Atomistry » Zinc » PDB 5c3h-5cde » 5c4a
Atomistry »
  Zinc »
    PDB 5c3h-5cde »
      5c4a »

Zinc in PDB 5c4a: 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: 5c4a was solved by C.O.Barnes, M.Calero, I.Malik, H.Saphr, 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) 39.91 / 4.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 219.830, 396.710, 273.640, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 24.2

Other elements in 5c4a:

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 5c4a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Transcribing Rna Polymerase II Complex Reveals A Complete Transcription Bubble, PDB code: 5c4a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 1 out of 8 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 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:0.3
occ:0.95
 SG A:CYS110 2.4 0.3 1.0
SG A:CYS148 2.7 0.6 1.0
O A:CYS167 2.8 0.3 1.0
CB A:CYS148 3.2 0.4 1.0
O A:MET108 3.6 0.3 1.0
SG A:CYS167 3.7 0.8 1.0
SG A:CYS107 3.8 0.2 1.0
CB A:CYS107 3.9 0.9 1.0
CB A:CYS110 4.0 0.9 1.0
C A:CYS167 4.0 0.1 1.0
N A:CYS167 4.5 0.8 1.0
N A:CYS110 4.6 1.0 1.0
CA A:CYS167 4.6 0.7 1.0
CA A:CYS148 4.7 0.6 1.0
CB A:CYS167 4.8 0.6 1.0
C A:MET108 4.8 0.1 1.0
N A:ASN169 4.8 0.7 1.0
CA A:CYS110 4.8 0.9 1.0
C A:CYS107 4.9 0.8 1.0

Zinc binding site 2 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 2 out of 8 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 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:68.6
occ:1.00
 SG A:CYS67 2.1 0.8 1.0
NE2 A:HIS80 2.4 0.6 1.0
SG A:CYS77 2.8 0.6 1.0
CD2 A:HIS80 3.1 0.1 1.0
CE1 A:HIS80 3.4 0.6 1.0
CB A:CYS77 3.6 0.1 1.0
CD A:PRO78 3.6 58.4 1.0
CB A:CYS67 3.7 0.8 1.0
SG A:CYS70 3.7 0.7 1.0
CA A:CYS77 3.9 0.1 1.0
NE2 A:GLN68 4.1 0.2 1.0
N A:PRO78 4.1 61.5 1.0
CG A:HIS80 4.3 0.5 1.0
N A:GLY79 4.3 0.5 1.0
C A:CYS77 4.3 0.1 1.0
ND1 A:HIS80 4.4 0.5 1.0
CG A:PRO78 4.8 55.7 1.0
O A:CYS67 4.8 0.7 1.0
CA A:CYS67 4.8 0.6 1.0
CA A:GLY79 4.9 0.5 1.0
O A:GLN71 4.9 0.0 1.0

Zinc binding site 3 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 3 out of 8 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 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:60.2
occ:1.00
 SG B:CYS1166 2.2 67.5 1.0
SG B:CYS1163 2.4 0.6 1.0
SG B:CYS1185 2.9 69.1 1.0
SG B:CYS1182 3.0 53.8 1.0
CB B:CYS1163 3.0 1.0 1.0
OG1 B:THR1170 3.3 91.9 1.0
CB B:CYS1166 3.4 76.5 1.0
CB B:CYS1185 3.6 81.8 1.0
N B:CYS1166 3.9 86.5 1.0
CA B:CYS1166 4.3 74.6 1.0
CB B:CYS1182 4.4 69.3 1.0
CA B:CYS1163 4.4 72.2 1.0
CB B:THR1170 4.5 89.6 1.0
CG2 B:THR1170 4.8 86.6 1.0
N B:CYS1185 4.8 85.1 1.0
CA B:CYS1185 4.8 96.6 1.0
O B:CYS1163 4.9 66.9 1.0
C B:CYS1163 4.9 69.6 1.0
CB B:ILE1165 4.9 86.6 1.0
C B:ILE1165 5.0 0.1 1.0

Zinc binding site 4 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 4 out of 8 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 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:82.9
occ:1.00
 SG C:CYS88 2.2 92.2 1.0
SG C:CYS92 2.2 86.4 1.0
SG C:CYS95 2.3 0.5 1.0
SG C:CYS86 2.7 86.3 1.0
CB C:CYS92 3.0 96.5 1.0
N C:CYS92 3.2 0.9 1.0
CB C:CYS88 3.4 90.3 1.0
CB C:CYS95 3.5 0.7 1.0
CB C:CYS86 3.6 0.6 1.0
CA C:CYS92 3.6 0.9 1.0
C C:HIS91 3.7 86.7 1.0
N C:CYS95 3.9 0.8 1.0
CA C:HIS91 4.1 91.0 1.0
CA C:CYS95 4.3 0.5 1.0
O C:HIS91 4.3 81.3 1.0
C C:CYS92 4.4 0.9 1.0
N C:CYS88 4.5 67.8 1.0
CA C:CYS88 4.5 68.8 1.0
NZ C:LYS94 4.6 0.7 1.0
N C:HIS91 4.6 83.6 1.0
N C:LYS94 4.9 0.8 1.0
N C:ASP93 4.9 0.1 1.0
C C:LYS94 4.9 0.6 1.0

Zinc binding site 5 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 5 out of 8 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 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
I:Zn201

b:0.1
occ:1.00
 SG I:CYS32 2.1 0.2 1.0
SG I:CYS29 2.3 1.0 1.0
SG I:CYS10 2.4 0.8 1.0
SG I:CYS7 2.9 83.4 1.0
CB I:CYS29 3.5 0.3 1.0
CB I:CYS32 3.5 0.3 1.0
CB I:CYS7 3.5 87.6 1.0
N I:CYS32 3.7 1.0 1.0
O I:CYS10 4.0 0.8 1.0
CB I:CYS10 4.1 0.7 1.0
CA I:CYS32 4.1 0.5 1.0
CB I:TYR34 4.4 80.3 1.0
CB I:THR31 4.4 0.8 1.0
N I:CYS10 4.5 0.2 1.0
CA I:CYS10 4.7 0.0 1.0
C I:THR31 4.7 0.9 1.0
CA I:CYS29 4.8 0.8 1.0
C I:CYS32 4.8 0.9 1.0
C I:CYS10 4.8 0.4 1.0
OG1 I:THR31 4.8 0.9 1.0
N I:THR31 4.9 0.2 1.0
CA I:THR31 4.9 0.2 1.0

Zinc binding site 6 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 6 out of 8 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 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:Zn202

b:0.2
occ:1.00
 SG I:CYS106 2.2 0.9 1.0
CB I:CYS78 2.3 0.5 1.0
SG I:CYS78 2.4 0.7 1.0
SG I:CYS75 2.8 0.7 1.0
CB I:CYS106 2.9 0.4 1.0
CB I:CYS75 3.3 0.0 1.0
OG I:SER80 3.4 57.2 1.0
CA I:CYS78 3.7 0.8 1.0
CB I:HIS108 3.9 0.7 1.0
CB I:SER80 4.1 86.4 1.0
SG I:CYS103 4.1 0.3 1.0
CB I:CYS103 4.2 0.0 1.0
N I:CYS78 4.3 0.1 1.0
C I:CYS78 4.3 0.0 1.0
CA I:CYS106 4.4 0.6 1.0
O I:SER105 4.4 0.8 1.0
N I:SER80 4.6 0.9 1.0
N I:HIS108 4.7 0.5 1.0
CG I:HIS108 4.7 0.8 1.0
N I:HIS79 4.8 0.8 1.0
CA I:CYS75 4.8 0.5 1.0
CD2 I:HIS108 4.9 0.9 1.0
CA I:HIS108 4.9 0.6 1.0
O I:CYS78 4.9 0.8 1.0
C I:CYS106 4.9 0.4 1.0

Zinc binding site 7 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 7 out of 8 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 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
J:Zn101

b:90.2
occ:1.00
 SG J:CYS10 2.2 0.3 1.0
SG J:CYS7 2.3 0.5 1.0
CB J:CYS7 2.6 0.7 1.0
SG J:CYS45 2.9 0.6 1.0
CB J:CYS46 3.0 0.8 1.0
N J:CYS46 3.2 0.6 1.0
CA J:CYS46 3.2 0.6 1.0
CB J:CYS10 3.5 1.0 1.0
C J:CYS45 3.7 0.5 1.0
N J:CYS10 3.7 0.3 1.0
SG J:CYS46 3.9 0.5 1.0
N J:GLY11 4.0 69.6 1.0
CB J:CYS45 4.0 0.7 1.0
CA J:CYS10 4.1 0.5 1.0
O J:CYS45 4.1 0.1 1.0
CA J:CYS7 4.1 74.3 1.0
NE J:ARG43 4.3 86.2 1.0
CA J:CYS45 4.5 0.8 1.0
NH2 J:ARG43 4.5 88.2 1.0
C J:CYS10 4.6 0.4 1.0
C J:CYS7 4.6 76.4 1.0
N J:LYS12 4.6 0.0 1.0
C J:CYS46 4.7 0.1 1.0
C J:SER9 4.8 0.9 1.0
CZ J:ARG43 4.9 88.2 1.0
N J:SER9 4.9 0.5 1.0
N J:CYS7 4.9 81.1 1.0
CB J:SER9 5.0 0.1 1.0
N J:PHE8 5.0 97.5 1.0

Zinc binding site 8 out of 8 in 5c4a

Go back to Zinc Binding Sites List in 5c4a
Zinc binding site 8 out of 8 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 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
L:Zn101

b:91.4
occ:1.00
 OG L:SER36 2.5 0.3 1.0
SG L:CYS51 2.7 94.6 1.0
SG L:CYS48 3.4 55.2 1.0
SG L:CYS34 3.4 0.4 1.0
CB L:SER36 3.6 0.4 1.0
CB L:CYS51 3.9 0.1 1.0
O L:ALA32 3.9 0.2 1.0
CB L:ASP50 4.0 0.9 1.0
CB L:CYS31 4.1 0.7 1.0
SG L:CYS31 4.1 0.5 1.0
N L:CYS51 4.2 0.2 1.0
O L:CYS34 4.4 0.1 1.0
N L:CYS34 4.6 0.6 1.0
CB L:CYS48 4.6 73.1 1.0
CG L:ASP50 4.7 0.7 1.0
CA L:CYS51 4.7 0.5 1.0
CB L:GLU33 4.7 0.8 1.0
C L:ASP50 4.7 0.2 1.0
OD1 L:ASP50 4.8 1.0 1.0
CA L:ASP50 4.9 0.2 1.0
CA L:SER36 4.9 0.2 1.0
CB L:CYS34 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: Wed Dec 16 06:06:00 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy