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Zinc in PDB 2nvy: Rna Polymerase II Form II in 150 Mm Mn+2

Enzymatic activity of Rna Polymerase II Form II in 150 Mm Mn+2

All present enzymatic activity of Rna Polymerase II Form II in 150 Mm Mn+2:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Form II in 150 Mm Mn+2, PDB code: 2nvy 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 / 3.40
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 118.036, 218.914, 369.549, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 32.3

Other elements in 2nvy:

The structure of Rna Polymerase II Form II in 150 Mm Mn+2 also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Form II in 150 Mm Mn+2 (pdb code 2nvy). 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 Form II in 150 Mm Mn+2, PDB code: 2nvy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2nvy

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Zinc binding site 1 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3001

b:68.8
occ:1.00
 SG J:CYS7 2.0 59.7 1.0
SG J:CYS45 2.1 66.3 1.0
SG J:CYS46 2.1 63.4 1.0
SG J:CYS10 2.3 60.2 1.0
N J:CYS46 3.1 64.0 1.0
CB J:CYS7 3.3 58.7 1.0
C J:CYS45 3.3 64.5 1.0
CB J:CYS46 3.3 63.1 1.0
CA J:CYS46 3.4 63.3 1.0
CB J:CYS45 3.4 65.3 1.0
CB J:CYS10 3.6 60.6 1.0
O J:CYS45 3.6 64.6 1.0
N J:CYS10 3.7 60.4 1.0
CA J:CYS45 4.0 65.0 1.0
NE J:ARG43 4.2 72.2 1.0
CB J:SER9 4.2 59.6 1.0
CA J:CYS10 4.2 60.6 1.0
CG J:ARG43 4.5 71.1 1.0
N J:GLY11 4.6 61.4 1.0
CD J:ARG43 4.6 72.0 1.0
CA J:CYS7 4.6 58.5 1.0
C J:SER9 4.6 60.0 1.0
CA J:SER9 4.7 59.6 1.0
N J:SER9 4.8 59.0 1.0
C J:CYS7 4.8 58.3 1.0
C J:CYS46 4.9 62.9 1.0
N J:CYS45 4.9 65.5 1.0
C J:CYS10 4.9 61.0 1.0
O J:CYS7 4.9 58.2 1.0
O J:ARG43 4.9 69.0 1.0
OG J:SER9 4.9 60.1 1.0
CB J:LYS12 5.0 63.1 1.0

Zinc binding site 2 out of 8 in 2nvy

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Zinc binding site 2 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3002

b:79.3
occ:1.00
 SG C:CYS88 2.0 81.9 1.0
SG C:CYS86 2.1 79.0 1.0
SG C:CYS95 2.5 74.9 1.0
SG C:CYS92 2.7 84.5 1.0
CB C:CYS88 3.1 81.0 1.0
CB C:CYS86 3.3 78.4 1.0
CB C:CYS95 3.4 75.4 1.0
N C:CYS92 3.6 83.7 1.0
CB C:CYS92 3.6 83.3 1.0
N C:CYS95 3.8 77.0 1.0
O C:CYS92 4.1 82.1 1.0
CA C:CYS92 4.1 83.0 1.0
C C:HIS91 4.2 84.5 1.0
CA C:CYS95 4.2 75.7 1.0
N C:CYS88 4.2 80.1 1.0
CA C:CYS88 4.3 81.0 1.0
CA C:HIS91 4.3 84.7 1.0
CB C:LYS94 4.3 78.3 1.0
C C:CYS92 4.4 82.2 1.0
CA C:CYS86 4.6 78.2 1.0
C C:CYS86 4.6 78.2 1.0
C C:LYS94 4.6 78.0 1.0
O C:CYS86 4.7 78.1 1.0
N C:LYS94 4.7 79.3 1.0
CA C:LYS94 4.8 78.5 1.0
N C:HIS91 4.9 84.7 1.0
O C:ASP90 5.0 85.1 1.0

Zinc binding site 3 out of 8 in 2nvy

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Zinc binding site 3 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3003

b:97.5
occ:1.00
 SG I:CYS10 1.9 96.0 1.0
SG I:CYS32 2.1 83.1 1.0
SG I:CYS29 2.3 83.1 1.0
SG I:CYS7 2.5 99.5 1.0
CB I:CYS32 3.1 81.8 1.0
CB I:CYS7 3.1 99.6 1.0
CB I:CYS29 3.2 83.0 1.0
N I:CYS32 3.3 81.8 1.0
CB I:CYS10 3.4 95.5 1.0
CA I:CYS32 3.7 81.7 1.0
N I:CYS10 3.9 96.1 1.0
CA I:CYS10 4.1 95.2 1.0
CB I:TYR34 4.3 75.4 1.0
C I:CYS32 4.4 81.2 1.0
CB I:THR31 4.4 82.8 1.0
C I:THR31 4.5 82.3 1.0
CA I:CYS7 4.6 99.7 1.0
O I:CYS32 4.6 81.3 1.0
N I:ASN11 4.6 93.0 1.0
CA I:CYS29 4.7 83.0 1.0
C I:CYS10 4.7 94.3 1.0
CA I:THR31 4.8 82.6 1.0
N I:THR31 4.8 82.5 1.0
CG2 I:THR31 4.9 83.3 1.0
N I:ASN12 5.0 90.9 1.0

Zinc binding site 4 out of 8 in 2nvy

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Zinc binding site 4 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3004

b:0.5
occ:1.00
 SG I:CYS75 2.2 0.0 1.0
SG I:CYS106 2.5 0.3 1.0
SG I:CYS103 2.7 0.4 1.0
CB I:CYS75 2.7 0.4 1.0
CB I:CYS103 3.0 0.4 1.0
SG I:CYS78 3.1 0.4 1.0
N I:CYS78 3.6 0.3 1.0
CB I:HIS108 3.6 0.8 1.0
CB I:CYS78 3.9 0.6 1.0
CB I:LYS77 4.0 0.5 1.0
CA I:CYS75 4.1 0.6 1.0
CA I:CYS78 4.2 0.6 1.0
CB I:CYS106 4.2 0.5 1.0
CG I:HIS108 4.3 0.0 1.0
O I:CYS75 4.3 0.6 1.0
CD2 I:HIS108 4.3 0.6 1.0
C I:CYS75 4.4 0.3 1.0
N I:LYS77 4.4 0.9 1.0
C I:LYS77 4.4 0.9 1.0
CA I:LYS77 4.5 0.5 1.0
CA I:CYS103 4.5 0.4 1.0
N I:HIS79 4.6 0.2 1.0
N I:HIS108 4.6 0.8 1.0
CA I:HIS108 4.6 0.8 1.0
C I:CYS78 4.7 0.9 1.0
OG I:SER80 4.8 0.6 1.0
O I:HIS108 4.9 0.7 1.0
N I:CYS75 4.9 0.8 1.0
N I:CYS106 5.0 0.8 1.0

Zinc binding site 5 out of 8 in 2nvy

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Zinc binding site 5 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn3005

b:0.2
occ:1.00
 SG L:CYS34 2.1 0.6 1.0
SG L:CYS48 2.6 0.7 1.0
CB L:CYS51 2.6 0.5 1.0
O L:CYS51 2.8 0.2 1.0
CB L:CYS48 3.0 0.1 1.0
SG L:CYS31 3.3 0.4 1.0
CB L:CYS34 3.5 0.2 1.0
CA L:CYS51 3.5 0.4 1.0
C L:CYS51 3.6 0.4 1.0
SG L:CYS51 3.6 0.8 1.0
CD2 L:HIS53 3.6 0.4 1.0
OG L:SER36 3.9 0.7 1.0
N L:CYS51 3.9 0.2 1.0
CB L:CYS31 4.0 0.0 1.0
N L:CYS34 4.2 0.8 1.0
CA L:CYS48 4.3 0.3 1.0
CG L:HIS53 4.3 0.5 1.0
CA L:CYS34 4.5 0.4 1.0
O L:LYS49 4.5 0.3 1.0
C L:CYS48 4.5 0.3 1.0
NE2 L:HIS53 4.5 0.1 1.0
CB L:HIS53 4.6 0.2 1.0
N L:LYS49 4.6 0.2 1.0
N L:HIS53 4.8 0.8 1.0
N L:GLY52 4.9 0.3 1.0
C L:LYS49 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 2nvy

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Zinc binding site 6 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3006

b:95.4
occ:1.00
 SG A:CYS110 2.0 98.2 1.0
SG A:CYS148 2.4 0.5 1.0
SG A:CYS107 2.8 96.3 1.0
SG A:CYS167 3.0 0.6 1.0
CB A:CYS148 3.0 0.6 1.0
O A:CYS167 3.0 0.7 1.0
CB A:CYS167 3.2 0.3 1.0
CB A:CYS107 3.3 96.6 1.0
CB A:CYS110 3.6 99.0 1.0
C A:CYS167 3.8 0.7 1.0
CA A:CYS167 4.1 0.2 1.0
N A:CYS110 4.3 99.1 1.0
CA A:CYS148 4.5 0.7 1.0
O A:CYS148 4.5 0.9 1.0
CA A:CYS110 4.6 99.0 1.0
CB A:LYS112 4.6 0.2 1.0
N A:CYS167 4.7 0.7 1.0
CA A:CYS107 4.8 96.6 1.0
C A:CYS148 4.9 1.0 1.0
N A:GLY168 5.0 0.2 1.0

Zinc binding site 7 out of 8 in 2nvy

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Zinc binding site 7 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3007

b:87.2
occ:1.00
 SG B:CYS1182 2.2 0.9 1.0
SG B:CYS1166 2.5 100.0 1.0
SG B:CYS1163 2.6 97.4 1.0
CB B:CYS1163 2.7 97.6 1.0
SG B:CYS1185 2.9 0.9 1.0
CB B:CYS1185 3.0 0.6 1.0
CB B:CYS1182 3.5 0.1 1.0
OG1 B:THR1170 4.1 0.2 1.0
O B:CYS1166 4.1 0.8 1.0
CB B:CYS1166 4.1 0.5 1.0
CA B:CYS1163 4.3 97.6 1.0
CA B:CYS1185 4.3 0.5 1.0
N B:CYS1185 4.3 0.2 1.0
N B:CYS1166 4.4 0.3 1.0
O B:LYS1183 4.5 0.9 1.0
O B:CYS1182 4.7 0.1 1.0
CA B:CYS1182 4.7 0.1 1.0
ND2 B:ASN1187 4.7 0.9 1.0
CA B:CYS1166 4.8 0.7 1.0
C B:CYS1182 4.8 0.1 1.0
C B:CYS1166 4.9 0.3 1.0
N B:CYS1163 5.0 97.4 1.0

Zinc binding site 8 out of 8 in 2nvy

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Zinc binding site 8 out of 8 in the Rna Polymerase II Form II in 150 Mm Mn+2


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 Form II in 150 Mm Mn+2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3008

b:0.4
occ:1.00
 NE2 A:HIS80 2.0 0.3 1.0
SG A:CYS77 2.0 0.1 1.0
SG A:CYS70 2.1 0.7 1.0
SG A:CYS67 2.4 0.8 1.0
CD2 A:HIS80 2.8 0.9 1.0
CE1 A:HIS80 3.1 0.6 1.0
CB A:CYS67 3.2 0.6 1.0
O A:CYS67 3.4 0.2 1.0
CB A:CYS77 3.4 0.6 1.0
CB A:CYS70 3.8 0.5 1.0
CG A:HIS80 4.0 0.6 1.0
ND1 A:HIS80 4.1 0.4 1.0
C A:CYS67 4.2 0.2 1.0
CA A:CYS67 4.3 0.5 1.0
CA A:CYS77 4.4 0.4 1.0
O A:GLN71 4.6 0.8 1.0
CA A:CYS70 4.9 0.5 1.0
CA A:GLY59 4.9 1.0 1.0
CD A:PRO78 4.9 0.6 1.0
C A:CYS70 4.9 0.7 1.0
C A:CYS77 5.0 0.0 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 02:20:34 2024

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