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Zinc in PDB 2r92: Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold

Enzymatic activity of Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold

All present enzymatic activity of Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold:
2.7.7.6;

Protein crystallography data

The structure of Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold, PDB code: 2r92 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 / 3.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 222.675, 393.853, 283.551, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 24.6

Other elements in 2r92:

The structure of Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold 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 Artificial Rdrp Scaffold (pdb code 2r92). 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 Artificial Rdrp Scaffold, PDB code: 2r92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2r92

Go back to Zinc Binding Sites List in 2r92
Zinc binding site 1 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1506

b:0.1
occ:1.00
 SG A:CYS110 2.6 0.9 1.0
SG A:CYS167 2.6 0.1 1.0
SG A:CYS148 2.9 0.5 1.0
CB A:CYS110 3.3 0.7 1.0
O A:MET108 3.4 0.3 1.0
O A:CYS167 3.5 0.1 1.0
CB A:CYS107 3.8 0.4 1.0
CB A:CYS148 3.8 0.5 1.0
N A:CYS110 3.9 0.5 1.0
SG A:CYS107 3.9 0.1 1.0
CA A:CYS110 4.1 0.0 1.0
O A:CYS107 4.2 0.7 1.0
CB A:CYS167 4.3 0.3 1.0
N A:GLY111 4.4 0.5 1.0
C A:CYS107 4.5 0.0 1.0
C A:CYS167 4.6 0.7 1.0
C A:MET108 4.6 0.3 1.0
O A:GLY166 4.7 0.5 1.0
C A:CYS110 4.7 0.9 1.0
CB A:HIS109 4.8 0.5 1.0
CA A:CYS107 4.8 0.4 1.0
C A:HIS109 4.9 0.3 1.0
CA A:CYS167 5.0 0.5 1.0

Zinc binding site 2 out of 8 in 2r92

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Zinc binding site 2 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1508

b:83.3
occ:1.00
 NE2 A:HIS80 2.4 90.9 1.0
SG A:CYS77 2.4 99.1 1.0
SG A:CYS67 2.6 0.6 1.0
CD2 A:HIS80 2.7 90.8 1.0
SG A:CYS70 2.7 0.3 1.0
CB A:CYS67 2.9 0.8 1.0
O A:CYS67 3.3 0.5 1.0
CB A:CYS70 3.3 1.0 1.0
CB A:CYS77 3.5 97.0 1.0
CE1 A:HIS80 3.7 90.5 1.0
CA A:CYS67 4.0 0.8 1.0
C A:CYS67 4.0 0.2 1.0
CG A:HIS80 4.0 91.9 1.0
ND1 A:HIS80 4.5 90.5 1.0
OE1 A:GLN68 4.5 0.8 1.0
O A:PRO78 4.6 91.9 1.0
CA A:CYS77 4.6 96.6 1.0
CA A:CYS70 4.7 0.7 1.0
CD A:GLN68 4.8 0.3 1.0
O A:CYS70 4.8 1.0 1.0
O A:GLN71 4.8 0.0 1.0
C A:CYS70 4.8 0.9 1.0

Zinc binding site 3 out of 8 in 2r92

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Zinc binding site 3 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:83.5
occ:1.00
 SG B:CYS1182 2.4 0.6 1.0
SG B:CYS1166 2.5 82.7 1.0
SG B:CYS1185 2.6 0.9 1.0
SG B:CYS1163 2.6 97.4 1.0
CB B:CYS1185 2.7 0.2 1.0
CB B:CYS1163 2.9 97.3 1.0
CB B:CYS1182 4.0 0.1 1.0
CA B:CYS1185 4.1 0.2 1.0
CB B:CYS1166 4.1 88.8 1.0
O B:CYS1182 4.2 0.3 1.0
N B:CYS1185 4.3 0.7 1.0
N B:CYS1166 4.3 93.9 1.0
O B:CYS1166 4.3 94.2 1.0
OG1 B:THR1170 4.4 93.5 1.0
CA B:CYS1163 4.4 96.3 1.0
CB B:THR1170 4.6 92.7 1.0
C B:CYS1185 4.7 0.6 1.0
CA B:CYS1166 4.8 91.7 1.0
CB B:ILE1165 4.9 98.1 1.0
CG2 B:THR1170 5.0 95.3 1.0
CG2 B:ILE1165 5.0 99.5 1.0

Zinc binding site 4 out of 8 in 2r92

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Zinc binding site 4 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:82.2
occ:1.00
 SG C:CYS95 2.4 95.6 1.0
SG C:CYS88 2.4 83.8 1.0
SG C:CYS86 2.5 77.7 1.0
SG C:CYS92 2.7 0.5 1.0
CB C:CYS86 2.9 82.6 1.0
N C:CYS92 3.0 0.3 1.0
CB C:CYS95 3.1 97.1 1.0
CB C:CYS92 3.6 0.2 1.0
CA C:CYS92 3.7 0.2 1.0
C C:HIS91 3.7 0.4 1.0
CB C:CYS88 3.8 86.6 1.0
CA C:HIS91 3.8 0.2 1.0
O C:CYS92 4.0 0.9 1.0
N C:CYS95 4.1 96.9 1.0
C C:CYS92 4.1 0.0 1.0
CA C:CYS95 4.2 96.6 1.0
CA C:CYS86 4.3 85.5 1.0
C C:LYS94 4.4 96.4 1.0
O C:CYS86 4.5 86.1 1.0
N C:CYS88 4.6 85.0 1.0
C C:CYS86 4.6 85.4 1.0
CA C:CYS88 4.7 87.8 1.0
O C:LYS94 4.7 95.6 1.0
O C:HIS91 4.8 99.7 1.0
N C:HIS91 4.8 0.3 1.0
O C:CYS88 4.8 91.1 1.0
N C:LYS94 4.8 98.4 1.0
CB C:HIS91 4.8 0.1 1.0
CB C:LYS94 4.9 96.5 1.0
CA C:LYS94 4.9 96.8 1.0

Zinc binding site 5 out of 8 in 2r92

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Zinc binding site 5 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn203

b:1.0
occ:1.00
 SG I:CYS32 2.4 0.4 1.0
SG I:CYS10 2.6 0.6 1.0
SG I:CYS7 2.6 0.4 1.0
SG I:CYS29 2.8 0.7 1.0
CB I:CYS32 3.2 0.3 1.0
CB I:CYS29 3.6 0.2 1.0
N I:CYS32 3.8 0.6 1.0
O I:CYS10 4.0 0.0 1.0
CB I:CYS7 4.0 0.0 1.0
O I:ARG8 4.0 0.7 1.0
CB I:CYS10 4.1 0.4 1.0
CA I:CYS32 4.1 0.3 1.0
N I:CYS10 4.2 0.8 1.0
C I:CYS10 4.2 0.8 1.0
CB I:THR31 4.4 0.2 1.0
CA I:CYS10 4.4 0.1 1.0
CB I:TYR34 4.8 0.8 1.0
C I:THR31 4.8 0.6 1.0
OG1 I:THR31 4.9 0.7 1.0
C I:CYS32 5.0 0.5 1.0
N I:ASN11 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 2r92

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Zinc binding site 6 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn204

b:0.1
occ:1.00
 SG I:CYS106 2.6 0.7 1.0
CB I:CYS75 2.7 0.7 1.0
SG I:CYS75 3.1 0.5 1.0
SG I:CYS78 3.3 0.5 1.0
CB I:CYS106 3.5 0.6 1.0
CB I:CYS103 3.6 0.5 1.0
CB I:HIS108 3.7 0.4 1.0
CB I:CYS78 3.7 1.0 1.0
N I:CYS78 3.7 0.9 1.0
SG I:CYS103 4.0 0.5 1.0
CA I:CYS75 4.1 0.4 1.0
CD I:PRO76 4.1 0.3 1.0
CA I:CYS78 4.2 0.2 1.0
N I:LYS77 4.4 0.5 1.0
N I:PRO76 4.5 0.1 1.0
N I:HIS108 4.5 0.6 1.0
C I:CYS75 4.6 0.6 1.0
CG I:HIS108 4.6 0.8 1.0
CA I:HIS108 4.7 0.8 1.0
C I:LYS77 4.7 0.1 1.0
CA I:LYS77 4.9 0.8 1.0
C I:CYS78 4.9 0.8 1.0
CB I:LYS77 4.9 0.0 1.0
CA I:CYS106 4.9 0.2 1.0
CD2 I:HIS108 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 2r92

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Zinc binding site 7 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.2
occ:1.00
 SG J:CYS10 2.3 96.8 1.0
SG J:CYS46 2.5 0.1 1.0
N J:CYS46 2.6 0.1 1.0
SG J:CYS7 2.6 91.4 1.0
SG J:CYS45 2.7 0.9 1.0
CB J:CYS46 2.7 0.9 1.0
CA J:CYS46 3.0 1.0 1.0
CB J:CYS10 3.0 95.5 1.0
CB J:CYS45 3.2 0.3 1.0
C J:CYS45 3.3 0.2 1.0
N J:CYS10 3.4 94.1 1.0
CB J:CYS7 3.7 91.2 1.0
CA J:CYS10 3.8 95.0 1.0
CA J:CYS45 3.8 0.1 1.0
O J:CYS45 4.1 0.5 1.0
CB J:SER9 4.3 89.9 1.0
NE J:ARG43 4.4 99.3 1.0
C J:CYS46 4.4 0.9 1.0
N J:GLY11 4.5 94.1 1.0
C J:SER9 4.6 92.2 1.0
N J:CYS45 4.6 0.7 1.0
C J:CYS10 4.7 93.9 1.0
NH2 J:ARG43 4.7 99.1 1.0
CG J:ARG43 4.7 0.2 1.0
CZ J:ARG43 4.9 99.5 1.0
CA J:SER9 4.9 90.6 1.0
O J:ARG43 4.9 0.0 1.0
N J:ARG47 5.0 0.3 1.0

Zinc binding site 8 out of 8 in 2r92

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Zinc binding site 8 out of 8 in the Elongation Complex of Rna Polymerase II with Artificial Rdrp Scaffold


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 Artificial Rdrp Scaffold within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn105

b:0.9
occ:1.00
 SG L:CYS34 2.4 0.8 1.0
SG L:CYS48 2.6 0.3 1.0
SG L:CYS31 2.9 0.8 1.0
SG L:CYS51 3.0 0.0 1.0
CB L:CYS48 3.1 0.6 1.0
CB L:CYS31 3.3 0.5 1.0
CB L:CYS51 3.3 0.2 1.0
O L:CYS51 3.4 0.1 1.0
CB L:CYS34 4.0 0.3 1.0
CA L:CYS51 4.1 0.3 1.0
C L:CYS51 4.1 0.6 1.0
N L:CYS51 4.2 0.8 1.0
CA L:CYS31 4.5 0.5 1.0
CA L:CYS48 4.5 0.7 1.0
OG L:SER36 4.6 0.6 1.0
O L:CYS34 4.8 0.0 1.0
N L:LYS49 4.9 0.9 1.0
C L:CYS48 4.9 0.9 1.0
CA L:CYS34 4.9 0.7 1.0
N L:CYS34 5.0 0.3 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 03:42:26 2024

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