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Zinc in PDB 2r93: Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop

Enzymatic activity of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop

All present enzymatic activity of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop:
2.7.7.6;

Protein crystallography data

The structure of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop, PDB code: 2r93 was solved by E.Lehmann, F.Brueckner, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 4.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 223.336, 394.884, 284.121, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.1

Other elements in 2r93:

The structure of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop (pdb code 2r93). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop, PDB code: 2r93:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2r93

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Zinc binding site 1 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1506

b:0.0
occ:1.00
 SG A:CYS110 2.7 0.2 1.0
SG A:CYS148 2.8 0.5 1.0
CB A:CYS110 3.2 0.0 1.0
SG A:CYS167 3.3 0.9 1.0
CB A:CYS148 3.6 0.1 1.0
O A:CYS167 3.7 0.1 1.0
O A:MET108 3.7 0.2 1.0
SG A:CYS107 3.7 0.3 1.0
CB A:CYS107 3.8 0.2 1.0
N A:CYS110 4.0 0.2 1.0
CA A:CYS110 4.1 0.5 1.0
N A:GLY111 4.5 0.2 1.0
O A:GLY166 4.6 0.1 1.0
C A:CYS167 4.7 0.7 1.0
C A:CYS107 4.8 0.8 1.0
C A:CYS110 4.8 0.5 1.0
C A:MET108 4.8 0.5 1.0
O A:CYS107 4.9 0.6 1.0
CA A:CYS107 4.9 0.3 1.0
CB A:CYS167 4.9 0.3 1.0

Zinc binding site 2 out of 8 in 2r93

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Zinc binding site 2 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1508

b:79.0
occ:1.00
 NE2 A:HIS80 2.5 93.7 1.0
SG A:CYS70 2.6 0.4 1.0
SG A:CYS77 2.7 96.5 1.0
SG A:CYS67 2.7 0.3 1.0
CD2 A:HIS80 2.8 94.2 1.0
CB A:CYS67 2.9 0.6 1.0
CB A:CYS70 3.2 0.1 1.0
O A:CYS67 3.4 0.3 1.0
CE1 A:HIS80 3.7 94.1 1.0
CB A:CYS77 3.8 98.6 1.0
OE1 A:GLN68 4.0 0.3 1.0
CG A:HIS80 4.1 94.9 1.0
CA A:CYS67 4.1 0.5 1.0
C A:CYS67 4.2 0.1 1.0
ND1 A:HIS80 4.5 93.9 1.0
CA A:CYS70 4.5 0.7 1.0
O A:PRO78 4.6 96.4 1.0
CD A:GLN68 4.6 0.4 1.0
O A:GLN71 4.6 0.9 1.0
C A:CYS70 4.7 0.1 1.0
CA A:CYS77 4.8 99.2 1.0
O A:CYS70 4.8 0.5 1.0
NE2 A:GLN68 4.9 0.3 1.0

Zinc binding site 3 out of 8 in 2r93

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Zinc binding site 3 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:78.2
occ:1.00
 SG B:CYS1163 2.5 95.1 1.0
CB B:CYS1185 2.5 0.9 1.0
SG B:CYS1166 2.6 90.2 1.0
SG B:CYS1182 2.6 0.6 1.0
SG B:CYS1185 2.6 0.9 1.0
CB B:CYS1163 2.9 94.2 1.0
CB B:CYS1166 3.9 94.4 1.0
CA B:CYS1185 4.0 0.9 1.0
N B:CYS1166 4.1 95.8 1.0
O B:CYS1166 4.1 98.6 1.0
O B:CYS1182 4.2 0.3 1.0
CB B:CYS1182 4.3 1.0 1.0
OG1 B:THR1170 4.4 90.8 1.0
N B:CYS1185 4.4 0.5 1.0
CA B:CYS1163 4.4 93.7 1.0
CA B:CYS1166 4.5 95.7 1.0
C B:CYS1166 4.8 97.3 1.0
C B:CYS1185 4.8 0.7 1.0
CB B:THR1170 4.9 89.5 1.0
CB B:ILE1165 4.9 100.0 1.0

Zinc binding site 4 out of 8 in 2r93

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Zinc binding site 4 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:71.1
occ:1.00
 SG C:CYS86 2.4 88.9 1.0
SG C:CYS88 2.6 99.8 1.0
SG C:CYS95 2.6 97.7 1.0
SG C:CYS92 2.7 0.1 1.0
CB C:CYS86 2.9 92.5 1.0
N C:CYS92 3.1 0.2 1.0
CB C:CYS95 3.3 99.3 1.0
CB C:CYS92 3.6 0.0 1.0
CA C:CYS92 3.7 0.5 1.0
CB C:CYS88 3.8 97.6 1.0
C C:HIS91 3.9 0.8 1.0
N C:CYS95 4.0 0.0 1.0
O C:CYS92 4.0 0.9 1.0
CA C:HIS91 4.1 0.4 1.0
C C:CYS92 4.1 0.5 1.0
CA C:CYS95 4.3 99.0 1.0
CA C:CYS86 4.3 95.5 1.0
O C:CYS86 4.5 98.5 1.0
C C:CYS86 4.5 96.7 1.0
C C:LYS94 4.6 0.4 1.0
N C:CYS88 4.6 95.6 1.0
CA C:CYS88 4.8 97.2 1.0
CB C:LYS94 4.8 0.4 1.0
N C:LYS94 4.8 1.0 1.0
N C:ASP93 5.0 0.3 1.0
CA C:LYS94 5.0 0.4 1.0
N C:HIS91 5.0 0.5 1.0

Zinc binding site 5 out of 8 in 2r93

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Zinc binding site 5 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:0.1
occ:1.00
 SG I:CYS7 2.4 0.2 1.0
SG I:CYS32 2.5 0.6 1.0
SG I:CYS10 2.5 0.7 1.0
SG I:CYS29 2.7 0.8 1.0
CB I:CYS29 3.5 0.7 1.0
CB I:CYS32 3.6 0.7 1.0
N I:CYS10 3.9 0.5 1.0
O I:ARG8 3.9 0.9 1.0
CB I:CYS10 4.0 0.9 1.0
N I:CYS32 4.0 0.7 1.0
CB I:CYS7 4.1 0.3 1.0
CA I:CYS10 4.3 0.1 1.0
CB I:THR31 4.3 0.8 1.0
C I:CYS10 4.4 0.5 1.0
CA I:CYS32 4.4 0.0 1.0
CB I:TYR34 4.6 0.8 1.0
OG1 I:THR31 4.6 0.3 1.0
CB I:ASP9 4.6 0.7 1.0
N I:ASN11 4.8 0.4 1.0
O I:CYS10 4.8 0.6 1.0

Zinc binding site 6 out of 8 in 2r93

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Zinc binding site 6 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.2
occ:1.00
 SG I:CYS106 2.5 0.2 1.0
SG I:CYS75 2.6 0.8 1.0
SG I:CYS78 3.0 0.6 1.0
CB I:CYS75 3.1 0.5 1.0
N I:CYS78 3.6 0.1 1.0
CB I:HIS108 3.6 1.0 1.0
CB I:CYS103 3.7 0.9 1.0
CB I:CYS106 3.8 0.9 1.0
CB I:CYS78 3.9 0.5 1.0
SG I:CYS103 4.1 0.1 1.0
CB I:LYS77 4.3 0.4 1.0
CA I:CYS78 4.3 0.1 1.0
CG I:HIS108 4.5 0.5 1.0
N I:LYS77 4.5 0.7 1.0
C I:LYS77 4.6 0.8 1.0
CA I:CYS75 4.6 0.3 1.0
CA I:LYS77 4.6 0.0 1.0
N I:HIS108 4.7 0.6 1.0
CD2 I:HIS108 4.8 0.7 1.0
CA I:HIS108 4.8 0.7 1.0
C I:CYS78 4.9 0.5 1.0
C I:CYS75 5.0 0.7 1.0

Zinc binding site 7 out of 8 in 2r93

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Zinc binding site 7 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:86.5
occ:1.00
 SG J:CYS10 2.4 0.8 1.0
SG J:CYS46 2.5 1.0 1.0
SG J:CYS45 2.6 0.6 1.0
SG J:CYS7 2.8 96.3 1.0
CB J:CYS10 2.8 98.1 1.0
N J:CYS46 3.0 0.3 1.0
CB J:CYS46 3.0 0.5 1.0
CB J:CYS45 3.3 0.6 1.0
CA J:CYS46 3.4 0.3 1.0
N J:CYS10 3.5 97.7 1.0
CB J:CYS7 3.6 93.8 1.0
C J:CYS45 3.7 0.1 1.0
CA J:CYS10 3.7 97.7 1.0
CA J:CYS45 4.1 0.6 1.0
NE J:ARG43 4.2 0.1 1.0
NH2 J:ARG43 4.4 0.4 1.0
N J:GLY11 4.5 95.8 1.0
O J:CYS45 4.5 0.9 1.0
CB J:SER9 4.6 96.4 1.0
CZ J:ARG43 4.6 0.7 1.0
C J:CYS10 4.7 96.5 1.0
C J:SER9 4.7 97.1 1.0
CG J:ARG43 4.7 0.9 1.0
N J:CYS45 4.8 0.4 1.0
C J:CYS46 4.9 0.9 1.0
O J:ARG43 4.9 0.1 1.0

Zinc binding site 8 out of 8 in 2r93

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Zinc binding site 8 out of 8 in the Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Elongation Complex of Rna Polymerase II with A Hepatitis Delta Virus- Derived Rna Stem Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.3
occ:1.00
 SG L:CYS34 2.4 1.0 1.0
SG L:CYS51 2.6 0.6 1.0
SG L:CYS48 2.7 0.2 1.0
CB L:CYS48 2.9 0.2 1.0
SG L:CYS31 3.0 0.6 1.0
O L:CYS51 3.0 0.8 1.0
CB L:CYS31 3.5 0.8 1.0
CB L:CYS34 4.0 0.0 1.0
CB L:CYS51 4.0 0.2 1.0
C L:CYS51 4.0 0.5 1.0
N L:CYS51 4.3 0.3 1.0
CA L:CYS48 4.3 1.0 1.0
CA L:CYS51 4.3 0.2 1.0
C L:CYS48 4.7 0.7 1.0
N L:LYS49 4.8 0.1 1.0
N L:CYS34 4.9 0.6 1.0
CA L:CYS34 4.9 0.3 1.0
CA L:CYS31 5.0 0.7 1.0
O L:CYS34 5.0 0.6 1.0

Reference:

E.Lehmann, F.Brueckner, P.Cramer. Molecular Basis of Rna-Dependent Rna Polymerase II Activity. Nature V. 450 445 2007.
ISSN: ISSN 0028-0836
PubMed: 18004386
DOI: 10.1038/NATURE06290
Page generated: Thu Oct 17 03:42:27 2024

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