binding site 8 out of 8 in the Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:173.1
occ:1.00
 SG L:CYS51 2.3 131.5 1.0
SG L:CYS34 2.3 145.0 1.0
SG L:CYS48 2.3 127.0 1.0
SG L:CYS31 2.3 186.0 1.0
CB L:CYS34 2.7 147.8 1.0
CB L:CYS31 2.9 155.6 1.0
CB L:CYS51 3.2 154.1 1.0
N L:CYS34 3.7 170.2 1.0
CB L:CYS48 3.7 127.3 1.0
CA L:CYS34 3.8 160.1 1.0
CD1 L:LEU38 4.1 120.0 1.0
OG L:SER36 4.2 136.2 1.0
CA L:CYS31 4.4 145.6 1.0
CG L:GLU33 4.5 170.5 1.0
CA L:CYS51 4.6 169.5 1.0
C L:CYS34 4.6 161.1 1.0
N L:SER35 4.7 176.5 1.0
OE2 L:GLU33 4.8 158.1 1.0
C L:CYS31 4.8 152.4 1.0
N L:CYS51 4.9 174.7 1.0
N L:ALA32 4.9 143.4 1.0
C L:GLU33 5.0 174.1 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: Thu Oct 31 12:05:02 2024

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