Zinc in PDB 8u9x: Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

Enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser

All present enzymatic activity of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser, PDB code: 8u9x 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) 18.00 / 3.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 220.167, 392.604, 280.921, 90, 90, 90
R / Rfree (%) 28.3 / 30.7

Other elements in 8u9x:

The structure of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser also contains other interesting chemical elements:

Manganese (Mn) 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser (pdb code 8u9x). 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser, PDB code: 8u9x:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:139.6
occ:1.00
 SG A:CYS167 2.3 168.0 1.0
SG A:CYS107 2.3 141.8 1.0
SG A:CYS110 2.5 153.2 1.0
CB A:CYS107 2.8 132.6 1.0
CB A:CYS167 3.4 148.9 1.0
SG A:CYS148 3.5 174.6 1.0
N A:CYS167 3.5 143.7 1.0
CB A:CYS110 3.7 156.5 1.0
CB A:CYS148 3.8 129.4 1.0
N A:CYS110 3.8 148.8 1.0
CA A:CYS167 3.9 135.5 1.0
CA A:CYS107 4.2 130.8 1.0
CA A:CYS110 4.2 151.2 1.0
O A:CYS107 4.3 129.2 1.0
C A:CYS167 4.3 145.1 1.0
N A:GLY111 4.4 134.0 1.0
C A:CYS107 4.5 125.4 1.0
ND1 A:HIS109 4.5 165.6 1.0
N A:GLY168 4.6 144.5 1.0
C A:CYS110 4.6 134.9 1.0
CB A:HIS109 4.7 128.8 1.0
C A:HIS109 4.9 143.3 1.0
N A:HIS109 4.9 123.6 1.0
N A:ASN169 4.9 134.0 1.0
CA A:CYS148 4.9 131.7 1.0
O A:CYS167 4.9 155.2 1.0

Zinc binding site 2 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 2 of Structural Basis of Transcription: Rna Polymerase II Substrate Binding and Metal Coordination at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:65.0
occ:1.00
 SG A:CYS70 2.3 80.5 1.0
CE1 A:HIS80 2.3 82.7 1.0
SG A:CYS67 2.5 78.5 1.0
SG A:CYS77 2.6 42.2 1.0
NE2 A:HIS80 2.8 99.1 1.0
CB A:CYS67 3.0 104.2 1.0
CB A:CYS70 3.3 97.0 1.0
ND1 A:HIS80 3.3 68.7 1.0
N A:CYS70 3.3 91.9 1.0
O A:CYS70 3.4 102.4 1.0
CA A:CYS70 3.6 98.5 1.0
CB A:CYS77 3.7 75.6 1.0
CD2 A:HIS80 3.9 88.8 1.0
C A:CYS70 4.0 95.6 1.0
CG A:HIS80 4.1 79.2 1.0
C A:THR69 4.4 99.9 1.0
CA A:CYS67 4.5 99.2 1.0
CB A:THR69 4.6 89.9 1.0
CA A:CYS77 4.7 86.5 1.0
CA A:GLY59 4.7 110.5 1.0
CA A:THR69 4.8 92.5 1.0
N A:THR69 4.8 87.8 1.0

Zinc binding site 3 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2502

b:77.8
occ:1.00
 SG B:CYS1185 2.0 63.5 1.0
SG B:CYS1166 2.3 60.4 1.0
CB B:CYS1166 2.6 76.6 1.0
N B:CYS1166 2.8 67.8 1.0
CB B:CYS1185 2.9 88.1 1.0
CA B:CYS1166 3.3 63.0 1.0
SG B:CYS1163 3.5 60.9 1.0
CB B:ILE1165 3.6 79.6 1.0
SG B:CYS1182 3.6 67.8 1.0
CG2 B:ILE1165 3.7 98.9 1.0
C B:ILE1165 3.9 77.6 1.0
CB B:CYS1163 4.2 59.5 1.0
CA B:ILE1165 4.2 78.3 1.0
CA B:CYS1185 4.3 102.3 1.0
C B:CYS1166 4.3 53.0 1.0
O B:CYS1166 4.3 62.0 1.0
N B:CYS1185 4.6 99.4 1.0
N B:ILE1165 4.6 70.8 1.0
O B:CYS1185 4.7 122.1 1.0
CG1 B:ILE1165 4.8 77.3 1.0
O B:ILE1165 5.0 80.8 1.0
CD1 B:ILE1165 5.0 87.0 1.0

Zinc binding site 4 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:69.8
occ:1.00
 SG C:CYS92 2.2 78.1 1.0
SG C:CYS88 2.4 38.1 1.0
SG C:CYS95 2.6 64.9 1.0
SG C:CYS86 2.9 132.9 1.0
CB C:CYS95 3.1 88.0 1.0
CB C:CYS86 3.3 104.2 1.0
CB C:CYS92 3.7 73.1 1.0
CB C:CYS88 3.7 65.5 1.0
N C:CYS92 3.9 75.4 1.0
N C:CYS95 4.0 78.9 1.0
CB C:LYS94 4.1 88.0 1.0
CA C:CYS95 4.2 82.0 1.0
N C:CYS88 4.2 62.8 1.0
C C:HIS91 4.3 79.0 1.0
CA C:CYS92 4.4 69.2 1.0
C C:LYS94 4.4 86.6 1.0
O C:ASP90 4.5 128.4 1.0
CA C:HIS91 4.5 90.5 1.0
CA C:CYS88 4.6 63.3 1.0
N C:PHE87 4.6 70.9 1.0
CG C:LYS94 4.6 90.0 1.0
CA C:LYS94 4.7 88.3 1.0
CA C:CYS86 4.7 95.5 1.0
N C:LYS94 4.8 74.4 1.0
CD C:LYS94 4.8 85.8 1.0
O C:HIS91 4.9 70.7 1.0
C C:CYS86 4.9 93.0 1.0
C C:CYS92 5.0 75.7 1.0

Zinc binding site 5 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:119.3
occ:1.00
 SG I:CYS32 2.0 97.8 1.0
SG I:CYS7 2.4 90.0 1.0
CB I:CYS7 2.5 105.1 1.0
SG I:CYS29 2.8 119.5 1.0
CB I:CYS10 3.1 112.5 1.0
CB I:CYS29 3.6 106.6 1.0
SG I:CYS10 3.7 108.6 1.0
CB I:CYS32 3.7 107.7 1.0
N I:CYS10 3.7 119.4 1.0
CB I:TYR34 3.9 88.3 1.0
CA I:CYS7 4.1 111.7 1.0
CA I:CYS10 4.1 111.7 1.0
N I:CYS32 4.3 119.1 1.0
CA I:CYS32 4.5 117.3 1.0
CD2 I:LEU14 4.6 85.2 1.0
CG I:TYR34 4.6 88.6 1.0
CB I:ASP9 4.6 129.7 1.0
C I:ASP9 4.7 115.7 1.0
N I:ASP9 4.8 121.3 1.0
N I:CYS7 4.8 119.3 1.0
C I:CYS7 4.8 118.4 1.0
C I:CYS32 4.8 132.0 1.0
CB I:THR31 4.9 129.0 1.0
O I:CYS32 4.9 134.6 1.0
N I:TYR34 4.9 108.2 1.0
C I:CYS10 4.9 96.2 1.0
CA I:ASP9 5.0 125.6 1.0

Zinc binding site 6 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:182.5
occ:1.00
 SG I:CYS78 2.3 176.6 1.0
SG I:CYS106 2.4 165.8 1.0
SG I:CYS75 2.5 166.6 1.0
CB I:CYS106 2.7 171.8 1.0
CB I:CYS78 3.2 173.7 1.0
CB I:CYS75 3.4 170.2 1.0
SG I:CYS103 3.6 199.8 1.0
N I:CYS106 3.7 190.9 1.0
N I:CYS78 3.7 187.0 1.0
CA I:CYS106 3.7 172.9 1.0
CB I:CYS103 3.9 166.6 1.0
CA I:CYS78 4.0 184.2 1.0
OG I:SER105 4.1 170.4 1.0
ND1 I:HIS108 4.2 172.5 1.0
N I:HIS79 4.3 243.1 1.0
C I:SER105 4.5 188.9 1.0
C I:CYS106 4.5 178.8 1.0
C I:CYS78 4.6 199.8 1.0
CE1 I:HIS108 4.6 170.5 1.0
CB I:SER105 4.8 170.4 1.0
C I:LYS77 4.8 191.6 1.0
CA I:CYS75 4.9 186.2 1.0
CB I:LYS77 4.9 177.4 1.0
N I:SER80 5.0 204.1 1.0

Zinc binding site 7 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:85.9
occ:1.00
 SG J:CYS46 2.4 93.3 1.0
SG J:CYS7 2.5 87.3 1.0
OG J:SER9 2.7 87.0 1.0
SG J:CYS10 2.8 78.2 1.0
CB J:CYS7 2.9 80.8 1.0
SG J:CYS45 3.0 93.9 1.0
N J:CYS46 3.3 95.0 1.0
CB J:CYS46 3.5 83.3 1.0
CA J:CYS46 3.5 87.6 1.0
N J:CYS10 3.6 87.5 1.0
NH2 J:ARG43 3.8 77.3 1.0
CB J:CYS45 3.9 96.6 1.0
C J:CYS45 3.9 89.6 1.0
CB J:CYS10 4.0 101.5 1.0
CB J:SER9 4.1 86.3 1.0
NE J:ARG43 4.1 92.4 1.0
CA J:CYS10 4.3 98.1 1.0
CA J:CYS7 4.4 88.7 1.0
CZ J:ARG43 4.4 88.9 1.0
O J:CYS45 4.5 78.5 1.0
N J:SER9 4.5 97.9 1.0
CA J:CYS45 4.5 81.2 1.0
C J:SER9 4.6 95.3 1.0
CA J:SER9 4.6 95.6 1.0
N J:GLY11 4.6 91.4 1.0
C J:CYS10 4.7 84.5 1.0
C J:CYS7 4.8 91.3 1.0
N J:LYS12 4.9 88.5 1.0
CB J:LYS12 5.0 80.7 1.0
O J:CYS7 5.0 102.6 1.0

Zinc binding site 8 out of 8 in 8u9x

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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 at 3.0 A of T834P Mutant 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 at 3.0 A of T834P Mutant Using A Free-Electron Laser within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:153.8
occ:1.00
 SG L:CYS48 1.8 171.1 1.0
SG L:CYS34 2.1 184.8 1.0
SG L:CYS51 2.2 211.7 1.0
SG L:CYS31 2.2 212.3 1.0
CB L:CYS51 2.9 198.3 1.0
CB L:CYS48 3.0 149.4 1.0
CB L:CYS31 3.3 159.2 1.0
CB L:CYS34 3.7 178.7 1.0
N L:CYS51 3.9 206.6 1.0
CA L:CYS51 4.0 203.0 1.0
CA L:CYS48 4.2 122.9 1.0
CB L:SER36 4.2 121.5 1.0
N L:SER36 4.3 121.6 1.0
N L:SER35 4.3 162.8 1.0
O L:CYS48 4.3 173.7 1.0
N L:CYS34 4.5 192.4 1.0
CA L:CYS34 4.5 185.5 1.0
C L:CYS48 4.6 145.7 1.0
N L:ALA32 4.6 135.3 1.0
N L:GLY52 4.6 151.9 1.0
CA L:CYS31 4.7 144.4 1.0
C L:CYS34 4.8 174.5 1.0
C L:CYS51 4.9 192.9 1.0
C L:ASP50 4.9 199.1 1.0
CA L:SER36 4.9 123.6 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 12:05:03 2024

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