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Zinc in PDB 2nvq: Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 150 Mm Mg+2 with 2'Dutp, PDB code: 2nvq 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) 48.45 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 170.646, 222.760, 195.281, 90.00, 101.31, 90.00
R / Rfree (%) 22.9 / 28.3

Other elements in 2nvq:

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

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1734

b:85.0
occ:1.00
 SG A:CYS110 2.4 72.8 1.0
SG A:CYS107 2.4 74.6 1.0
SG A:CYS148 2.4 74.2 1.0
SG A:CYS167 2.4 76.4 1.0
O A:CYS167 3.4 70.5 1.0
CB A:CYS107 3.4 73.8 1.0
CB A:CYS110 3.4 71.6 1.0
N A:CYS167 3.6 70.6 1.0
CB A:CYS148 3.6 73.0 1.0
O A:MET108 3.8 72.8 1.0
CB A:CYS167 3.8 72.0 1.0
CA A:CYS167 4.0 71.3 1.0
C A:CYS167 4.0 70.6 1.0
N A:CYS110 4.1 71.6 1.0
ND2 A:ASN169 4.2 65.8 1.0
CA A:CYS110 4.3 71.1 1.0
C A:GLY166 4.7 70.0 1.0
N A:GLY111 4.7 70.0 1.0
CA A:CYS107 4.8 73.2 1.0
C A:CYS110 4.9 70.5 1.0
CA A:GLY166 4.9 69.5 1.0
C A:MET108 5.0 72.9 1.0

Zinc binding site 2 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1735

b:78.3
occ:1.00
 NE2 A:HIS80 2.0 62.2 1.0
SG A:CYS67 2.3 78.6 1.0
SG A:CYS70 2.3 79.5 1.0
SG A:CYS77 2.4 75.7 1.0
CE1 A:HIS80 2.9 62.1 1.0
O A:CYS67 3.0 79.0 1.0
CD2 A:HIS80 3.1 61.8 1.0
CB A:CYS67 3.1 78.8 1.0
CB A:CYS70 3.2 79.5 1.0
CB A:CYS77 3.3 74.3 1.0
C A:CYS67 3.8 79.2 1.0
CA A:CYS67 4.0 79.0 1.0
CA A:CYS77 4.0 73.9 1.0
ND1 A:HIS80 4.1 61.6 1.0
CG A:HIS80 4.2 63.0 1.0
NE2 A:GLN68 4.4 73.8 1.0
CA A:CYS70 4.5 79.7 1.0
CD A:GLN68 4.6 75.7 1.0
O A:GLN71 4.6 80.0 1.0
N A:GLN71 4.6 79.9 1.0
CD A:PRO78 4.7 71.9 1.0
C A:CYS70 4.7 79.9 1.0
C A:CYS77 4.7 73.0 1.0
CG A:GLN68 4.7 77.9 1.0
N A:PRO78 4.9 72.0 1.0

Zinc binding site 3 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:80.9
occ:1.00
 SG B:CYS1163 2.3 69.8 1.0
SG B:CYS1185 2.3 72.1 1.0
SG B:CYS1182 2.4 69.0 1.0
SG B:CYS1166 2.4 70.2 1.0
CB B:CYS1185 3.3 71.3 1.0
CB B:CYS1163 3.3 68.4 1.0
CB B:CYS1182 3.3 69.0 1.0
CB B:ASN1187 3.7 64.4 1.0
O B:CYS1185 3.9 69.3 1.0
CB B:CYS1166 4.1 69.4 1.0
C B:CYS1185 4.1 69.5 1.0
N B:CYS1166 4.1 67.5 1.0
O B:CYS1182 4.2 69.6 1.0
CA B:CYS1163 4.3 67.4 1.0
CA B:CYS1185 4.3 70.6 1.0
ND2 B:ASN1187 4.3 64.9 1.0
CG B:ASN1187 4.6 63.8 1.0
CB B:ILE1165 4.6 66.2 1.0
N B:ASN1187 4.6 65.6 1.0
CA B:CYS1182 4.6 68.6 1.0
CA B:CYS1166 4.7 68.2 1.0
C B:CYS1182 4.8 69.6 1.0
CA B:ASN1187 4.8 64.5 1.0
N B:ILE1165 4.8 66.5 1.0
N B:ASP1186 4.8 68.3 1.0
C B:CYS1163 4.9 67.3 1.0

Zinc binding site 4 out of 8 in 2nvq

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Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn319

b:48.5
occ:1.00
 SG C:CYS86 2.3 49.1 1.0
SG C:CYS92 2.3 50.8 1.0
SG C:CYS88 2.3 37.0 1.0
SG C:CYS95 2.4 48.0 1.0
N C:CYS92 2.9 53.6 1.0
CB C:CYS95 3.2 46.9 1.0
CB C:CYS86 3.4 49.1 1.0
CB C:CYS88 3.4 43.8 1.0
CB C:CYS92 3.5 52.1 1.0
C C:HIS91 3.6 54.9 1.0
CA C:CYS92 3.6 52.5 1.0
CA C:HIS91 3.7 55.3 1.0
N C:CYS95 4.0 47.0 1.0
C C:CYS92 4.2 52.9 1.0
O C:CYS92 4.2 52.9 1.0
CA C:CYS95 4.2 46.4 1.0
C C:LYS94 4.5 48.2 1.0
O C:HIS91 4.5 55.5 1.0
N C:CYS88 4.6 45.7 1.0
CB C:LYS94 4.6 49.2 1.0
CA C:CYS88 4.6 45.2 1.0
CB C:HIS91 4.7 55.6 1.0
N C:HIS91 4.7 55.4 1.0
N C:LYS94 4.7 49.6 1.0
CA C:CYS86 4.8 49.4 1.0
CA C:LYS94 4.9 49.2 1.0

Zinc binding site 5 out of 8 in 2nvq

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Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:83.0
occ:1.00
 SG I:CYS10 2.3 50.8 1.0
SG I:CYS7 2.3 50.6 1.0
SG I:CYS29 2.3 50.3 1.0
SG I:CYS32 2.3 54.1 1.0
CB I:CYS10 3.1 50.2 1.0
CB I:CYS7 3.2 51.2 1.0
CB I:CYS29 3.3 49.0 1.0
CB I:CYS32 3.4 51.0 1.0
N I:CYS10 3.7 50.1 1.0
N I:CYS32 3.8 50.0 1.0
CA I:CYS10 4.0 50.2 1.0
CB I:TYR34 4.1 41.4 1.0
CA I:CYS32 4.1 50.5 1.0
N I:SER33 4.4 48.1 1.0
CB I:THR31 4.4 49.5 1.0
CA I:CYS7 4.6 51.3 1.0
N I:TYR34 4.6 43.4 1.0
CA I:CYS29 4.7 48.5 1.0
C I:THR31 4.7 49.7 1.0
C I:ASP9 4.8 49.7 1.0
CB I:ASP9 4.9 49.2 1.0
C I:CYS32 4.9 49.6 1.0
N I:THR31 4.9 49.0 1.0
CA I:THR31 5.0 49.4 1.0
C I:CYS29 5.0 48.3 1.0

Zinc binding site 6 out of 8 in 2nvq

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Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:57.1
occ:1.00
 SG I:CYS78 2.2 46.0 1.0
SG I:CYS75 2.3 52.0 1.0
SG I:CYS106 2.4 51.1 1.0
SG I:CYS103 2.6 41.6 1.0
CB I:CYS103 2.8 41.3 1.0
N I:CYS78 2.9 45.8 1.0
CB I:CYS78 3.1 45.1 1.0
O I:CYS78 3.2 43.6 1.0
CA I:CYS78 3.3 45.2 1.0
CB I:CYS75 3.4 49.3 1.0
CB I:HIS108 3.6 44.0 1.0
C I:CYS78 3.6 44.4 1.0
C I:LYS77 3.9 45.6 1.0
CG I:LYS77 4.0 48.5 1.0
CB I:CYS106 4.1 48.3 1.0
N I:LYS77 4.2 45.6 1.0
CG I:HIS108 4.3 43.2 1.0
CA I:CYS103 4.4 40.5 1.0
CA I:LYS77 4.4 46.1 1.0
CD2 I:HIS108 4.4 42.3 1.0
N I:CYS106 4.5 45.5 1.0
N I:HIS108 4.6 45.4 1.0
CA I:CYS75 4.7 48.8 1.0
CA I:HIS108 4.7 44.3 1.0
CA I:CYS106 4.7 47.1 1.0
CB I:LYS77 4.7 46.0 1.0
C I:CYS75 4.8 47.8 1.0
O I:CYS103 4.9 41.6 1.0
O I:CYS75 4.9 47.7 1.0
N I:HIS79 4.9 42.3 1.0
CD I:LYS77 4.9 48.4 1.0
O I:LYS77 4.9 45.3 1.0
C I:CYS106 5.0 47.2 1.0

Zinc binding site 7 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:50.2
occ:1.00
 SG J:CYS46 2.3 46.4 1.0
SG J:CYS10 2.3 45.3 1.0
SG J:CYS45 2.3 51.6 1.0
SG J:CYS7 2.4 42.0 1.0
N J:CYS46 2.7 45.7 1.0
CB J:CYS10 3.2 46.3 1.0
CA J:CYS46 3.3 45.0 1.0
CB J:CYS46 3.3 45.2 1.0
CB J:CYS7 3.4 43.3 1.0
CB J:CYS45 3.5 48.4 1.0
CD J:ARG43 3.5 57.3 1.0
C J:CYS45 3.5 47.2 1.0
OG J:SER9 3.7 46.4 1.0
CG J:ARG43 3.8 55.9 1.0
N J:CYS10 3.9 45.3 1.0
CA J:CYS45 4.0 48.2 1.0
CA J:CYS10 4.1 45.9 1.0
O J:CYS45 4.3 48.7 1.0
NE J:ARG43 4.3 55.6 1.0
N J:CYS45 4.7 48.8 1.0
C J:CYS46 4.8 44.9 1.0
CB J:SER9 4.8 46.8 1.0
CA J:CYS7 4.8 44.9 1.0
C J:SER9 4.9 46.1 1.0
O J:ARG43 4.9 53.1 1.0
N J:GLY11 5.0 46.3 1.0
C J:CYS10 5.0 45.4 1.0

Zinc binding site 8 out of 8 in 2nvq

Go back to Zinc Binding Sites List in 2nvq
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex in 150 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 150 Mm Mg+2 with 2'Dutp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:91.6
occ:1.00
 SG L:CYS51 2.3 88.4 1.0
SG L:CYS34 2.3 87.5 1.0
SG L:CYS31 2.3 85.6 1.0
SG L:CYS48 2.4 88.3 1.0
CB L:CYS51 2.4 88.0 1.0
CB L:CYS31 3.1 85.3 1.0
CB L:CYS34 3.5 87.2 1.0
CB L:SER36 3.6 88.3 1.0
CA L:CYS51 3.6 88.5 1.0
N L:CYS51 3.7 88.8 1.0
CB L:CYS48 3.9 89.6 1.0
OG L:SER36 4.3 89.5 1.0
C L:ASP50 4.4 89.2 1.0
O L:ASP50 4.5 88.9 1.0
CA L:CYS34 4.6 87.5 1.0
CA L:CYS31 4.6 84.8 1.0
CD1 L:LEU38 4.6 90.8 1.0
N L:SER36 4.6 87.9 1.0
C L:CYS51 4.7 88.3 1.0
CA L:SER36 4.7 88.3 1.0
O L:LYS49 4.8 90.7 1.0
N L:CYS34 4.8 87.3 1.0
C L:CYS34 4.9 87.7 1.0
N L:LYS49 4.9 91.5 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 02:17:54 2024

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