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Zinc in PDB 5c4j: 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: 5c4j 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) 174.08 / 4.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 280.711, 223.384, 156.422, 90.00, 98.14, 90.00
R / Rfree (%) 21.2 / 27.1

Other elements in 5c4j:

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) 1 atom

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 5c4j). 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: 5c4j:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 5c4j

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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:0.2
occ:1.00
 SG A:CYS110 2.3 0.7 1.0
SG A:CYS107 2.6 0.1 1.0
O A:CYS167 3.5 0.6 1.0
CB A:CYS110 3.6 0.3 1.0
SG A:CYS148 3.6 0.8 1.0
CB A:CYS107 3.8 0.9 1.0
O A:MET108 3.8 0.1 1.0
SG A:CYS167 3.8 0.5 1.0
N A:CYS167 4.2 0.5 1.0
C A:CYS167 4.3 0.7 1.0
CB A:CYS148 4.4 0.8 1.0
N A:GLY166 4.6 0.1 1.0
N A:CYS110 4.6 0.8 1.0
CA A:CYS110 4.6 0.3 1.0
C A:GLY166 4.7 0.6 1.0
CA A:CYS167 4.7 0.9 1.0
C A:HIS109 4.7 0.0 1.0
C A:MET108 4.7 0.5 1.0
OD1 A:ASN169 4.8 0.4 1.0
O A:HIS109 4.8 1.0 1.0
CA A:GLY166 4.8 0.5 1.0
CB A:CYS167 4.9 0.1 1.0
C A:CYS107 4.9 0.6 1.0
CA A:CYS107 5.0 0.8 1.0

Zinc binding site 2 out of 9 in 5c4j

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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:0.0
occ:1.00
 SG A:CYS67 2.2 0.4 1.0
CE1 A:HIS80 2.4 0.9 1.0
CB B:ALA1173 3.1 90.6 1.0
NE2 A:HIS80 3.3 0.8 1.0
ND1 A:HIS80 3.3 0.6 1.0
SG A:CYS70 3.4 0.8 1.0
SG A:CYS77 3.5 0.9 1.0
CB A:CYS67 3.6 0.6 1.0
OE1 A:GLN68 3.9 0.8 1.0
O B:ALA1173 4.0 0.9 1.0
CB A:CYS77 4.1 0.1 1.0
CA B:ALA1173 4.1 0.8 1.0
N B:ALA1173 4.1 0.7 1.0
O A:CYS67 4.2 0.3 1.0
O A:GLN71 4.4 0.6 1.0
CD2 A:HIS80 4.4 0.3 1.0
CG A:HIS80 4.5 0.2 1.0
C B:ALA1173 4.5 0.5 1.0
CD A:GLN68 4.6 0.0 1.0
CB A:GLU72 4.6 0.6 1.0
C A:CYS67 4.7 0.4 1.0
CG A:GLN68 4.7 0.1 1.0
CA A:CYS67 4.7 0.4 1.0
CA A:CYS77 5.0 0.8 1.0

Zinc binding site 3 out of 9 in 5c4j

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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:0.0
occ:1.00
 SG B:CYS1163 2.9 0.3 1.0
CB B:CYS1163 2.9 0.9 1.0
SG B:CYS1166 3.0 0.6 1.0
CB B:CYS1185 3.2 0.6 1.0
SG B:CYS1182 3.4 0.1 1.0
SG B:CYS1185 3.5 0.4 1.0
CB B:CYS1166 3.7 0.1 1.0
OG1 B:THR1170 3.9 0.9 1.0
CA B:CYS1163 4.4 0.6 1.0
OD1 B:ASN1187 4.5 0.8 1.0
N B:CYS1166 4.5 0.4 1.0
CB B:THR1170 4.6 0.6 1.0
CA B:CYS1185 4.7 0.6 1.0
CA B:CYS1166 4.7 0.9 1.0
CD1 A:ILE30 4.8 0.8 1.0
O B:GLY1184 4.8 1.0 1.0
CB B:CYS1182 5.0 0.8 1.0

Zinc binding site 4 out of 9 in 5c4j

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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:0.9
occ:1.00
 O C:PHE87 4.2 0.8 1.0
C C:PHE87 4.7 0.6 1.0
CB C:PHE87 4.9 1.0 1.0
CA C:CYS88 5.0 0.1 1.0

Zinc binding site 5 out of 9 in 5c4j

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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:0.2
occ:1.00
 SG C:CYS92 1.6 0.8 1.0
SG C:CYS95 2.2 0.2 1.0
SG C:CYS88 2.2 0.9 1.0
SG C:CYS86 2.2 0.6 1.0
O C:HIS91 3.0 0.4 1.0
CB C:CYS92 3.0 0.9 1.0
CB C:CYS86 3.2 0.8 1.0
C C:HIS91 3.3 0.8 1.0
CB C:CYS88 3.3 0.1 1.0
CB C:CYS95 3.4 0.6 1.0
N C:CYS92 3.6 0.2 1.0
CA C:CYS92 3.8 0.2 1.0
CA C:HIS91 4.0 0.6 1.0
N C:CYS95 4.1 0.6 1.0
N C:HIS91 4.3 0.6 1.0
CA C:CYS95 4.3 0.9 1.0
C C:CYS92 4.4 0.5 1.0
N C:CYS88 4.4 0.2 1.0
CA C:CYS88 4.4 0.1 1.0
O C:CYS92 4.6 0.5 1.0
CA C:CYS86 4.7 0.2 1.0
C C:LYS94 4.8 0.1 1.0
N C:LYS94 4.9 0.8 1.0
C C:CYS95 5.0 1.0 1.0

Zinc binding site 6 out of 9 in 5c4j

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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:0.4
occ:1.00
 SG I:CYS32 2.3 0.4 1.0
SG I:CYS7 2.8 0.1 1.0
SG I:CYS29 2.8 1.0 1.0
SG I:CYS10 2.9 0.3 1.0
O I:ASP9 3.0 0.4 1.0
CB I:CYS32 3.5 0.7 1.0
O I:CYS10 3.5 0.2 1.0
C I:ASP9 3.8 0.0 1.0
CB I:CYS7 3.9 0.8 1.0
CB I:CYS29 3.9 0.0 1.0
N I:CYS32 4.0 0.3 1.0
C I:CYS10 4.0 0.3 1.0
CB I:CYS10 4.3 0.6 1.0
CB I:THR31 4.3 0.3 1.0
CA I:CYS32 4.3 0.7 1.0
CA I:CYS10 4.4 0.8 1.0
N I:CYS10 4.4 0.2 1.0
CB I:ASN12 4.5 0.7 1.0
CB I:ASP9 4.8 0.1 1.0
C I:THR31 4.8 0.7 1.0
CA I:ASP9 4.8 0.9 1.0
N I:ASN11 4.8 0.8 1.0
CB I:TYR34 4.8 0.1 1.0
CG2 I:THR31 4.9 0.3 1.0
N I:ASN12 4.9 0.8 1.0

Zinc binding site 7 out of 9 in 5c4j

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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:0.9
occ:1.00
 SG I:CYS106 2.2 0.7 1.0
SG I:CYS103 3.1 0.0 1.0
SG I:CYS75 3.1 0.8 1.0
CB I:CYS78 3.1 0.1 1.0
CB I:CYS75 3.1 0.0 1.0
CB I:CYS106 3.3 0.8 1.0
CB I:CYS103 3.5 0.2 1.0
OG I:SER80 3.6 0.2 1.0
N I:CYS106 3.6 0.5 1.0
N I:CYS78 3.7 0.2 1.0
SG I:CYS78 3.8 0.7 1.0
CA I:CYS78 3.9 0.5 1.0
CA I:CYS106 4.0 0.6 1.0
CB I:SER80 4.0 0.8 1.0
C I:CYS78 4.4 0.0 1.0
N I:SER80 4.4 0.7 1.0
N I:HIS79 4.5 0.5 1.0
CB I:SER105 4.5 0.5 1.0
C I:SER105 4.6 0.9 1.0
CA I:CYS75 4.7 0.4 1.0
C I:CYS106 4.7 0.8 1.0
CB I:HIS108 4.7 0.5 1.0
CB I:LYS77 4.8 0.8 1.0
CA I:SER80 4.8 0.8 1.0
CA I:CYS103 4.9 0.9 1.0
C I:LYS77 4.9 0.7 1.0
CA I:SER105 5.0 0.9 1.0

Zinc binding site 8 out of 9 in 5c4j

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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:0.9
occ:1.00
 SG J:CYS7 2.1 0.2 1.0
SG J:CYS10 2.2 0.5 1.0
CB J:CYS7 2.5 0.8 1.0
SG J:CYS45 2.5 0.5 1.0
N J:CYS46 2.9 0.7 1.0
CA J:CYS46 3.2 0.5 1.0
CB J:CYS10 3.2 0.7 1.0
CB J:CYS46 3.3 0.6 1.0
C J:CYS45 3.4 0.7 1.0
CB J:CYS45 3.5 0.8 1.0
N J:CYS10 3.6 0.1 1.0
CA J:CYS10 3.9 0.1 1.0
CA J:CYS7 4.0 0.4 1.0
O J:CYS45 4.0 0.2 1.0
N J:GLY11 4.1 0.2 1.0
CA J:CYS45 4.1 0.2 1.0
C J:CYS7 4.5 0.0 1.0
C J:CYS10 4.6 0.4 1.0
SG J:CYS46 4.6 0.4 1.0
C J:CYS46 4.7 0.7 1.0
NE J:ARG43 4.7 0.4 1.0
N J:LYS12 4.8 0.1 1.0
N J:CYS7 4.8 0.2 1.0
N J:CYS45 4.8 0.6 1.0
C J:SER9 4.8 0.1 1.0
N J:SER9 4.9 0.1 1.0
NH2 J:ARG43 5.0 0.7 1.0
O J:CYS7 5.0 0.2 1.0

Zinc binding site 9 out of 9 in 5c4j

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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


Mono view


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:0.7
occ:1.00
 SG L:CYS34 1.8 0.5 1.0
SG L:CYS48 2.5 0.8 1.0
CB L:CYS51 2.6 0.1 1.0
SG L:CYS51 3.0 0.9 1.0
SG L:CYS31 3.1 0.4 1.0
N L:CYS51 3.3 0.9 1.0
CB L:CYS48 3.5 0.7 1.0
CB L:CYS34 3.5 0.4 1.0
CA L:CYS51 3.5 0.7 1.0
CB L:CYS31 3.9 0.2 1.0
O L:ALA32 4.1 0.8 1.0
O L:CYS34 4.2 0.6 1.0
CB L:SER36 4.3 0.8 1.0
N L:CYS34 4.4 0.8 1.0
CA L:CYS34 4.4 0.7 1.0
CB L:ASP50 4.4 0.5 1.0
C L:ASP50 4.5 0.9 1.0
C L:CYS51 4.6 0.8 1.0
O L:CYS51 4.7 0.6 1.0
C L:CYS34 4.7 0.8 1.0
OD2 L:ASP50 4.9 0.8 1.0
CA L:ASP50 4.9 0.7 1.0
CA L:CYS48 4.9 0.8 1.0
N L:ASP50 5.0 0.1 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 13:51:18 2024

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