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Zinc in PDB 5c3e: Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble

Enzymatic activity of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble

All present enzymatic activity of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble, PDB code: 5c3e was solved by C.O.Barnes, M.Calero, I.Malik, H.Spahr, Q.Zhang, F.Pullara, C.D.Kaplan, G.Calero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 219.050, 390.940, 278.080, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 22

Other elements in 5c3e:

The structure of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble (pdb code 5c3e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble, PDB code: 5c3e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5c3e

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Zinc binding site 1 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:90.5
occ:0.95
 SG A:CYS110 2.2 0.8 1.0
O A:CYS167 2.7 0.8 1.0
CB A:CYS110 3.0 0.2 1.0
SG A:CYS148 3.1 0.6 1.0
O A:MET108 3.4 0.3 1.0
SG A:CYS167 3.5 0.9 1.0
CB A:CYS148 3.6 1.0 1.0
C A:CYS167 3.8 0.8 1.0
N A:CYS110 4.1 0.8 1.0
CA A:CYS110 4.1 0.1 1.0
SG A:CYS107 4.2 0.8 1.0
N A:CYS167 4.3 0.8 1.0
CA A:CYS167 4.4 0.0 1.0
CB A:CYS107 4.5 0.6 1.0
CB A:CYS167 4.6 0.3 1.0
C A:MET108 4.7 0.8 1.0
N A:ASN169 4.8 0.6 1.0
C A:GLY166 4.8 0.6 1.0
C A:HIS109 4.8 0.1 1.0
O A:CYS107 4.9 0.7 1.0
N A:GLY168 4.9 0.4 1.0
C A:CYS110 5.0 0.8 1.0

Zinc binding site 2 out of 9 in 5c3e

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Zinc binding site 2 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:67.9
occ:1.00
 NE2 A:HIS80 2.0 96.4 1.0
SG A:CYS67 2.2 54.2 1.0
CD2 A:HIS80 3.0 88.4 1.0
CE1 A:HIS80 3.1 0.6 1.0
SG A:CYS70 3.3 71.0 1.0
SG A:CYS77 3.4 0.1 1.0
CB A:CYS67 3.7 55.1 1.0
CB A:CYS77 3.8 0.5 1.0
CA A:CYS77 4.0 88.1 1.0
CD A:PRO78 4.1 56.2 1.0
CG A:HIS80 4.2 88.5 1.0
ND1 A:HIS80 4.2 96.2 1.0
NE2 A:GLN68 4.3 0.5 1.0
O A:GLN71 4.4 0.7 1.0
N A:PRO78 4.7 70.6 1.0
C A:CYS77 4.7 84.3 1.0
CG A:GLN68 4.7 1.0 1.0
O A:CYS67 4.8 0.4 1.0
N A:GLY79 4.8 90.2 1.0
CD A:GLN68 4.9 0.6 1.0
CA A:CYS67 4.9 79.0 1.0

Zinc binding site 3 out of 9 in 5c3e

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Zinc binding site 3 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:72.3
occ:1.00
 SG B:CYS1185 2.5 0.2 1.0
SG B:CYS1163 2.5 84.9 1.0
CB B:CYS1163 2.9 98.2 1.0
SG B:CYS1182 2.9 0.3 1.0
CB B:CYS1166 3.1 0.6 1.0
SG B:CYS1166 3.2 0.0 1.0
OG1 B:THR1170 3.5 0.7 1.0
CB B:CYS1185 3.6 1.0 1.0
N B:CYS1166 3.8 84.9 1.0
CA B:CYS1166 4.1 86.7 1.0
CB B:CYS1182 4.2 0.3 1.0
CA B:CYS1163 4.4 91.0 1.0
CG2 B:ILE1165 4.7 0.4 1.0
CB B:ILE1165 4.8 0.7 1.0
C B:ILE1165 4.8 72.8 1.0
CB B:THR1170 4.9 0.9 1.0
C B:CYS1163 4.9 92.4 1.0
CA B:CYS1185 4.9 79.9 1.0
N B:GLY1167 5.0 0.4 1.0

Zinc binding site 4 out of 9 in 5c3e

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Zinc binding site 4 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.7
occ:1.00
 NZ C:LYS94 3.7 1.0 1.0
CB C:CYS88 3.9 0.9 1.0
CE C:LYS94 4.0 0.5 1.0
SG C:CYS92 4.1 0.3 1.0
SG C:CYS86 4.2 70.5 1.0
CB C:CYS92 4.2 0.7 1.0
N C:CYS88 4.3 53.0 1.0
CA C:CYS88 4.4 53.2 1.0
ZN C:ZN402 4.6 74.1 1.0
C C:PHE87 4.9 62.0 1.0

Zinc binding site 5 out of 9 in 5c3e

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Zinc binding site 5 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:74.1
occ:1.00
 SG C:CYS88 2.2 0.1 1.0
SG C:CYS95 2.3 0.1 1.0
SG C:CYS86 2.4 70.5 1.0
SG C:CYS92 2.5 0.3 1.0
CB C:CYS92 2.9 0.7 1.0
CB C:CYS88 3.1 0.9 1.0
CB C:CYS95 3.2 0.3 1.0
CB C:CYS86 3.2 82.4 1.0
N C:CYS92 3.6 0.7 1.0
C C:HIS91 3.8 0.9 1.0
CA C:CYS92 3.8 0.7 1.0
O C:HIS91 4.1 0.8 1.0
N C:CYS88 4.2 53.0 1.0
N C:CYS95 4.3 69.1 1.0
CA C:CYS88 4.3 53.2 1.0
CA C:CYS95 4.3 71.7 1.0
CA C:HIS91 4.4 0.7 1.0
N C:HIS91 4.5 0.8 1.0
C C:CYS92 4.6 0.8 1.0
ZN C:ZN401 4.6 0.7 1.0
CA C:CYS86 4.6 75.1 1.0
O C:CYS92 4.7 0.1 1.0
N C:PHE87 5.0 67.5 1.0

Zinc binding site 6 out of 9 in 5c3e

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Zinc binding site 6 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.2
occ:1.00
 SG I:CYS32 2.2 0.1 1.0
SG I:CYS10 2.4 0.1 1.0
SG I:CYS29 2.6 99.3 1.0
SG I:CYS7 3.0 87.0 1.0
CB I:CYS32 3.1 0.8 1.0
N I:CYS32 3.5 0.1 1.0
O I:CYS10 3.5 0.7 1.0
CB I:CYS29 3.7 0.1 1.0
CB I:CYS7 3.7 89.2 1.0
CA I:CYS32 3.9 0.7 1.0
CB I:CYS10 4.0 0.8 1.0
CB I:THR31 4.1 1.0 1.0
ND2 I:ASN12 4.2 0.7 1.0
C I:THR31 4.3 0.7 1.0
N I:CYS10 4.3 0.2 1.0
C I:CYS10 4.4 0.8 1.0
CA I:CYS10 4.5 1.0 1.0
CA I:THR31 4.6 1.0 1.0
CB I:TYR34 4.7 78.7 1.0
N I:THR31 4.7 0.7 1.0
C I:CYS32 4.7 0.9 1.0
OG1 I:THR31 4.8 0.3 1.0
CG2 I:THR31 4.9 0.2 1.0
CB I:ASN12 5.0 1.0 1.0

Zinc binding site 7 out of 9 in 5c3e

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Zinc binding site 7 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.5
occ:1.00
 SG I:CYS75 2.2 0.5 1.0
CB I:CYS78 2.3 0.5 1.0
CB I:CYS75 2.5 0.5 1.0
SG I:CYS106 2.6 0.7 1.0
SG I:CYS78 2.8 0.5 1.0
CA I:CYS78 3.4 0.4 1.0
CB I:HIS108 3.5 0.2 1.0
OG I:SER80 3.7 0.3 1.0
N I:CYS78 3.7 0.3 1.0
CB I:CYS106 3.8 0.3 1.0
C I:CYS78 4.0 0.7 1.0
CA I:CYS75 4.0 0.3 1.0
CG I:HIS108 4.0 1.0 1.0
N I:HIS79 4.1 0.6 1.0
CD2 I:HIS108 4.2 0.5 1.0
CB I:SER80 4.3 0.4 1.0
N I:SER80 4.4 0.5 1.0
CB I:CYS103 4.5 0.4 1.0
N I:CYS75 4.6 0.6 1.0
SG I:CYS103 4.7 0.7 1.0
O I:CYS78 4.8 0.7 1.0
CA I:HIS108 4.8 0.3 1.0
C I:CYS75 4.9 0.0 1.0
C I:LYS77 5.0 0.7 1.0
CA I:SER80 5.0 0.2 1.0

Zinc binding site 8 out of 9 in 5c3e

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Zinc binding site 8 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:93.4
occ:1.00
 SG J:CYS7 2.2 92.2 1.0
SG J:CYS10 2.2 84.6 1.0
SG J:CYS46 2.6 0.7 1.0
CB J:CYS7 2.8 88.4 1.0
SG J:CYS45 2.8 87.9 1.0
N J:CYS46 3.0 75.5 1.0
CA J:CYS46 3.2 85.7 1.0
CB J:CYS46 3.2 0.1 1.0
C J:CYS45 3.4 98.3 1.0
CB J:CYS10 3.6 93.5 1.0
O J:CYS45 3.8 0.4 1.0
CB J:CYS45 3.8 0.9 1.0
N J:CYS10 3.9 0.9 1.0
CA J:CYS45 4.2 95.8 1.0
CA J:CYS10 4.3 0.9 1.0
CA J:CYS7 4.3 74.5 1.0
N J:GLY11 4.4 74.7 1.0
NE J:ARG43 4.6 89.2 1.0
C J:CYS46 4.7 91.1 1.0
C J:CYS7 4.8 71.7 1.0
N J:CYS45 4.9 0.2 1.0
C J:CYS10 4.9 0.3 1.0
N J:LYS12 4.9 0.7 1.0
CB J:SER9 5.0 0.4 1.0
NH2 J:ARG43 5.0 0.6 1.0

Zinc binding site 9 out of 9 in 5c3e

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Zinc binding site 9 out of 9 in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:93.9
occ:1.00
 SG L:CYS51 2.4 0.5 1.0
SG L:CYS34 2.6 0.3 1.0
OG L:SER36 3.1 0.6 1.0
SG L:CYS48 3.2 79.9 1.0
OE2 L:GLU33 3.3 0.4 1.0
OE1 L:GLU33 3.6 0.7 1.0
SG L:CYS31 3.7 0.5 1.0
CD L:GLU33 3.8 0.9 1.0
CB L:CYS51 3.8 0.3 1.0
O L:ALA32 4.0 0.9 1.0
CB L:CYS31 4.0 0.2 1.0
O L:CYS34 4.1 0.9 1.0
CB L:CYS34 4.1 0.1 1.0
CB L:CYS48 4.2 99.8 1.0
N L:CYS51 4.3 0.9 1.0
CB L:SER36 4.3 0.5 1.0
CB L:ASP50 4.4 0.9 1.0
N L:CYS34 4.6 0.4 1.0
CA L:CYS51 4.7 0.1 1.0
CA L:CYS34 4.7 0.4 1.0
C L:CYS34 4.8 0.2 1.0
C L:ASP50 4.9 0.6 1.0

Reference:

C.O.Barnes, M.Calero, I.Malik, B.W.Graham, H.Spahr, G.Lin, A.E.Cohen, I.S.Brown, Q.Zhang, F.Pullara, M.A.Trakselis, C.D.Kaplan, G.Calero. Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble. Mol.Cell V. 59 258 2015.
ISSN: ISSN 1097-2765
PubMed: 26186291
DOI: 10.1016/J.MOLCEL.2015.06.034
Page generated: Sun Oct 27 13:46:04 2024

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