Atomistry » Zinc » PDB 2yu5-2z4g » 2yu9
Atomistry »
  Zinc »
    PDB 2yu5-2z4g »
      2yu9 »

Zinc in PDB 2yu9: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp

Enzymatic activity of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp

All present enzymatic activity of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp, PDB code: 2yu9 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) 19.98 / 3.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.610, 222.729, 196.160, 90.00, 101.87, 90.00
R / Rfree (%) 28.3 / 34.4

Other elements in 2yu9:

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp (pdb code 2yu9). 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 150 Mm Mg+2 with Utp, PDB code: 2yu9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.1
occ:1.00
 SG A:CYS110 2.3 0.3 1.0
SG A:CYS148 2.4 0.7 1.0
SG A:CYS107 2.4 0.3 1.0
SG A:CYS167 2.4 0.8 1.0
O A:CYS167 3.2 0.2 1.0
CB A:CYS110 3.3 0.4 1.0
CB A:CYS107 3.5 0.1 1.0
N A:CYS167 3.5 0.4 1.0
CB A:CYS148 3.6 0.9 1.0
CB A:CYS167 3.6 0.6 1.0
CA A:CYS167 3.9 0.5 1.0
C A:CYS167 4.0 0.2 1.0
O A:MET108 4.2 0.4 1.0
CA A:CYS110 4.4 0.2 1.0
N A:CYS110 4.5 0.1 1.0
C A:GLY166 4.7 0.3 1.0
ND2 A:ASN169 4.8 0.5 1.0
CA A:CYS107 4.9 0.8 1.0
CA A:GLY166 4.9 0.2 1.0
CA A:CYS148 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.3
occ:1.00
 NE2 A:HIS80 2.0 0.4 1.0
SG A:CYS77 2.3 0.7 1.0
SG A:CYS70 2.3 0.5 1.0
SG A:CYS67 2.3 0.0 1.0
CE1 A:HIS80 2.6 1.0 1.0
O A:CYS67 3.1 0.9 1.0
CD2 A:HIS80 3.3 0.5 1.0
CB A:CYS70 3.3 0.8 1.0
CB A:CYS67 3.3 0.5 1.0
CB A:CYS77 3.4 0.1 1.0
NE2 A:GLN68 3.6 0.2 1.0
ND1 A:HIS80 3.9 0.8 1.0
C A:CYS67 4.1 0.8 1.0
CA A:CYS77 4.1 0.8 1.0
CG A:HIS80 4.2 0.1 1.0
CA A:CYS67 4.3 0.7 1.0
O A:GLN71 4.5 0.2 1.0
CA A:CYS70 4.7 1.0 1.0
CD A:GLN68 4.8 0.6 1.0
C A:CYS77 4.9 0.1 1.0
CD A:PRO78 5.0 0.4 1.0
C A:CYS70 5.0 1.0 1.0

Zinc binding site 3 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.6
occ:1.00
 SG B:CYS1163 2.3 0.8 1.0
SG B:CYS1185 2.3 0.1 1.0
SG B:CYS1166 2.4 0.5 1.0
SG B:CYS1182 2.4 0.1 1.0
CB B:CYS1163 3.2 0.9 1.0
CB B:CYS1185 3.3 0.7 1.0
CB B:CYS1182 3.5 0.4 1.0
CB B:CYS1166 3.5 0.2 1.0
CB B:ASN1187 4.2 0.1 1.0
N B:CYS1185 4.2 0.6 1.0
CA B:CYS1185 4.3 0.5 1.0
N B:CYS1166 4.5 0.5 1.0
CA B:CYS1166 4.6 0.2 1.0
CA B:CYS1163 4.7 0.8 1.0
C B:CYS1185 4.7 0.3 1.0
ND2 B:ASN1187 4.8 0.2 1.0
CB B:THR1170 4.9 0.1 1.0
OG1 B:THR1170 4.9 0.8 1.0
CA B:CYS1182 5.0 0.5 1.0

Zinc binding site 4 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.0
occ:1.00
 SG C:CYS95 2.3 0.7 1.0
SG C:CYS86 2.3 0.7 1.0
SG C:CYS88 2.3 0.8 1.0
SG C:CYS92 2.3 0.4 1.0
N C:CYS92 3.1 0.4 1.0
CB C:CYS86 3.3 0.9 1.0
CB C:CYS92 3.4 0.7 1.0
CB C:CYS95 3.4 0.4 1.0
CB C:CYS88 3.5 0.9 1.0
CA C:CYS92 3.7 0.8 1.0
C C:HIS91 4.0 1.0 1.0
O C:CYS92 4.0 0.3 1.0
C C:CYS92 4.1 0.3 1.0
CA C:HIS91 4.2 0.3 1.0
N C:CYS95 4.3 0.8 1.0
N C:CYS88 4.4 0.6 1.0
CA C:CYS95 4.5 0.1 1.0
CA C:CYS88 4.5 0.1 1.0
CA C:CYS86 4.8 0.1 1.0
CB C:LYS94 4.8 0.8 1.0
C C:LYS94 4.8 0.7 1.0
N C:LYS94 4.9 0.2 1.0

Zinc binding site 5 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.5
occ:1.00
 SG I:CYS32 2.3 0.8 1.0
SG I:CYS7 2.3 0.2 1.0
SG I:CYS10 2.3 0.1 1.0
SG I:CYS29 2.4 0.4 1.0
CB I:CYS32 3.4 0.9 1.0
CB I:CYS7 3.4 0.2 1.0
CB I:CYS29 3.4 0.3 1.0
CB I:TYR34 3.5 0.2 1.0
CB I:CYS10 3.6 0.3 1.0
N I:TYR34 4.0 0.8 1.0
N I:CYS10 4.0 0.9 1.0
N I:SER33 4.1 0.8 1.0
CA I:CYS10 4.3 0.4 1.0
CA I:TYR34 4.4 0.6 1.0
CA I:CYS32 4.4 0.7 1.0
N I:CYS32 4.5 0.9 1.0
CG I:TYR34 4.5 0.6 1.0
CA I:CYS7 4.7 0.5 1.0
C I:CYS32 4.8 0.2 1.0
CA I:CYS29 4.8 0.1 1.0
N I:ASP9 4.9 0.6 1.0
C I:SER33 5.0 0.1 1.0
CB I:ASP9 5.0 0.4 1.0

Zinc binding site 6 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.0
occ:1.00
 SG I:CYS78 2.3 0.8 1.0
SG I:CYS106 2.3 0.7 1.0
SG I:CYS103 2.3 0.2 1.0
SG I:CYS75 2.4 0.4 1.0
CB I:CYS103 3.2 0.2 1.0
O I:CYS78 3.2 0.3 1.0
CB I:CYS78 3.3 0.5 1.0
CB I:CYS106 3.4 0.2 1.0
CB I:CYS75 3.4 0.0 1.0
N I:CYS78 3.5 0.4 1.0
CA I:CYS78 3.7 0.3 1.0
C I:CYS78 3.9 0.1 1.0
N I:CYS106 4.1 0.9 1.0
CB I:HIS108 4.2 0.6 1.0
CA I:CYS106 4.3 0.2 1.0
CG I:LYS77 4.6 0.2 1.0
C I:LYS77 4.7 0.4 1.0
CA I:CYS103 4.7 0.2 1.0
N I:HIS108 4.8 0.6 1.0
CA I:CYS75 4.8 0.9 1.0
C I:CYS106 4.9 0.4 1.0

Zinc binding site 7 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.2
occ:1.00
 N J:CYS46 2.2 0.9 1.0
SG J:CYS45 2.3 0.5 1.0
SG J:CYS10 2.3 0.4 1.0
SG J:CYS46 2.4 0.7 1.0
SG J:CYS7 2.5 0.7 1.0
C J:CYS45 2.9 0.2 1.0
CA J:CYS46 2.9 0.2 1.0
CB J:CYS46 3.1 0.3 1.0
CB J:CYS45 3.2 0.8 1.0
CB J:CYS10 3.4 0.5 1.0
CA J:CYS45 3.5 0.0 1.0
O J:CYS45 3.7 0.2 1.0
CB J:CYS7 3.7 0.6 1.0
N J:CYS10 3.9 0.6 1.0
CD J:ARG43 4.2 0.8 1.0
O J:ARG43 4.2 0.4 1.0
CA J:CYS10 4.2 0.1 1.0
N J:CYS45 4.2 0.6 1.0
C J:CYS46 4.4 0.4 1.0
CG J:ARG43 4.5 0.1 1.0
C J:SER9 4.6 0.1 1.0
N J:GLY11 4.8 0.1 1.0
CB J:ARG43 4.9 0.8 1.0
CB J:SER9 4.9 0.4 1.0
N J:ARG47 4.9 0.3 1.0
N J:SER9 4.9 0.6 1.0
C J:ARG43 4.9 0.6 1.0
CE J:MET49 5.0 0.8 1.0

Zinc binding site 8 out of 8 in 2yu9

Go back to Zinc Binding Sites List in 2yu9
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with Utp


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 150 Mm Mg+2 with Utp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.8
occ:1.00
 SG L:CYS51 2.3 0.5 1.0
SG L:CYS48 2.3 0.6 1.0
SG L:CYS31 2.3 0.7 1.0
SG L:CYS34 2.4 0.8 1.0
CB L:CYS31 3.2 0.7 1.0
CB L:CYS51 3.3 0.7 1.0
CB L:CYS48 3.5 0.5 1.0
CB L:CYS34 3.5 0.1 1.0
N L:CYS51 4.2 1.0 1.0
CA L:CYS51 4.3 0.5 1.0
N L:LYS49 4.5 0.5 1.0
CA L:CYS34 4.6 1.0 1.0
N L:GLY52 4.6 0.9 1.0
CB L:SER36 4.7 0.5 1.0
CA L:CYS31 4.7 0.6 1.0
N L:CYS34 4.7 0.9 1.0
CA L:CYS48 4.8 0.7 1.0
CD1 L:LEU38 4.9 0.8 1.0
C L:CYS51 4.9 0.8 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: Thu Oct 24 10:27:57 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy