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 Dec 16 03:22:41 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy