Atomistry » Zinc » PDB 2dqv-2e2i » 2e2i
Atomistry »
  Zinc »
    PDB 2dqv-2e2i »
      2e2i »

Zinc in PDB 2e2i: Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp

Enzymatic activity of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp

All present enzymatic activity of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp, PDB code: 2e2i was solved by D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.682, 223.524, 193.938, 90.00, 100.54, 90.00
R / Rfree (%) 26.6 / 31.6

Other elements in 2e2i:

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp (pdb code 2e2i). 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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp, PDB code: 2e2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.1
occ:1.00
 SG A:CYS110 2.3 0.2 1.0
N A:CYS110 2.8 0.0 1.0
SG A:CYS167 3.0 0.4 1.0
CB A:CYS167 3.1 0.5 1.0
CB A:CYS110 3.2 0.7 1.0
SG A:CYS107 3.3 0.5 1.0
SG A:CYS148 3.4 0.0 1.0
CA A:CYS110 3.5 0.7 1.0
CB A:CYS107 3.7 0.2 1.0
N A:HIS109 3.7 0.5 1.0
C A:HIS109 3.9 0.2 1.0
N A:GLY111 4.0 0.3 1.0
CA A:HIS109 4.1 0.4 1.0
CB A:HIS109 4.2 0.5 1.0
C A:CYS110 4.2 0.5 1.0
N A:MET108 4.4 0.9 1.0
CA A:CYS167 4.6 0.4 1.0
C A:MET108 4.6 0.5 1.0
C A:CYS107 4.8 0.4 1.0
CA A:CYS107 4.8 0.9 1.0
CB A:CYS148 4.9 0.3 1.0

Zinc binding site 2 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.3
occ:1.00
 SG A:CYS77 2.0 0.8 1.0
SG A:CYS70 2.3 0.2 1.0
CE1 A:HIS80 2.4 0.3 1.0
SG A:CYS67 2.8 0.2 1.0
NE2 A:HIS80 2.9 0.5 1.0
O A:CYS67 3.1 0.1 1.0
CB A:CYS67 3.2 0.8 1.0
CB A:CYS77 3.4 0.9 1.0
ND1 A:HIS80 3.6 0.6 1.0
CB A:CYS70 3.9 0.5 1.0
C A:CYS67 4.0 1.0 1.0
CA A:CYS67 4.2 0.5 1.0
CA A:CYS77 4.2 0.1 1.0
CD2 A:HIS80 4.3 0.2 1.0
CG A:HIS80 4.6 0.3 1.0
CD A:PRO78 4.7 0.3 1.0
CG A:GLN68 4.9 0.1 1.0
C A:CYS77 4.9 0.2 1.0

Zinc binding site 3 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.1
occ:1.00
 SG B:CYS1166 1.7 0.1 1.0
SG B:CYS1185 2.5 0.6 1.0
SG B:CYS1163 2.5 0.1 1.0
CB B:CYS1163 2.9 0.4 1.0
CB B:CYS1185 3.0 0.6 1.0
SG B:CYS1182 3.0 0.8 1.0
CB B:CYS1166 3.2 0.4 1.0
O B:CYS1166 3.4 0.8 1.0
N B:CYS1166 3.7 0.4 1.0
CA B:CYS1166 3.8 0.7 1.0
C B:CYS1166 4.0 0.6 1.0
CB B:CYS1182 4.2 0.9 1.0
CA B:CYS1163 4.4 0.5 1.0
CA B:CYS1185 4.5 0.1 1.0
OG1 B:THR1170 4.8 0.1 1.0
C B:ILE1165 4.8 0.0 1.0
C B:CYS1163 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:95.5
occ:1.00
 SG C:CYS92 2.2 90.6 1.0
SG C:CYS95 2.3 83.4 1.0
SG C:CYS88 2.4 90.4 1.0
SG C:CYS86 2.5 87.2 1.0
N C:CYS92 2.8 91.7 1.0
CB C:CYS92 3.1 91.1 1.0
CB C:CYS95 3.2 81.9 1.0
CA C:CYS92 3.4 91.2 1.0
CB C:CYS88 3.5 90.8 1.0
C C:HIS91 3.6 92.3 1.0
CB C:CYS86 3.7 87.3 1.0
CA C:HIS91 3.9 92.5 1.0
N C:CYS95 3.9 84.1 1.0
CA C:CYS95 4.1 81.6 1.0
C C:CYS92 4.3 91.1 1.0
O C:HIS91 4.5 92.8 1.0
O C:CYS92 4.7 91.0 1.0
CA C:CYS88 4.8 91.0 1.0
C C:LYS94 4.8 86.5 1.0
N C:HIS91 4.8 93.7 1.0
N C:CYS88 4.9 89.8 1.0
CB C:LYS94 4.9 88.0 1.0
C C:CYS95 4.9 79.6 1.0
N C:LYS94 4.9 88.5 1.0
N C:ASP93 5.0 90.9 1.0

Zinc binding site 5 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.9
occ:1.00
 SG I:CYS10 2.0 0.0 1.0
SG I:CYS29 2.1 0.1 1.0
SG I:CYS32 2.3 0.9 1.0
CB I:CYS29 3.1 0.0 1.0
SG I:CYS7 3.3 0.2 1.0
N I:CYS32 3.5 0.1 1.0
CB I:CYS10 3.5 0.6 1.0
CB I:CYS32 3.5 0.2 1.0
CB I:THR31 3.9 0.6 1.0
CA I:CYS32 4.1 0.9 1.0
N I:CYS10 4.3 0.4 1.0
CB I:CYS7 4.3 0.8 1.0
C I:THR31 4.3 0.4 1.0
OG1 I:THR31 4.4 0.1 1.0
N I:THR31 4.4 0.0 1.0
CA I:THR31 4.4 0.5 1.0
CA I:CYS10 4.5 0.5 1.0
CB I:ASP9 4.6 0.8 1.0
CA I:CYS29 4.6 0.4 1.0
CB I:TYR34 4.6 0.9 1.0
C I:CYS32 4.7 0.4 1.0
C I:CYS29 4.9 1.0 1.0
CG2 I:THR31 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.9
occ:1.00
 SG I:CYS106 2.0 0.1 1.0
CB I:CYS78 2.2 0.3 1.0
SG I:CYS78 2.2 0.3 1.0
SG I:CYS103 2.3 93.8 1.0
SG I:CYS75 2.5 0.0 1.0
CB I:CYS75 3.1 0.1 1.0
CB I:CYS103 3.2 93.5 1.0
OG I:SER80 3.4 0.6 1.0
CA I:CYS78 3.4 0.6 1.0
N I:CYS78 3.5 0.7 1.0
CB I:CYS106 3.7 0.2 1.0
N I:CYS106 3.9 0.9 1.0
CA I:CYS106 4.3 0.7 1.0
CB I:HIS108 4.3 99.3 1.0
C I:CYS78 4.5 0.4 1.0
CA I:CYS103 4.6 93.5 1.0
CA I:CYS75 4.6 0.1 1.0
CB I:SER80 4.7 0.0 1.0
C I:LYS77 4.8 0.8 1.0
CB I:SER105 4.8 0.3 1.0
N I:HIS79 4.8 0.0 1.0
CB I:LYS77 4.8 0.1 1.0
N I:HIS108 4.8 0.2 1.0
C I:SER105 4.8 0.5 1.0
N I:SER80 4.9 0.9 1.0
C I:CYS106 4.9 0.8 1.0
N I:SER105 4.9 98.7 1.0

Zinc binding site 7 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.9
occ:1.00
 SG J:CYS7 2.0 67.1 1.0
SG J:CYS46 2.0 64.3 1.0
SG J:CYS10 2.3 65.8 1.0
SG J:CYS45 2.4 65.6 1.0
CB J:CYS10 2.8 63.9 1.0
N J:CYS10 3.1 63.3 1.0
N J:CYS46 3.1 66.8 1.0
CB J:CYS46 3.1 64.1 1.0
C J:CYS45 3.2 68.3 1.0
CB J:CYS45 3.3 69.5 1.0
CA J:CYS46 3.3 65.4 1.0
CA J:CYS10 3.4 64.2 1.0
CB J:CYS7 3.5 64.7 1.0
O J:CYS45 3.6 67.3 1.0
OG J:SER9 3.6 62.6 1.0
CA J:CYS45 3.8 69.0 1.0
C J:SER9 4.1 63.8 1.0
O J:CYS7 4.6 63.8 1.0
CB J:SER9 4.6 63.2 1.0
C J:CYS10 4.6 63.8 1.0
CA J:SER9 4.7 63.5 1.0
N J:GLY11 4.7 64.8 1.0
CA J:CYS7 4.7 64.8 1.0
N J:CYS45 4.7 70.8 1.0
C J:CYS7 4.8 63.6 1.0
C J:CYS46 4.9 64.7 1.0
O J:SER9 4.9 64.6 1.0
N J:SER9 4.9 62.9 1.0
NE J:ARG43 4.9 79.0 1.0

Zinc binding site 8 out of 8 in 2e2i

Go back to Zinc Binding Sites List in 2e2i
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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 Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.2
occ:1.00
 SG L:CYS34 1.9 0.0 1.0
SG L:CYS48 2.2 0.3 1.0
SG L:CYS51 2.5 0.7 1.0
SG L:CYS31 3.1 0.1 1.0
CB L:CYS48 3.2 0.7 1.0
CB L:CYS31 3.3 0.3 1.0
CB L:CYS34 3.6 1.0 1.0
CB L:CYS51 3.9 0.9 1.0
CB L:SER36 3.9 0.0 1.0
N L:CYS34 4.4 0.8 1.0
CA L:CYS34 4.4 1.0 1.0
CA L:CYS48 4.6 0.0 1.0
N L:SER36 4.7 0.8 1.0
C L:CYS34 4.8 0.1 1.0
CA L:CYS31 4.8 0.4 1.0
OG L:SER36 4.8 0.9 1.0
N L:SER35 4.9 0.3 1.0

Reference:

D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg. Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis Cell(Cambridge,Mass.) V. 127 941 2006.
ISSN: ISSN 0092-8674
PubMed: 17129781
DOI: 10.1016/J.CELL.2006.11.023
Page generated: Wed Oct 16 22:56:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy