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

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dutp, PDB code: 2nvx 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 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.719, 222.414, 193.071, 90.00, 101.29, 90.00
R / Rfree (%) 28.5 / 30.4

Other elements in 2nvx:

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

Zinc binding site 1 out of 8 in 2nvx

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


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:0.2
occ:1.00
 SG A:CYS148 1.8 0.2 1.0
SG A:CYS107 2.7 0.5 1.0
SG A:CYS110 3.0 0.5 1.0
CB A:CYS148 3.1 0.0 1.0
O A:CYS167 3.5 0.9 1.0
N A:CYS167 4.0 0.3 1.0
O A:MET108 4.1 0.9 1.0
C A:CYS167 4.4 0.8 1.0
CA A:CYS148 4.4 0.9 1.0
CB A:CYS107 4.4 0.7 1.0
CA A:GLY166 4.5 0.2 1.0
CB A:CYS110 4.6 0.2 1.0
C A:GLY166 4.7 0.2 1.0
CA A:CYS167 4.7 0.4 1.0
SG A:CYS167 4.8 0.6 1.0

Zinc binding site 2 out of 8 in 2nvx

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Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dutp


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:0.9
occ:1.00
 SG A:CYS70 1.9 0.2 1.0
CE1 A:HIS80 2.3 0.4 1.0
SG A:CYS67 2.4 0.2 1.0
CB A:CYS77 2.6 0.5 1.0
SG A:CYS77 2.6 0.8 1.0
CB A:CYS70 3.0 0.6 1.0
NE2 A:HIS80 3.2 0.8 1.0
ND1 A:HIS80 3.2 0.5 1.0
CA A:CYS77 3.6 0.3 1.0
CB A:CYS67 3.7 0.1 1.0
N A:GLY79 4.1 0.9 1.0
C A:CYS77 4.1 0.7 1.0
CD2 A:HIS80 4.3 0.6 1.0
O A:CYS67 4.3 0.1 1.0
CG A:HIS80 4.3 0.8 1.0
CA A:GLY79 4.4 0.3 1.0
CA A:CYS70 4.4 1.0 1.0
N A:PRO78 4.5 0.2 1.0
CD A:PRO78 4.5 0.2 1.0
O A:CYS77 4.7 0.7 1.0
N A:HIS80 4.8 0.4 1.0
C A:CYS70 4.8 0.2 1.0
N A:CYS77 4.9 0.5 1.0
CA A:CYS67 4.9 0.2 1.0
N A:GLY59 5.0 0.1 1.0

Zinc binding site 3 out of 8 in 2nvx

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


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:0.7
occ:1.00
 SG B:CYS1166 1.8 0.8 1.0
CB B:CYS1166 2.5 0.9 1.0
CB B:CYS1163 3.0 0.5 1.0
SG B:CYS1163 3.2 0.7 1.0
CA B:CYS1166 3.5 0.9 1.0
SG B:CYS1185 3.5 0.7 1.0
OG1 B:THR1170 3.6 0.2 1.0
SG B:CYS1182 3.7 0.0 1.0
N B:CYS1166 3.8 0.1 1.0
C B:CYS1166 3.9 0.4 1.0
N B:GLY1167 4.0 0.3 1.0
CB B:THR1170 4.1 0.2 1.0
N B:LEU1168 4.4 0.4 1.0
CA B:CYS1163 4.5 0.5 1.0
O B:CYS1166 4.6 0.3 1.0
CD1 A:ILE30 4.6 0.3 1.0
CB B:CYS1185 4.7 0.2 1.0
CG2 B:THR1170 4.9 0.2 1.0
N B:CYS1163 5.0 0.4 1.0

Zinc binding site 4 out of 8 in 2nvx

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dutp


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:0.9
occ:1.00
 SG C:CYS88 2.0 97.4 1.0
SG C:CYS95 2.2 91.0 1.0
SG C:CYS92 2.5 0.4 1.0
SG C:CYS86 2.6 0.1 1.0
CB C:CYS88 3.1 0.9 1.0
N C:CYS92 3.1 0.7 1.0
CB C:CYS92 3.3 0.4 1.0
CB C:CYS95 3.3 92.7 1.0
CB C:CYS86 3.4 1.0 1.0
CA C:CYS92 3.7 0.3 1.0
C C:HIS91 3.8 0.1 1.0
CA C:HIS91 4.0 0.6 1.0
N C:CYS95 4.2 94.5 1.0
CA C:CYS88 4.3 0.3 1.0
CA C:CYS95 4.4 92.8 1.0
N C:CYS88 4.4 0.1 1.0
C C:CYS92 4.4 0.7 1.0
O C:ASP90 4.7 1.0 1.0
O C:HIS91 4.8 0.1 1.0
O C:CYS92 4.8 0.7 1.0
N C:HIS91 4.8 1.0 1.0
CA C:CYS86 4.9 0.8 1.0
C C:CYS88 4.9 0.4 1.0

Zinc binding site 5 out of 8 in 2nvx

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dutp


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:97.2
occ:1.00
 SG I:CYS29 1.9 96.2 1.0
SG I:CYS10 2.1 0.1 1.0
SG I:CYS32 2.6 0.2 1.0
O I:CYS10 2.8 0.9 1.0
OG1 I:THR31 3.2 96.6 1.0
CB I:THR31 3.3 96.3 1.0
N I:CYS32 3.6 97.6 1.0
CB I:CYS29 3.6 94.2 1.0
C I:CYS10 3.7 1.0 1.0
CB I:CYS10 3.7 0.8 1.0
SG I:CYS7 3.8 0.3 1.0
N I:THR31 4.0 95.9 1.0
CB I:CYS32 4.0 99.0 1.0
CA I:THR31 4.1 96.5 1.0
C I:THR31 4.2 97.0 1.0
CA I:CYS10 4.3 0.7 1.0
CA I:CYS32 4.4 98.5 1.0
CG2 I:THR31 4.5 96.5 1.0
CB I:ASN12 4.5 0.1 1.0
N I:ASN11 4.6 1.0 1.0
C I:CYS29 4.7 94.4 1.0
C I:ASN11 4.7 0.5 1.0
O I:ASP9 4.7 0.5 1.0
CA I:CYS29 4.7 94.1 1.0
N I:ASN12 4.8 0.8 1.0
O I:ASN11 4.9 0.4 1.0
O I:CYS29 4.9 94.7 1.0
CB I:CYS7 4.9 0.8 1.0
N I:ARG30 5.0 94.8 1.0
CA I:ASN11 5.0 0.9 1.0

Zinc binding site 6 out of 8 in 2nvx

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dutp


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.9
occ:1.00
 SG I:CYS78 1.5 99.6 1.0
SG I:CYS106 2.0 0.2 1.0
SG I:CYS75 2.3 0.7 1.0
SG I:CYS103 2.9 95.3 1.0
CB I:CYS75 3.0 1.0 1.0
CB I:CYS78 3.0 99.5 1.0
N I:CYS78 3.3 0.6 1.0
CB I:CYS103 3.4 95.3 1.0
CA I:CYS78 3.6 99.6 1.0
CB I:CYS106 3.6 0.7 1.0
OG I:SER80 3.9 95.5 1.0
C I:CYS78 4.1 99.2 1.0
N I:HIS79 4.2 98.7 1.0
CB I:HIS108 4.2 0.1 1.0
N I:CYS106 4.2 0.0 1.0
CA I:CYS75 4.4 0.8 1.0
CA I:CYS106 4.5 0.6 1.0
C I:LYS77 4.5 0.4 1.0
O I:CYS75 4.6 0.2 1.0
C I:CYS75 4.7 0.1 1.0
CB I:LYS77 4.8 0.1 1.0
N I:SER80 4.8 96.3 1.0
O I:SER80 4.9 94.5 1.0
N I:HIS108 4.9 0.0 1.0
CA I:CYS103 4.9 95.5 1.0
CA I:LYS77 5.0 0.0 1.0
N I:LYS77 5.0 0.8 1.0
C I:CYS106 5.0 0.7 1.0

Zinc binding site 7 out of 8 in 2nvx

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


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.6
occ:1.00
 SG J:CYS7 1.7 92.9 1.0
SG J:CYS45 2.0 0.6 1.0
SG J:CYS10 2.1 0.8 1.0
SG J:CYS46 2.1 94.6 1.0
CB J:CYS10 2.4 96.5 1.0
N J:CYS10 2.8 94.8 1.0
CB J:CYS46 3.0 96.3 1.0
N J:CYS46 3.0 98.3 1.0
CA J:CYS10 3.1 96.2 1.0
CA J:CYS46 3.2 97.3 1.0
CB J:CYS7 3.4 92.3 1.0
CB J:CYS45 3.5 0.3 1.0
C J:CYS45 3.7 98.7 1.0
CB J:SER9 3.9 93.1 1.0
C J:SER9 3.9 93.7 1.0
O J:CYS7 4.1 91.6 1.0
N J:GLY11 4.1 95.2 1.0
N J:SER9 4.2 93.3 1.0
C J:CYS10 4.2 95.5 1.0
CA J:SER9 4.2 93.4 1.0
CA J:CYS45 4.3 99.6 1.0
C J:CYS7 4.3 92.0 1.0
OG J:SER9 4.4 94.0 1.0
CD J:ARG43 4.4 0.1 1.0
O J:CYS45 4.4 98.1 1.0
CA J:CYS7 4.5 92.3 1.0
C J:CYS46 4.7 97.5 1.0
CG J:ARG43 4.7 0.0 1.0
O J:SER9 5.0 93.1 1.0
N J:PHE8 5.0 92.2 1.0

Zinc binding site 8 out of 8 in 2nvx

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


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'- Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.2
occ:1.00
 SG L:CYS34 2.3 0.7 1.0
SG L:CYS31 2.4 0.6 1.0
CB L:CYS51 2.5 0.8 1.0
CB L:CYS31 2.8 0.0 1.0
SG L:CYS51 3.0 0.8 1.0
CB L:SER36 3.5 0.8 1.0
SG L:CYS48 3.5 0.4 1.0
CA L:CYS51 3.7 0.6 1.0
CB L:CYS34 4.0 0.3 1.0
N L:CYS51 4.1 0.6 1.0
CA L:CYS31 4.3 0.1 1.0
N L:SER36 4.3 0.5 1.0
OG L:SER36 4.4 0.3 1.0
N L:CYS34 4.6 0.8 1.0
CA L:SER36 4.6 0.8 1.0
CA L:CYS34 4.6 0.2 1.0
O L:CYS31 4.6 0.4 1.0
N L:SER35 4.7 0.4 1.0
C L:CYS34 4.7 0.3 1.0
C L:CYS31 4.8 0.4 1.0
CB L:CYS48 4.8 0.8 1.0
C L:ASP50 4.9 0.8 1.0
N L:CYS31 4.9 0.8 1.0
C L:CYS51 5.0 0.5 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 02:18:49 2024

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