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Zinc in PDB 1sfo: Rna Polymerase II Strand Separated Elongation Complex

Enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex

All present enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Strand Separated Elongation Complex, PDB code: 1sfo was solved by K.D.Westover, D.A.Bushnell, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.86 / 3.61
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 167.076, 221.256, 193.685, 90.00, 100.10, 90.00
R / Rfree (%) 31.5 / 34.3

Other elements in 1sfo:

The structure of Rna Polymerase II Strand Separated Elongation Complex also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Strand Separated Elongation Complex (pdb code 1sfo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Rna Polymerase II Strand Separated Elongation Complex, PDB code: 1sfo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1sfo

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Zinc binding site 1 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:22.8
occ:1.00
 SG A:CYS148 2.7 55.6 1.0
SG A:CYS107 2.9 0.8 1.0
CB A:CYS148 3.3 55.6 1.0
O A:MET108 3.4 0.7 1.0
CB A:CYS107 3.5 0.8 1.0
SG A:CYS110 3.5 30.0 1.0
SG A:CYS167 3.6 99.2 1.0
O A:CYS107 3.8 0.6 1.0
C A:CYS107 3.9 0.6 1.0
CA A:CYS107 4.3 0.6 1.0
N A:MET108 4.4 0.7 1.0
CA A:CYS148 4.5 0.1 1.0
N A:LYS112 4.5 63.4 1.0
C A:MET108 4.5 0.7 1.0
O A:CYS167 4.6 0.0 1.0
N A:GLY111 4.6 88.2 1.0
O A:GLY166 4.7 0.3 1.0
CB A:LYS112 4.7 0.2 1.0
N A:CYS110 4.8 85.8 1.0
CD2 A:LEU114 4.8 89.6 1.0
N A:CYS107 4.9 0.6 1.0
CA A:MET108 5.0 0.7 1.0

Zinc binding site 2 out of 8 in 1sfo

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Zinc binding site 2 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:22.8
occ:1.00
 SG A:CYS77 2.2 30.0 1.0
SG A:CYS70 2.3 30.0 1.0
CE1 A:HIS80 2.5 30.0 1.0
CB A:CYS67 3.0 0.4 1.0
SG A:CYS67 3.0 0.4 1.0
CB A:CYS77 3.2 30.0 1.0
NE2 A:HIS80 3.4 30.0 1.0
ND1 A:HIS80 3.5 30.0 1.0
NE2 A:GLN68 3.6 0.8 1.0
CA A:CYS77 3.6 30.0 1.0
CB A:CYS70 3.6 30.0 1.0
CD A:PRO78 4.2 30.9 1.0
O A:CYS67 4.4 33.6 1.0
C A:CYS77 4.4 30.0 1.0
O A:PRO78 4.4 91.4 1.0
CA A:CYS67 4.5 33.6 1.0
N A:PRO78 4.6 91.4 1.0
CD2 A:HIS80 4.6 30.0 1.0
CG A:HIS80 4.7 30.0 1.0
O A:GLN71 4.7 30.0 1.0
N A:CYS77 4.7 30.0 1.0
CD A:GLN68 4.8 0.8 1.0
C A:CYS70 4.8 0.4 1.0
CA A:CYS70 4.8 0.4 1.0
O A:GLU76 4.9 31.7 1.0
O A:CYS70 4.9 0.4 1.0
C A:CYS67 4.9 33.6 1.0

Zinc binding site 3 out of 8 in 1sfo

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Zinc binding site 3 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:22.8
occ:1.00
 SG B:CYS1166 2.2 83.8 1.0
SG B:CYS1182 2.5 30.0 1.0
CB B:CYS1163 2.5 30.0 1.0
SG B:CYS1163 2.7 30.0 1.0
CB B:CYS1166 3.5 83.8 1.0
O B:CYS1166 3.7 37.1 1.0
SG B:CYS1185 3.7 30.0 1.0
CB B:THR1170 3.9 85.0 1.0
OG1 B:THR1170 4.0 85.0 1.0
CA B:CYS1163 4.0 80.3 1.0
C B:CYS1166 4.0 37.1 1.0
CB B:LEU1168 4.1 32.4 1.0
CA B:CYS1166 4.1 37.1 1.0
CB B:CYS1182 4.1 30.0 1.0
CB B:CYS1185 4.2 30.0 1.0
N B:CYS1166 4.2 37.1 1.0
CG2 B:THR1170 4.3 85.0 1.0
N B:LEU1168 4.3 1.0 1.0
CA B:LEU1168 4.6 1.0 1.0
N B:CYS1163 4.6 80.3 1.0
O B:LEU1168 4.6 1.0 1.0
O B:CYS1182 4.8 56.0 1.0
C B:LEU1168 4.9 1.0 1.0
C B:CYS1163 5.0 80.3 1.0
N B:GLY1167 5.0 81.4 1.0

Zinc binding site 4 out of 8 in 1sfo

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Zinc binding site 4 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:22.8
occ:1.00
 SG C:CYS88 2.2 30.0 1.0
SG C:CYS92 2.4 30.0 1.0
SG C:CYS95 2.4 30.0 1.0
SG C:CYS86 2.5 30.0 1.0
CB C:CYS92 2.7 30.0 1.0
CB C:CYS86 3.0 30.0 1.0
CB C:CYS88 3.2 30.0 1.0
N C:CYS92 3.3 30.0 1.0
C C:HIS91 3.5 30.0 1.0
CA C:CYS92 3.6 30.0 1.0
CB C:CYS95 3.7 30.0 1.0
O C:HIS91 3.7 30.0 1.0
CA C:HIS91 4.1 30.0 1.0
O C:ASP90 4.1 37.8 1.0
N C:CYS95 4.3 30.0 1.0
C C:CYS92 4.3 30.0 1.0
N C:CYS88 4.3 30.0 1.0
CA C:CYS88 4.4 30.0 1.0
O C:CYS92 4.4 30.0 1.0
CA C:CYS86 4.5 44.7 1.0
CA C:CYS95 4.6 30.0 1.0
CB C:LYS94 4.7 30.0 1.0
C C:ASP90 4.9 37.8 1.0
C C:CYS86 4.9 44.7 1.0
N C:HIS91 4.9 30.0 1.0

Zinc binding site 5 out of 8 in 1sfo

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Zinc binding site 5 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:22.8
occ:1.00
 CB I:CYS10 2.2 30.1 1.0
SG I:CYS7 2.2 37.3 1.0
CB I:CYS7 2.2 37.3 1.0
SG I:CYS10 2.3 30.1 1.0
N I:CYS10 2.4 30.0 1.0
CA I:CYS10 2.5 30.0 1.0
O I:ARG8 2.6 30.0 1.0
C I:CYS10 3.1 30.0 1.0
CA I:CYS7 3.4 30.0 1.0
N I:ASN11 3.4 30.0 1.0
C I:ASP9 3.5 45.4 1.0
C I:CYS7 3.5 30.0 1.0
SG I:CYS29 3.6 30.0 1.0
O I:CYS7 3.8 30.0 1.0
C I:ARG8 3.9 30.0 1.0
CB I:CYS29 3.9 30.0 1.0
O I:CYS10 3.9 30.0 1.0
N I:ASN12 4.1 30.0 1.0
N I:ARG8 4.1 30.0 1.0
O I:ASP9 4.1 45.4 1.0
N I:CYS7 4.2 30.0 1.0
CB I:ASP9 4.3 0.3 1.0
SG I:CYS32 4.3 0.5 1.0
CA I:ASP9 4.3 45.4 1.0
CG2 I:THR31 4.5 77.3 1.0
CA I:ASN11 4.5 30.0 1.0
N I:ASP9 4.6 45.4 1.0
CB I:ASN12 4.7 30.0 1.0
CD2 I:LEU14 4.8 30.0 1.0
C I:ASN11 4.8 30.0 1.0
CA I:ARG8 4.9 30.0 1.0
CB I:THR31 4.9 77.3 1.0
CA I:ASN12 4.9 30.0 1.0

Zinc binding site 6 out of 8 in 1sfo

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Zinc binding site 6 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:22.8
occ:1.00
 SG I:CYS78 2.1 30.0 1.0
O I:CYS78 2.1 40.3 1.0
SG I:CYS75 2.3 0.7 1.0
C I:CYS78 2.4 40.3 1.0
CB I:CYS78 2.5 30.0 1.0
OG I:SER80 2.9 30.0 1.0
CA I:CYS78 2.9 40.3 1.0
SG I:CYS103 3.0 59.2 1.0
N I:SER80 3.1 30.0 1.0
N I:HIS79 3.2 30.0 1.0
CB I:SER80 3.6 30.0 1.0
SG I:CYS106 3.8 30.0 1.0
CB I:CYS75 3.9 0.7 1.0
CA I:HIS79 3.9 30.0 1.0
CA I:SER80 4.0 30.0 1.0
C I:HIS79 4.0 30.0 1.0
N I:CYS78 4.0 40.3 1.0
CB I:CYS103 4.2 59.2 1.0
O I:SER80 4.3 30.0 1.0
C I:SER80 4.6 30.0 1.0
CB I:SER105 4.7 30.0 1.0
CB I:CYS106 4.8 30.0 1.0
N I:CYS75 4.9 30.0 1.0
CA I:CYS75 4.9 30.0 1.0
N I:SER105 5.0 69.4 1.0
O I:CYS75 5.0 30.0 1.0

Zinc binding site 7 out of 8 in 1sfo

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Zinc binding site 7 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:22.8
occ:1.00
 SG J:CYS7 2.1 30.0 1.0
SG J:CYS46 2.2 30.0 1.0
CB J:CYS10 2.2 30.0 1.0
SG J:CYS45 2.4 96.7 1.0
N J:CYS46 2.6 0.2 1.0
SG J:CYS10 2.7 30.0 1.0
CB J:CYS46 2.7 30.0 1.0
CA J:CYS46 2.8 0.2 1.0
CB J:CYS7 3.0 30.0 1.0
C J:CYS45 3.2 30.0 1.0
CB J:CYS45 3.3 96.7 1.0
N J:CYS10 3.5 30.0 1.0
CA J:CYS10 3.5 30.0 1.0
OG J:SER9 3.6 30.0 1.0
O J:CYS45 3.8 30.0 1.0
CA J:CYS45 3.9 30.0 1.0
CD J:ARG43 4.1 30.0 1.0
CG J:ARG43 4.2 30.0 1.0
C J:CYS46 4.3 0.2 1.0
CA J:CYS7 4.4 30.0 1.0
N J:GLY11 4.5 30.0 1.0
C J:CYS10 4.5 30.0 1.0
N J:CYS45 4.5 30.0 1.0
C J:CYS7 4.6 30.0 1.0
CB J:SER9 4.7 30.0 1.0
C J:SER9 4.7 30.0 1.0
O J:CYS7 4.7 30.0 1.0
NE J:ARG43 4.8 30.0 1.0
O J:CYS46 5.0 0.2 1.0

Zinc binding site 8 out of 8 in 1sfo

Go back to Zinc Binding Sites List in 1sfo
Zinc binding site 8 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rna Polymerase II Strand Separated Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:22.8
occ:1.00
 SG L:CYS51 2.0 30.0 1.0
SG L:CYS34 2.0 30.0 1.0
CB L:CYS34 2.5 30.0 1.0
CB L:CYS51 2.5 30.0 1.0
SG L:CYS31 3.1 0.3 1.0
SG L:CYS48 3.2 30.0 1.0
N L:CYS34 3.2 60.6 1.0
CA L:CYS34 3.4 60.6 1.0
CA L:CYS51 4.0 85.0 1.0
O L:CYS51 4.1 85.0 1.0
N L:SER35 4.2 67.2 1.0
C L:CYS34 4.3 60.6 1.0
CB L:CYS31 4.3 0.3 1.0
C L:GLU33 4.4 81.9 1.0
C L:CYS51 4.6 85.0 1.0
CB L:GLU33 4.6 58.5 1.0
CB L:CYS48 4.7 30.0 1.0
N L:CYS51 4.7 85.0 1.0
CA L:GLU33 4.8 81.9 1.0
N L:GLU33 5.0 81.9 1.0

Reference:

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Separation of Rna From Dna By Rna Polymerase II Science V. 303 1014 2004.
ISSN: ISSN 0036-8075
PubMed: 14963331
DOI: 10.1126/SCIENCE.1090839
Page generated: Wed Oct 16 18:49:53 2024

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