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Zinc in PDB 1r9t: Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide

Enzymatic activity of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide

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

Protein crystallography data

The structure of Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide, PDB code: 1r9t 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) 40.00 / 3.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.846, 222.958, 193.602, 90.00, 101.17, 90.00
R / Rfree (%) 23 / 31.7

Other elements in 1r9t:

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

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide (pdb code 1r9t). 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, Mismatched Nucleotide, PDB code: 1r9t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.3
occ:1.00
 SG A:CYS167 2.6 0.8 1.0
SG A:CYS148 2.7 0.3 1.0
SG A:CYS110 2.8 0.5 1.0
O A:MET108 2.9 0.1 1.0
SG A:CYS107 3.0 0.7 1.0
CB A:CYS148 3.7 0.1 1.0
O A:GLY166 4.0 0.9 1.0
N A:CYS110 4.0 0.7 1.0
C A:MET108 4.1 0.2 1.0
CB A:CYS167 4.1 0.1 1.0
CB A:CYS110 4.2 0.9 1.0
N A:GLY111 4.2 0.6 1.0
O A:CYS167 4.3 0.1 1.0
O A:CYS107 4.4 0.2 1.0
CA A:CYS110 4.5 0.5 1.0
C A:CYS107 4.6 0.3 1.0
CB A:CYS107 4.6 0.6 1.0
C A:GLY166 4.7 0.6 1.0
C A:CYS110 4.8 0.3 1.0
C A:CYS167 4.9 0.0 1.0
CA A:CYS167 4.9 0.1 1.0

Zinc binding site 2 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:75.6
occ:1.00
 CE1 A:HIS80 2.0 73.2 1.0
SG A:CYS77 2.1 56.5 1.0
SG A:CYS67 2.2 0.4 1.0
SG A:CYS70 2.3 80.3 1.0
NE2 A:GLN68 2.7 75.5 1.0
NE2 A:HIS80 2.7 72.6 1.0
CB A:CYS67 3.0 0.8 1.0
ND1 A:HIS80 3.0 73.4 1.0
CB A:CYS70 3.2 82.8 1.0
CB A:CYS77 3.5 51.7 1.0
CD2 A:HIS80 3.9 73.2 1.0
CD A:GLN68 4.0 76.0 1.0
O A:CYS67 4.1 0.3 1.0
CG A:HIS80 4.1 73.0 1.0
CA A:CYS77 4.3 68.8 1.0
CA A:CYS67 4.3 0.8 1.0
C A:CYS67 4.6 0.5 1.0
CD A:PRO78 4.6 93.4 1.0
CA A:CYS70 4.7 0.9 1.0
O A:PRO78 4.7 0.8 1.0
OE1 A:GLN68 4.7 73.5 1.0
O A:GLN71 4.9 0.1 1.0
C A:CYS70 4.9 1.0 1.0
N A:GLY59 4.9 1.0 1.0
CA A:GLY59 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:80.5
occ:1.00
 SG B:CYS1166 1.9 86.7 1.0
SG B:CYS1163 2.3 33.9 1.0
SG B:CYS1185 2.3 0.7 1.0
SG B:CYS1182 2.3 0.4 1.0
CB B:CYS1163 3.0 41.1 1.0
CB B:CYS1185 3.1 0.2 1.0
CB B:CYS1166 3.4 78.8 1.0
CB B:CYS1182 3.6 0.8 1.0
O B:CYS1182 4.2 0.5 1.0
O B:CYS1166 4.3 98.9 1.0
CA B:CYS1166 4.4 97.6 1.0
CA B:CYS1163 4.4 59.6 1.0
N B:CYS1166 4.4 93.1 1.0
C B:CYS1166 4.6 98.4 1.0
CB B:THR1170 4.6 0.7 1.0
CG2 B:THR1170 4.7 0.5 1.0
CA B:CYS1185 4.8 0.7 1.0
CG2 B:ILE1165 4.8 78.5 1.0
OG1 B:THR1170 4.9 0.5 1.0
CB B:LEU1168 4.9 53.5 1.0
CA B:CYS1182 4.9 0.2 1.0

Zinc binding site 4 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:31.0
occ:1.00
 SG C:CYS88 2.1 7.4 1.0
SG C:CYS86 2.1 43.7 1.0
SG C:CYS92 2.3 45.0 1.0
SG C:CYS95 2.5 10.4 1.0
CB C:CYS86 2.7 43.5 1.0
N C:CYS92 2.9 45.8 1.0
CB C:CYS88 3.2 13.1 1.0
CB C:CYS95 3.3 18.9 1.0
CB C:CYS92 3.3 42.7 1.0
CA C:CYS92 3.6 46.4 1.0
C C:HIS91 3.6 28.5 1.0
O C:HIS91 3.9 29.0 1.0
CA C:CYS86 4.1 41.0 1.0
N C:CYS88 4.1 11.3 1.0
O C:ASP90 4.2 43.1 1.0
CA C:CYS88 4.3 12.9 1.0
CA C:HIS91 4.4 28.9 1.0
N C:CYS95 4.4 53.9 1.0
CB C:LYS94 4.4 53.7 1.0
C C:CYS92 4.4 47.4 1.0
CA C:CYS95 4.6 49.3 1.0
C C:CYS86 4.6 39.4 1.0
O C:CYS92 4.8 47.7 1.0
N C:LYS94 4.9 43.1 1.0
C C:LYS94 5.0 39.6 1.0
N C:CYS86 5.0 42.7 1.0

Zinc binding site 5 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:98.1
occ:1.00
 SG I:CYS10 1.7 59.9 1.0
SG I:CYS29 1.9 49.6 1.0
SG I:CYS7 2.4 60.6 1.0
CB I:CYS7 2.7 60.4 1.0
CG2 I:THR31 2.9 54.9 1.0
CB I:CYS29 3.0 49.2 1.0
SG I:CYS32 3.1 0.8 1.0
CB I:CYS10 3.5 62.3 1.0
CB I:CYS32 3.6 0.0 1.0
O I:ARG8 3.7 62.1 1.0
N I:CYS32 3.7 82.7 1.0
N I:CYS10 3.7 70.9 1.0
CB I:THR31 3.8 57.1 1.0
CA I:CYS7 4.1 83.7 1.0
CA I:CYS10 4.2 68.5 1.0
C I:THR31 4.2 48.4 1.0
CB I:TYR34 4.3 32.8 1.0
C I:ASP9 4.4 61.0 1.0
CA I:CYS32 4.4 84.3 1.0
CA I:THR31 4.6 49.2 1.0
CA I:CYS29 4.8 52.2 1.0
N I:TYR34 4.8 38.8 1.0
C I:ARG8 4.8 63.0 1.0
C I:CYS7 4.8 86.0 1.0
CB I:ASP9 4.8 86.7 1.0
O I:THR31 4.9 48.7 1.0
OG1 I:THR31 4.9 57.3 1.0
C I:CYS10 4.9 66.9 1.0
N I:CYS7 4.9 82.0 1.0
CA I:ASP9 4.9 64.5 1.0
CD2 I:LEU14 5.0 54.2 1.0

Zinc binding site 6 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:31.9
occ:1.00
 CB I:CYS78 1.6 41.7 1.0
SG I:CYS78 1.7 41.0 1.0
SG I:CYS75 2.0 76.0 1.0
SG I:CYS106 2.2 80.0 1.0
SG I:CYS103 2.7 18.9 1.0
CA I:CYS78 3.0 38.6 1.0
CB I:CYS75 3.0 74.2 1.0
CB I:CYS103 3.2 19.9 1.0
O I:CYS78 3.2 37.1 1.0
C I:CYS78 3.4 37.8 1.0
CB I:CYS106 3.5 74.4 1.0
N I:CYS78 3.5 40.9 1.0
OG I:SER80 4.0 46.9 1.0
CB I:HIS108 4.0 49.9 1.0
N I:CYS106 4.0 64.8 1.0
CA I:CYS106 4.3 66.3 1.0
CA I:CYS75 4.4 65.5 1.0
N I:HIS79 4.6 53.9 1.0
CA I:CYS103 4.6 11.2 1.0
C I:LYS77 4.8 48.8 1.0
N I:CYS75 4.9 65.3 1.0
CG I:HIS108 4.9 49.5 1.0
N I:SER80 4.9 54.3 1.0
C I:CYS75 4.9 64.4 1.0
C I:CYS106 5.0 63.8 1.0
C I:SER105 5.0 37.2 1.0

Zinc binding site 7 out of 8 in 1r9t

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


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:39.6
occ:1.00
 SG J:CYS46 1.6 26.9 1.0
SG J:CYS10 2.0 42.7 1.0
SG J:CYS45 2.2 61.7 1.0
SG J:CYS7 2.4 5.9 1.0
N J:CYS46 2.6 50.2 1.0
CB J:CYS10 2.8 44.0 1.0
CB J:CYS46 2.9 23.1 1.0
CA J:CYS46 3.0 47.6 1.0
CB J:CYS45 3.1 64.2 1.0
CB J:CYS7 3.4 7.6 1.0
C J:CYS45 3.4 14.9 1.0
CG J:ARG43 3.8 59.1 1.0
CD J:ARG43 3.8 59.9 1.0
CA J:CYS45 3.9 14.6 1.0
CA J:CYS10 3.9 34.8 1.0
N J:CYS10 3.9 35.9 1.0
OG J:SER9 4.0 30.1 1.0
O J:CYS45 4.2 14.5 1.0
NE J:ARG43 4.4 60.8 1.0
N J:CYS45 4.4 14.2 1.0
N J:GLY11 4.5 35.5 1.0
C J:CYS46 4.5 49.0 1.0
C J:CYS10 4.7 34.0 1.0
O J:ARG43 4.8 74.8 1.0
CA J:CYS7 4.8 21.2 1.0
CB J:SER9 4.8 30.6 1.0
CB J:ARG43 4.9 57.2 1.0

Zinc binding site 8 out of 8 in 1r9t

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Zinc binding site 8 out of 8 in the Rna Polymerase II Strand Separated Elongation Complex, Mismatched Nucleotide


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, Mismatched Nucleotide within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:77.0
occ:1.00
 SG L:CYS51 2.0 0.7 1.0
SG L:CYS34 2.3 0.3 1.0
CB L:CYS51 2.4 0.7 1.0
SG L:CYS48 2.6 50.5 1.0
SG L:CYS31 2.9 95.7 1.0
CB L:CYS34 3.1 0.1 1.0
O L:CYS51 3.5 0.5 1.0
N L:CYS34 3.7 0.0 1.0
CA L:CYS51 3.8 1.0 1.0
CA L:CYS34 4.0 0.3 1.0
C L:CYS51 4.1 0.0 1.0
CB L:CYS48 4.1 53.3 1.0
CB L:CYS31 4.3 94.0 1.0
N L:CYS51 4.6 0.4 1.0
N L:SER35 4.6 88.6 1.0
C L:GLU33 4.7 0.7 1.0
CB L:GLU33 4.8 0.7 1.0
C L:CYS34 4.9 0.6 1.0

Reference:

K.D.Westover, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Nucleotide Selection By Rotation in the Rna Polymerase II Active Center. Cell(Cambridge,Mass.) V. 119 481 2004.
ISSN: ISSN 0092-8674
PubMed: 15537538
DOI: 10.1016/J.CELL.2004.10.016
Page generated: Wed Oct 16 18:30:01 2024

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