Atomistry » Zinc » PDB 1hxy-1i95 » 1i3q
Atomistry »
  Zinc »
    PDB 1hxy-1i95 »
      1i3q »

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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Go back to Zinc Binding Sites List in 1i3q
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy