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Zinc in PDB 1i3q: Rna Polymerase II Crystal Form I at 3.1 A Resolution

Enzymatic activity of Rna Polymerase II Crystal Form I at 3.1 A Resolution

All present enzymatic activity of Rna Polymerase II Crystal Form I at 3.1 A Resolution:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Crystal Form I at 3.1 A Resolution, PDB code: 1i3q was solved by P.Cramer, 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 / 3.10
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 130.700, 224.800, 369.400, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 28.3

Other elements in 1i3q:

The structure of Rna Polymerase II Crystal Form I at 3.1 A Resolution also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Crystal Form I at 3.1 A Resolution (pdb code 1i3q). 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 Crystal Form I at 3.1 A Resolution, PDB code: 1i3q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1i3q

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Zinc binding site 1 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn2001

b:87.8
occ:1.00
 SG J:CYS7 2.2 49.6 1.0
SG J:CYS10 2.3 55.2 1.0
SG J:CYS46 2.3 52.5 1.0
SG J:CYS45 2.7 43.1 1.0
N J:CYS46 3.1 44.3 1.0
CA J:CYS46 3.3 45.1 1.0
CB J:CYS7 3.3 47.5 1.0
CB J:CYS46 3.3 46.0 1.0
CB J:CYS45 3.7 39.7 1.0
C J:CYS45 3.7 43.0 1.0
CB J:CYS10 3.7 48.9 1.0
N J:CYS10 3.8 45.1 1.0
CA J:CYS10 4.3 49.0 1.0
CA J:CYS45 4.4 40.7 1.0
O J:CYS45 4.4 46.0 1.0
CD J:ARG43 4.4 54.7 1.0
NE J:ARG43 4.4 58.4 1.0
CG J:ARG43 4.4 52.1 1.0
N J:GLY11 4.6 48.6 1.0
CB J:LYS12 4.7 44.4 1.0
CA J:CYS7 4.7 42.4 1.0
CB J:SER9 4.7 41.3 1.0
N J:LYS12 4.8 46.2 1.0
C J:SER9 4.8 42.8 1.0
C J:CYS46 4.8 47.0 1.0
C J:CYS10 4.9 47.1 1.0
C J:CYS7 4.9 42.6 1.0
O J:CYS7 4.9 46.8 1.0

Zinc binding site 2 out of 8 in 1i3q

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Zinc binding site 2 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2002

b:77.9
occ:1.00
 SG C:CYS86 2.2 47.0 1.0
SG C:CYS92 2.4 53.1 1.0
SG C:CYS88 2.5 60.6 1.0
SG C:CYS95 2.5 56.5 1.0
CB C:CYS86 3.0 47.8 1.0
CB C:CYS88 3.2 53.8 1.0
CB C:CYS92 3.5 54.0 1.0
CB C:CYS95 3.5 55.0 1.0
N C:CYS92 3.6 58.5 1.0
C C:HIS91 3.9 59.0 1.0
CA C:CYS92 4.0 58.2 1.0
N C:CYS95 4.1 59.4 1.0
N C:CYS88 4.1 43.9 1.0
CA C:HIS91 4.2 61.1 1.0
CA C:CYS88 4.3 47.8 1.0
CA C:CYS86 4.4 48.3 1.0
CB C:LYS94 4.4 63.4 1.0
CA C:CYS95 4.4 54.9 1.0
O C:HIS91 4.5 60.2 1.0
C C:CYS92 4.6 60.5 1.0
O C:CYS92 4.6 56.1 1.0
C C:CYS86 4.7 47.9 1.0
C C:LYS94 4.7 61.1 1.0
O C:ASP90 4.8 50.8 1.0
N C:LYS94 4.9 59.7 1.0
N C:HIS91 4.9 59.4 1.0
CA C:LYS94 4.9 61.1 1.0
N C:PHE87 5.0 47.5 1.0

Zinc binding site 3 out of 8 in 1i3q

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Zinc binding site 3 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2003

b:0.0
occ:1.00
 SG I:CYS32 1.8 81.1 1.0
SG I:CYS10 2.2 77.4 1.0
SG I:CYS7 2.5 69.2 1.0
SG I:CYS29 2.6 70.2 1.0
CB I:CYS32 3.2 78.1 1.0
CB I:CYS29 3.6 66.5 1.0
CB I:CYS10 3.6 74.0 1.0
CG2 I:THR31 3.8 64.4 1.0
N I:CYS32 3.8 76.6 1.0
CB I:CYS7 3.9 78.1 1.0
CA I:CYS32 4.1 76.3 1.0
N I:CYS10 4.2 74.3 1.0
O I:ARG8 4.3 73.7 1.0
CB I:TYR34 4.3 67.4 1.0
CA I:CYS10 4.4 72.8 1.0
CB I:THR31 4.4 65.7 1.0
N I:SER33 4.6 70.6 1.0
N I:TYR34 4.7 70.1 1.0
C I:CYS32 4.7 74.7 1.0
CB I:ASP9 4.7 70.4 1.0
C I:THR31 4.8 73.2 1.0
C I:CYS10 4.9 69.4 1.0
O I:CYS10 4.9 69.9 1.0

Zinc binding site 4 out of 8 in 1i3q

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Zinc binding site 4 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn2004

b:0.5
occ:1.00
 SG I:CYS78 2.1 97.9 1.0
SG I:CYS75 2.3 71.0 1.0
SG I:CYS106 2.3 76.8 1.0
SG I:CYS103 2.8 88.8 1.0
CB I:CYS106 3.0 68.5 1.0
CB I:CYS78 3.1 99.9 1.0
N I:CYS78 3.3 97.2 1.0
CB I:CYS103 3.3 75.5 1.0
CB I:CYS75 3.5 83.2 1.0
CA I:CYS78 3.6 98.2 1.0
N I:CYS106 3.9 66.5 1.0
OG I:SER80 3.9 0.8 1.0
CA I:CYS106 4.0 67.5 1.0
C I:CYS78 4.2 99.0 1.0
C I:LYS77 4.4 97.2 1.0
CB I:LYS77 4.5 95.6 1.0
O I:CYS78 4.6 99.9 1.0
CB I:HIS108 4.7 62.5 1.0
C I:CYS106 4.7 68.5 1.0
CA I:CYS103 4.8 69.1 1.0
CA I:LYS77 4.8 95.8 1.0
N I:HIS79 4.8 0.1 1.0
CA I:CYS75 4.9 86.2 1.0

Zinc binding site 5 out of 8 in 1i3q

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Zinc binding site 5 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn2005

b:0.4
occ:1.00
 CB L:CYS51 2.0 0.7 1.0
SG L:CYS34 2.1 0.8 1.0
SG L:CYS51 2.2 0.9 1.0
SG L:CYS31 3.0 0.3 1.0
SG L:CYS48 3.1 0.9 1.0
CB L:CYS34 3.4 0.1 1.0
CB L:CYS48 3.4 1.0 1.0
CB L:CYS31 3.4 0.1 1.0
CA L:CYS51 3.5 0.6 1.0
CD2 L:HIS53 3.7 0.2 1.0
N L:CYS34 3.9 0.0 1.0
O L:CYS51 4.0 0.3 1.0
N L:CYS51 4.2 0.4 1.0
C L:CYS51 4.2 0.2 1.0
CA L:CYS34 4.2 0.2 1.0
NE2 L:HIS53 4.4 0.6 1.0
CB L:GLU33 4.6 0.3 1.0
CG L:HIS53 4.7 0.7 1.0
C L:GLU33 4.7 0.0 1.0
CA L:CYS48 4.9 0.5 1.0
CA L:CYS31 4.9 0.7 1.0

Zinc binding site 6 out of 8 in 1i3q

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Zinc binding site 6 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2006

b:0.1
occ:1.00
 SG A:CYS110 1.9 0.8 1.0
SG A:CYS167 2.0 0.1 1.0
SG A:CYS107 2.6 0.1 1.0
CB A:CYS110 3.1 0.9 1.0
CB A:CYS107 3.3 0.7 1.0
SG A:CYS148 3.3 0.3 1.0
CB A:CYS167 3.6 1.0 1.0
N A:CYS110 3.6 0.4 1.0
O A:MET108 3.8 0.7 1.0
CB A:CYS148 3.8 0.5 1.0
CA A:CYS110 3.9 0.6 1.0
O A:CYS167 4.2 0.8 1.0
C A:CYS107 4.4 0.6 1.0
CA A:CYS107 4.5 0.7 1.0
O A:CYS107 4.5 0.2 1.0
C A:MET108 4.6 0.1 1.0
C A:CYS110 4.7 0.9 1.0
N A:GLY111 4.7 0.3 1.0
C A:HIS109 4.7 0.1 1.0
CB A:HIS109 4.8 0.6 1.0
CA A:CYS167 4.8 0.6 1.0
N A:MET108 4.9 0.8 1.0
ND2 A:ASN169 4.9 0.2 1.0
C A:CYS167 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 1i3q

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Zinc binding site 7 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2007

b:97.3
occ:1.00
 SG B:CYS1182 2.2 0.4 1.0
SG B:CYS1166 2.3 88.6 1.0
SG B:CYS1163 2.6 68.2 1.0
SG B:CYS1185 2.8 93.4 1.0
CB B:CYS1185 3.1 0.3 1.0
CB B:CYS1163 3.1 64.8 1.0
CB B:CYS1182 3.8 0.2 1.0
CB B:CYS1166 3.9 82.8 1.0
O B:CYS1166 4.1 83.5 1.0
N B:CYS1166 4.3 75.0 1.0
CA B:CYS1185 4.5 0.2 1.0
CA B:CYS1166 4.6 79.2 1.0
CA B:CYS1163 4.6 62.3 1.0
O B:LYS1183 4.7 0.2 1.0
C B:CYS1166 4.8 79.3 1.0
O B:CYS1182 4.8 0.4 1.0
N B:CYS1185 4.9 0.6 1.0
ND2 B:ASN1187 4.9 0.5 1.0
CA B:CYS1182 5.0 0.8 1.0

Zinc binding site 8 out of 8 in 1i3q

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Zinc binding site 8 out of 8 in the Rna Polymerase II Crystal Form I at 3.1 A Resolution


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 Crystal Form I at 3.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2008

b:0.7
occ:1.00
 SG A:CYS70 2.2 0.8 1.0
SG A:CYS67 2.2 0.9 1.0
NE2 A:HIS80 2.8 94.3 1.0
SG A:CYS77 2.8 0.9 1.0
CD2 A:HIS80 3.1 93.4 1.0
CB A:CYS67 3.4 0.8 1.0
CE1 A:HIS80 3.9 96.0 1.0
O A:CYS67 3.9 0.8 1.0
CB A:CYS70 4.0 0.2 1.0
CB A:CYS77 4.2 0.4 1.0
O A:GLN71 4.3 0.7 1.0
CG A:HIS80 4.4 95.8 1.0
C A:CYS67 4.4 0.0 1.0
CA A:CYS67 4.5 0.8 1.0
CA A:CYS77 4.6 0.9 1.0
ND1 A:HIS80 4.7 95.0 1.0
C A:CYS77 4.9 0.2 1.0

Reference:

P.Cramer, D.A.Bushnell, R.D.Kornberg. Structural Basis of Transcription: Rna Polymerase II at 2.8 Angstrom Resolution. Science V. 292 1863 2001.
ISSN: ISSN 0036-8075
PubMed: 11313498
DOI: 10.1126/SCIENCE.1059493
Page generated: Sun Oct 13 02:48:06 2024

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