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Zinc in PDB 2nvz: Rna Polymerase II Elongation Complex with Utp, Updated 11/2006

Enzymatic activity of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006

All present enzymatic activity of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006, PDB code: 2nvz 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) 40.00 / 4.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 169.647, 222.338, 194.316, 90.00, 101.67, 90.00
R / Rfree (%) 27 / 33.2

Other elements in 2nvz:

The structure of Rna Polymerase II Elongation Complex with Utp, Updated 11/2006 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 with Utp, Updated 11/2006 (pdb code 2nvz). 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 with Utp, Updated 11/2006, PDB code: 2nvz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.2
occ:1.00
 SG A:CYS167 2.3 0.7 1.0
SG A:CYS110 2.3 0.7 1.0
SD A:MET108 3.0 0.1 1.0
CB A:MET108 3.1 0.9 1.0
CG A:MET108 3.2 0.2 1.0
CB A:CYS167 3.4 0.6 1.0
CB A:CYS110 3.5 0.3 1.0
N A:CYS110 4.2 0.5 1.0
CE A:MET108 4.3 0.5 1.0
CA A:CYS110 4.3 0.0 1.0
N A:GLY111 4.3 0.9 1.0
O A:CYS107 4.4 0.6 1.0
CA A:MET108 4.5 0.9 1.0
C A:CYS110 4.8 0.9 1.0
CA A:CYS167 4.8 0.8 1.0
N A:HIS109 4.9 0.9 1.0
C A:MET108 4.9 0.3 1.0
SG A:CYS148 5.0 0.8 1.0
C A:CYS107 5.0 0.6 1.0

Zinc binding site 2 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.4
occ:1.00
 SG A:CYS77 1.0 1.0 1.0
SG A:CYS70 2.3 0.0 1.0
SG A:CYS67 2.3 0.9 1.0
NE2 A:HIS80 2.4 0.3 1.0
CE1 A:HIS80 2.5 0.3 1.0
CB A:CYS77 2.7 0.7 1.0
CB A:CYS70 3.2 0.2 1.0
CB A:CYS67 3.5 0.3 1.0
CD2 A:HIS80 3.7 0.2 1.0
OE1 A:GLN68 3.8 0.4 1.0
CA A:CYS77 3.8 0.6 1.0
ND1 A:HIS80 3.8 0.3 1.0
C A:CYS77 4.0 0.2 1.0
O A:CYS77 4.2 0.2 1.0
CG A:HIS80 4.4 0.1 1.0
N A:PRO78 4.6 0.8 1.0
N A:GLY79 4.6 0.0 1.0
CD A:GLN68 4.7 0.7 1.0
CA A:CYS70 4.7 0.4 1.0
CA A:GLY59 4.7 0.3 1.0
CD A:PRO78 4.7 0.8 1.0
NE2 A:GLN68 4.8 0.8 1.0
CA A:CYS67 4.9 0.5 1.0
N A:GLY59 5.0 0.8 1.0

Zinc binding site 3 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.4
occ:1.00
 SG B:CYS1166 2.3 0.9 1.0
SG B:CYS1182 2.4 0.6 1.0
SG B:CYS1185 2.5 0.2 1.0
CB B:CYS1185 3.0 0.2 1.0
SG B:CYS1163 3.2 0.6 1.0
CB B:CYS1166 3.4 0.5 1.0
CB B:CYS1182 3.5 0.4 1.0
CB B:CYS1163 3.7 0.8 1.0
O B:CYS1166 4.1 0.5 1.0
CA B:CYS1185 4.3 0.2 1.0
CD1 A:ILE30 4.4 0.6 1.0
CA B:CYS1166 4.5 0.4 1.0
N B:CYS1185 4.5 0.0 1.0
N B:CYS1166 4.7 0.9 1.0
C B:CYS1166 4.7 0.6 1.0
O B:LYS1183 4.8 0.9 1.0
O B:CYS1182 4.8 0.0 1.0
CA B:CYS1182 4.8 0.4 1.0
C B:CYS1182 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.1
occ:1.00
 SG C:CYS95 2.3 0.8 1.0
SG C:CYS92 2.3 0.5 1.0
SG C:CYS88 2.3 0.0 1.0
SG C:CYS86 2.3 0.9 1.0
N C:CYS92 3.3 0.2 1.0
CB C:CYS95 3.3 0.5 1.0
CB C:CYS92 3.3 0.8 1.0
CB C:CYS86 3.4 0.8 1.0
CB C:CYS88 3.4 0.4 1.0
C C:HIS91 3.9 0.5 1.0
CA C:CYS92 3.9 0.8 1.0
CA C:HIS91 4.0 0.8 1.0
N C:CYS88 4.1 0.3 1.0
CA C:CYS88 4.3 0.5 1.0
O C:ASP90 4.6 0.2 1.0
CA C:CYS95 4.6 0.3 1.0
CA C:CYS86 4.7 0.9 1.0
N C:HIS91 4.7 0.9 1.0
N C:PHE87 4.8 0.4 1.0
O C:HIS91 4.8 0.5 1.0
N C:CYS95 4.8 0.8 1.0
C C:CYS86 4.8 0.7 1.0
C C:CYS92 4.8 0.6 1.0
C C:CYS88 4.9 0.7 1.0
C C:ASP90 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.1
occ:1.00
 SG I:CYS29 2.3 0.2 1.0
SG I:CYS10 2.3 0.0 1.0
SG I:CYS32 2.3 0.0 1.0
CB I:CYS10 3.4 0.0 1.0
CB I:CYS29 3.4 0.6 1.0
CB I:CYS32 3.5 0.2 1.0
CG I:ARG30 3.6 0.0 1.0
SG I:CYS7 3.9 0.5 1.0
O I:CYS32 4.1 0.5 1.0
C I:CYS32 4.2 0.6 1.0
CA I:CYS32 4.2 0.4 1.0
N I:ARG30 4.3 0.1 1.0
CD I:ARG30 4.3 0.6 1.0
N I:CYS32 4.4 0.2 1.0
CB I:CYS7 4.7 0.5 1.0
CA I:CYS29 4.7 0.6 1.0
CA I:CYS10 4.7 0.2 1.0
CB I:ARG30 4.9 0.3 1.0
N I:SER33 4.9 0.9 1.0

Zinc binding site 6 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.0
occ:1.00
 SG I:CYS103 2.3 0.5 1.0
SG I:CYS78 2.3 0.3 1.0
SG I:CYS75 2.3 0.9 1.0
SG I:CYS106 2.3 0.6 1.0
O I:CYS78 2.8 0.9 1.0
OG I:SER80 3.0 1.0 1.0
CB I:CYS103 3.3 0.6 1.0
CB I:SER80 3.3 0.8 1.0
CB I:CYS75 3.3 0.9 1.0
CB I:CYS78 3.4 0.4 1.0
CB I:CYS106 3.5 1.0 1.0
C I:CYS78 3.5 0.9 1.0
CA I:CYS78 3.9 0.2 1.0
N I:CYS78 4.2 0.1 1.0
CD2 I:HIS108 4.3 0.8 1.0
CA I:CYS103 4.5 0.6 1.0
N I:HIS79 4.5 0.5 1.0
NE2 I:HIS108 4.6 0.5 1.0
N I:CYS106 4.6 0.2 1.0
CB I:SER105 4.7 0.7 1.0
CA I:CYS75 4.7 0.8 1.0
CA I:CYS106 4.7 0.3 1.0
CA I:SER80 4.7 0.8 1.0
O I:SER80 4.8 0.4 1.0
O I:CYS75 4.8 0.0 1.0
C I:CYS75 5.0 1.0 1.0
C I:SER105 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.8
occ:1.00
 SG J:CYS7 2.2 0.1 1.0
SG J:CYS10 2.3 0.2 1.0
SG J:CYS45 2.3 1.0 1.0
SG J:CYS46 2.4 0.3 1.0
N J:CYS10 2.5 1.0 1.0
CB J:CYS10 3.1 0.2 1.0
OG J:SER9 3.2 0.8 1.0
C J:CYS45 3.3 0.8 1.0
CB J:CYS46 3.3 0.2 1.0
N J:CYS46 3.3 0.2 1.0
CA J:CYS10 3.3 0.9 1.0
CA J:CYS46 3.4 0.4 1.0
CB J:CYS45 3.4 0.1 1.0
CB J:CYS7 3.5 0.6 1.0
O J:CYS45 3.5 0.8 1.0
CB J:SER9 3.5 0.7 1.0
C J:SER9 3.6 0.2 1.0
O J:CYS7 3.6 0.1 1.0
CA J:SER9 3.7 0.7 1.0
N J:SER9 3.8 0.1 1.0
CA J:CYS45 4.0 0.2 1.0
N J:GLY11 4.0 0.5 1.0
C J:CYS7 4.1 0.9 1.0
C J:CYS10 4.2 0.2 1.0
CA J:CYS7 4.4 0.8 1.0
O J:SER9 4.7 0.1 1.0
C J:PHE8 4.8 0.6 1.0
C J:CYS46 4.9 0.1 1.0
N J:PHE8 4.9 0.1 1.0

Zinc binding site 8 out of 8 in 2nvz

Go back to Zinc Binding Sites List in 2nvz
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex with Utp, Updated 11/2006


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 with Utp, Updated 11/2006 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.2
occ:1.00
 SG L:CYS48 1.9 0.8 1.0
SG L:CYS51 2.3 0.8 1.0
SG L:CYS34 2.4 0.3 1.0
CB L:CYS48 3.0 0.8 1.0
SG L:CYS31 3.0 0.3 1.0
CB L:CYS51 3.4 0.2 1.0
CB L:CYS34 3.5 0.1 1.0
CB L:CYS31 3.6 0.3 1.0
O L:CYS34 3.9 0.2 1.0
O L:GLU33 4.3 0.3 1.0
CA L:CYS48 4.4 1.0 1.0
CA L:CYS34 4.6 0.3 1.0
C L:CYS34 4.6 0.2 1.0
CA L:CYS51 4.7 0.7 1.0
N L:LYS49 4.8 0.3 1.0
C L:CYS48 4.8 0.7 1.0
OE2 L:GLU33 4.8 0.4 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 17 02:20:44 2024

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