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Zinc in PDB 2e2i: Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp

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

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

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp, PDB code: 2e2i 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 / 3.41
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.682, 223.524, 193.938, 90.00, 100.54, 90.00
R / Rfree (%) 26.6 / 31.6

Other elements in 2e2i:

The structure of Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp 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'- Dgtp (pdb code 2e2i). 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'- Dgtp, PDB code: 2e2i:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2e2i

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Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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

b:0.1
occ:1.00
 SG A:CYS110 2.3 0.2 1.0
N A:CYS110 2.8 0.0 1.0
SG A:CYS167 3.0 0.4 1.0
CB A:CYS167 3.1 0.5 1.0
CB A:CYS110 3.2 0.7 1.0
SG A:CYS107 3.3 0.5 1.0
SG A:CYS148 3.4 0.0 1.0
CA A:CYS110 3.5 0.7 1.0
CB A:CYS107 3.7 0.2 1.0
N A:HIS109 3.7 0.5 1.0
C A:HIS109 3.9 0.2 1.0
N A:GLY111 4.0 0.3 1.0
CA A:HIS109 4.1 0.4 1.0
CB A:HIS109 4.2 0.5 1.0
C A:CYS110 4.2 0.5 1.0
N A:MET108 4.4 0.9 1.0
CA A:CYS167 4.6 0.4 1.0
C A:MET108 4.6 0.5 1.0
C A:CYS107 4.8 0.4 1.0
CA A:CYS107 4.8 0.9 1.0
CB A:CYS148 4.9 0.3 1.0

Zinc binding site 2 out of 8 in 2e2i

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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'- Dgtp


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

b:0.3
occ:1.00
 SG A:CYS77 2.0 0.8 1.0
SG A:CYS70 2.3 0.2 1.0
CE1 A:HIS80 2.4 0.3 1.0
SG A:CYS67 2.8 0.2 1.0
NE2 A:HIS80 2.9 0.5 1.0
O A:CYS67 3.1 0.1 1.0
CB A:CYS67 3.2 0.8 1.0
CB A:CYS77 3.4 0.9 1.0
ND1 A:HIS80 3.6 0.6 1.0
CB A:CYS70 3.9 0.5 1.0
C A:CYS67 4.0 1.0 1.0
CA A:CYS67 4.2 0.5 1.0
CA A:CYS77 4.2 0.1 1.0
CD2 A:HIS80 4.3 0.2 1.0
CG A:HIS80 4.6 0.3 1.0
CD A:PRO78 4.7 0.3 1.0
CG A:GLN68 4.9 0.1 1.0
C A:CYS77 4.9 0.2 1.0

Zinc binding site 3 out of 8 in 2e2i

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Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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

b:0.1
occ:1.00
 SG B:CYS1166 1.7 0.1 1.0
SG B:CYS1185 2.5 0.6 1.0
SG B:CYS1163 2.5 0.1 1.0
CB B:CYS1163 2.9 0.4 1.0
CB B:CYS1185 3.0 0.6 1.0
SG B:CYS1182 3.0 0.8 1.0
CB B:CYS1166 3.2 0.4 1.0
O B:CYS1166 3.4 0.8 1.0
N B:CYS1166 3.7 0.4 1.0
CA B:CYS1166 3.8 0.7 1.0
C B:CYS1166 4.0 0.6 1.0
CB B:CYS1182 4.2 0.9 1.0
CA B:CYS1163 4.4 0.5 1.0
CA B:CYS1185 4.5 0.1 1.0
OG1 B:THR1170 4.8 0.1 1.0
C B:ILE1165 4.8 0.0 1.0
C B:CYS1163 4.9 0.1 1.0

Zinc binding site 4 out of 8 in 2e2i

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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'- Dgtp


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

b:95.5
occ:1.00
 SG C:CYS92 2.2 90.6 1.0
SG C:CYS95 2.3 83.4 1.0
SG C:CYS88 2.4 90.4 1.0
SG C:CYS86 2.5 87.2 1.0
N C:CYS92 2.8 91.7 1.0
CB C:CYS92 3.1 91.1 1.0
CB C:CYS95 3.2 81.9 1.0
CA C:CYS92 3.4 91.2 1.0
CB C:CYS88 3.5 90.8 1.0
C C:HIS91 3.6 92.3 1.0
CB C:CYS86 3.7 87.3 1.0
CA C:HIS91 3.9 92.5 1.0
N C:CYS95 3.9 84.1 1.0
CA C:CYS95 4.1 81.6 1.0
C C:CYS92 4.3 91.1 1.0
O C:HIS91 4.5 92.8 1.0
O C:CYS92 4.7 91.0 1.0
CA C:CYS88 4.8 91.0 1.0
C C:LYS94 4.8 86.5 1.0
N C:HIS91 4.8 93.7 1.0
N C:CYS88 4.9 89.8 1.0
CB C:LYS94 4.9 88.0 1.0
C C:CYS95 4.9 79.6 1.0
N C:LYS94 4.9 88.5 1.0
N C:ASP93 5.0 90.9 1.0

Zinc binding site 5 out of 8 in 2e2i

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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'- Dgtp


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

b:0.9
occ:1.00
 SG I:CYS10 2.0 0.0 1.0
SG I:CYS29 2.1 0.1 1.0
SG I:CYS32 2.3 0.9 1.0
CB I:CYS29 3.1 0.0 1.0
SG I:CYS7 3.3 0.2 1.0
N I:CYS32 3.5 0.1 1.0
CB I:CYS10 3.5 0.6 1.0
CB I:CYS32 3.5 0.2 1.0
CB I:THR31 3.9 0.6 1.0
CA I:CYS32 4.1 0.9 1.0
N I:CYS10 4.3 0.4 1.0
CB I:CYS7 4.3 0.8 1.0
C I:THR31 4.3 0.4 1.0
OG1 I:THR31 4.4 0.1 1.0
N I:THR31 4.4 0.0 1.0
CA I:THR31 4.4 0.5 1.0
CA I:CYS10 4.5 0.5 1.0
CB I:ASP9 4.6 0.8 1.0
CA I:CYS29 4.6 0.4 1.0
CB I:TYR34 4.6 0.9 1.0
C I:CYS32 4.7 0.4 1.0
C I:CYS29 4.9 1.0 1.0
CG2 I:THR31 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 2e2i

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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'- Dgtp


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

b:0.9
occ:1.00
 SG I:CYS106 2.0 0.1 1.0
CB I:CYS78 2.2 0.3 1.0
SG I:CYS78 2.2 0.3 1.0
SG I:CYS103 2.3 93.8 1.0
SG I:CYS75 2.5 0.0 1.0
CB I:CYS75 3.1 0.1 1.0
CB I:CYS103 3.2 93.5 1.0
OG I:SER80 3.4 0.6 1.0
CA I:CYS78 3.4 0.6 1.0
N I:CYS78 3.5 0.7 1.0
CB I:CYS106 3.7 0.2 1.0
N I:CYS106 3.9 0.9 1.0
CA I:CYS106 4.3 0.7 1.0
CB I:HIS108 4.3 99.3 1.0
C I:CYS78 4.5 0.4 1.0
CA I:CYS103 4.6 93.5 1.0
CA I:CYS75 4.6 0.1 1.0
CB I:SER80 4.7 0.0 1.0
C I:LYS77 4.8 0.8 1.0
CB I:SER105 4.8 0.3 1.0
N I:HIS79 4.8 0.0 1.0
CB I:LYS77 4.8 0.1 1.0
N I:HIS108 4.8 0.2 1.0
C I:SER105 4.8 0.5 1.0
N I:SER80 4.9 0.9 1.0
C I:CYS106 4.9 0.8 1.0
N I:SER105 4.9 98.7 1.0

Zinc binding site 7 out of 8 in 2e2i

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Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in 5 Mm Mg+2 with 2'- Dgtp


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

b:0.9
occ:1.00
 SG J:CYS7 2.0 67.1 1.0
SG J:CYS46 2.0 64.3 1.0
SG J:CYS10 2.3 65.8 1.0
SG J:CYS45 2.4 65.6 1.0
CB J:CYS10 2.8 63.9 1.0
N J:CYS10 3.1 63.3 1.0
N J:CYS46 3.1 66.8 1.0
CB J:CYS46 3.1 64.1 1.0
C J:CYS45 3.2 68.3 1.0
CB J:CYS45 3.3 69.5 1.0
CA J:CYS46 3.3 65.4 1.0
CA J:CYS10 3.4 64.2 1.0
CB J:CYS7 3.5 64.7 1.0
O J:CYS45 3.6 67.3 1.0
OG J:SER9 3.6 62.6 1.0
CA J:CYS45 3.8 69.0 1.0
C J:SER9 4.1 63.8 1.0
O J:CYS7 4.6 63.8 1.0
CB J:SER9 4.6 63.2 1.0
C J:CYS10 4.6 63.8 1.0
CA J:SER9 4.7 63.5 1.0
N J:GLY11 4.7 64.8 1.0
CA J:CYS7 4.7 64.8 1.0
N J:CYS45 4.7 70.8 1.0
C J:CYS7 4.8 63.6 1.0
C J:CYS46 4.9 64.7 1.0
O J:SER9 4.9 64.6 1.0
N J:SER9 4.9 62.9 1.0
NE J:ARG43 4.9 79.0 1.0

Zinc binding site 8 out of 8 in 2e2i

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


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

b:0.2
occ:1.00
 SG L:CYS34 1.9 0.0 1.0
SG L:CYS48 2.2 0.3 1.0
SG L:CYS51 2.5 0.7 1.0
SG L:CYS31 3.1 0.1 1.0
CB L:CYS48 3.2 0.7 1.0
CB L:CYS31 3.3 0.3 1.0
CB L:CYS34 3.6 1.0 1.0
CB L:CYS51 3.9 0.9 1.0
CB L:SER36 3.9 0.0 1.0
N L:CYS34 4.4 0.8 1.0
CA L:CYS34 4.4 1.0 1.0
CA L:CYS48 4.6 0.0 1.0
N L:SER36 4.7 0.8 1.0
C L:CYS34 4.8 0.1 1.0
CA L:CYS31 4.8 0.4 1.0
OG L:SER36 4.8 0.9 1.0
N L:SER35 4.9 0.3 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: Wed Oct 16 22:56:55 2024

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