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Zinc in PDB 2b63: Complete Rna Polymerase II-Rna Inhibitor Complex

Enzymatic activity of Complete Rna Polymerase II-Rna Inhibitor Complex

All present enzymatic activity of Complete Rna Polymerase II-Rna Inhibitor Complex:
2.7.7.6;

Protein crystallography data

The structure of Complete Rna Polymerase II-Rna Inhibitor Complex, PDB code: 2b63 was solved by H.Kettenberger, A.Eisenfuehr, F.Brueckner, M.Theis, M.Famulok, 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 (°) 224.585, 399.815, 286.727, 90.00, 90.00, 90.00
R / Rfree (%) 25.2 / 27.3

Other elements in 2b63:

The structure of Complete Rna Polymerase II-Rna Inhibitor Complex also contains other interesting chemical elements:

Bromine (Br) 4 atoms
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Complete Rna Polymerase II-Rna Inhibitor Complex (pdb code 2b63). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Complete Rna Polymerase II-Rna Inhibitor Complex, PDB code: 2b63:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2b63

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Zinc binding site 1 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:73.5
occ:1.00
 SG A:CYS167 2.5 0.8 1.0
SG A:CYS110 2.5 0.7 1.0
SG A:CYS148 3.3 0.1 1.0
CB A:CYS110 3.4 0.2 1.0
O A:MET108 3.6 0.4 1.0
O A:CYS167 3.8 0.8 1.0
N A:CYS110 4.0 0.4 1.0
CB A:CYS167 4.1 0.8 1.0
CA A:CYS110 4.1 0.6 1.0
O A:CYS107 4.5 0.5 1.0
N A:GLY111 4.5 0.9 1.0
C A:CYS110 4.6 1.0 1.0
CB A:CYS148 4.6 0.8 1.0
C A:CYS167 4.7 0.2 1.0
O A:GLY166 4.7 0.6 1.0
C A:MET108 4.8 0.8 1.0
CB A:CYS107 4.8 0.4 1.0
CA A:CYS167 4.9 0.1 1.0
C A:GLY166 5.0 0.7 1.0
C A:CYS107 5.0 0.0 1.0

Zinc binding site 2 out of 8 in 2b63

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Zinc binding site 2 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:46.6
occ:1.00
 SG A:CYS77 2.1 98.1 1.0
NE2 A:HIS80 2.2 61.4 1.0
CB A:CYS67 2.4 1.0 1.0
SG A:CYS67 2.5 0.1 1.0
SG A:CYS70 2.5 0.9 1.0
O A:CYS67 2.8 0.3 1.0
CD2 A:HIS80 3.0 61.6 1.0
CE1 A:HIS80 3.2 62.1 1.0
CB A:CYS70 3.2 0.4 1.0
CA A:CYS67 3.4 0.7 1.0
C A:CYS67 3.5 0.9 1.0
CB A:CYS77 3.5 89.3 1.0
CG A:HIS80 4.1 62.9 1.0
ND1 A:HIS80 4.2 61.0 1.0
CA A:CYS70 4.4 0.9 1.0
CA A:CYS77 4.4 83.0 1.0
C A:CYS70 4.5 0.1 1.0
O A:CYS70 4.6 0.7 1.0
N A:CYS67 4.6 0.9 1.0
O A:PRO78 4.6 69.7 1.0
OE1 A:GLN68 4.7 0.5 1.0
O A:GLN71 4.7 0.7 1.0
N A:GLN68 4.8 0.2 1.0
C A:CYS77 4.9 77.3 1.0

Zinc binding site 3 out of 8 in 2b63

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Zinc binding site 3 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:66.2
occ:1.00
 SG B:CYS1185 2.1 67.8 1.0
SG B:CYS1166 2.2 53.8 1.0
SG B:CYS1163 2.5 69.0 1.0
CB B:CYS1182 2.5 71.3 1.0
SG B:CYS1182 2.6 74.0 1.0
CB B:CYS1185 2.7 69.9 1.0
CB B:CYS1163 2.7 62.5 1.0
O B:CYS1182 4.0 78.8 1.0
CB B:CYS1166 4.0 59.9 1.0
CA B:CYS1182 4.1 74.2 1.0
CA B:CYS1185 4.1 74.3 1.0
O B:CYS1166 4.1 64.2 1.0
CA B:CYS1163 4.2 59.6 1.0
N B:CYS1166 4.3 62.5 1.0
C B:CYS1182 4.5 76.4 1.0
C B:CYS1185 4.6 74.5 1.0
N B:CYS1185 4.6 77.0 1.0
OG1 B:THR1170 4.7 53.9 1.0
CA B:CYS1166 4.7 61.3 1.0
CB B:ILE1165 4.7 66.0 1.0
C B:CYS1166 4.8 62.7 1.0
N B:CYS1182 4.9 74.4 1.0
CB B:ASN1187 4.9 74.9 1.0
C B:CYS1163 5.0 60.8 1.0

Zinc binding site 4 out of 8 in 2b63

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Zinc binding site 4 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:49.0
occ:1.00
 SG C:CYS92 2.3 67.2 1.0
SG C:CYS95 2.3 64.5 1.0
CB C:CYS86 2.4 61.7 1.0
SG C:CYS86 2.4 63.3 1.0
SG C:CYS88 2.5 63.9 1.0
N C:CYS92 2.6 71.6 1.0
CB C:CYS92 2.7 66.5 1.0
CA C:CYS92 3.2 70.6 1.0
CB C:CYS95 3.3 66.0 1.0
C C:HIS91 3.5 73.0 1.0
CA C:HIS91 3.8 73.6 1.0
CB C:CYS88 3.8 65.7 1.0
CA C:CYS86 3.8 63.7 1.0
O C:CYS92 3.9 73.1 1.0
O C:CYS86 3.9 65.0 1.0
C C:CYS92 4.0 72.1 1.0
C C:CYS86 4.2 63.6 1.0
N C:CYS95 4.5 66.0 1.0
CA C:CYS95 4.5 64.6 1.0
N C:HIS91 4.6 75.0 1.0
O C:HIS91 4.6 73.7 1.0
N C:CYS88 4.6 62.5 1.0
N C:CYS86 4.7 66.2 1.0
CA C:CYS88 4.8 65.5 1.0
CB C:HIS91 4.9 72.9 1.0
O C:SER83 5.0 71.9 1.0
C C:LYS94 5.0 67.0 1.0

Zinc binding site 5 out of 8 in 2b63

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Zinc binding site 5 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:85.7
occ:1.00
 SG I:CYS32 2.2 99.0 1.0
SG I:CYS7 2.3 0.9 1.0
SG I:CYS29 2.5 0.5 1.0
SG I:CYS10 2.5 0.4 1.0
CB I:CYS29 3.4 0.9 1.0
CB I:CYS7 3.7 0.5 1.0
N I:CYS10 3.8 0.7 1.0
CB I:CYS10 3.9 0.2 1.0
CB I:CYS32 3.9 0.3 1.0
O I:ARG8 4.0 0.1 1.0
CA I:CYS10 4.2 0.4 1.0
CB I:TYR34 4.4 83.7 1.0
C I:CYS10 4.4 0.7 1.0
N I:ASN11 4.5 0.3 1.0
CA I:CYS29 4.6 0.9 1.0
N I:CYS32 4.6 0.8 1.0
CD1 I:TYR34 4.7 79.0 1.0
CB I:ASP9 4.7 0.9 1.0
OG1 I:THR31 4.7 0.6 1.0
C I:ARG8 4.8 0.5 1.0
CA I:CYS32 4.9 0.7 1.0
CB I:THR31 4.9 0.2 1.0
C I:ASP9 5.0 0.1 1.0
CA I:CYS7 5.0 0.4 1.0
N I:ASN12 5.0 0.7 1.0
CG I:TYR34 5.0 79.5 1.0

Zinc binding site 6 out of 8 in 2b63

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Zinc binding site 6 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:0.8
occ:1.00
 SG I:CYS78 2.5 0.8 1.0
CB I:CYS75 2.6 0.5 1.0
SG I:CYS75 2.7 1.0 1.0
SG I:CYS106 2.7 0.2 1.0
CB I:HIS108 3.4 0.6 1.0
CB I:CYS103 3.6 0.5 1.0
CA I:CYS75 3.7 0.6 1.0
CB I:CYS106 3.9 0.6 1.0
CD I:PRO76 4.0 0.7 1.0
SG I:CYS103 4.0 1.0 1.0
N I:CYS78 4.1 0.1 1.0
CB I:CYS78 4.1 0.3 1.0
CG I:HIS108 4.2 0.2 1.0
CD2 I:HIS108 4.4 0.2 1.0
N I:PRO76 4.4 0.7 1.0
C I:CYS75 4.5 0.2 1.0
CA I:HIS108 4.5 0.2 1.0
N I:HIS108 4.5 0.2 1.0
N I:LYS77 4.6 1.0 1.0
CA I:CYS78 4.7 0.4 1.0
N I:CYS75 4.8 0.8 1.0
CB I:LYS77 4.8 0.5 1.0
O I:HIS108 4.9 0.1 1.0
C I:LYS77 5.0 0.8 1.0

Zinc binding site 7 out of 8 in 2b63

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Zinc binding site 7 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:65.8
occ:1.00
 SG J:CYS46 2.2 70.7 1.0
N J:CYS46 2.2 71.4 1.0
SG J:CYS45 2.4 73.8 1.0
CB J:CYS46 2.4 71.1 1.0
SG J:CYS7 2.4 56.6 1.0
CB J:CYS10 2.5 63.5 1.0
SG J:CYS10 2.6 68.4 1.0
CA J:CYS46 2.6 72.3 1.0
C J:CYS45 3.0 71.3 1.0
CB J:CYS45 3.2 71.8 1.0
N J:CYS10 3.4 62.0 1.0
CA J:CYS10 3.5 62.8 1.0
CA J:CYS45 3.6 71.1 1.0
CB J:CYS7 3.7 56.7 1.0
O J:CYS45 3.8 71.3 1.0
C J:CYS46 4.1 73.2 1.0
CB J:SER9 4.4 54.8 1.0
N J:CYS45 4.4 70.8 1.0
C J:CYS10 4.5 61.7 1.0
N J:GLY11 4.5 62.0 1.0
C J:SER9 4.6 58.8 1.0
N J:ARG47 4.8 74.9 1.0
NE J:ARG43 4.8 72.5 1.0
CG J:ARG43 4.9 75.0 1.0
O J:CYS46 4.9 73.7 1.0
OG J:SER9 4.9 55.4 1.0
O J:ARG43 4.9 73.6 1.0
CA J:SER9 5.0 55.8 1.0

Zinc binding site 8 out of 8 in 2b63

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Zinc binding site 8 out of 8 in the Complete Rna Polymerase II-Rna Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complete Rna Polymerase II-Rna Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.8
occ:1.00
 SG L:CYS34 2.3 0.9 1.0
SG L:CYS51 2.4 0.4 1.0
SG L:CYS48 2.6 0.9 1.0
O L:CYS51 2.8 0.9 1.0
SG L:CYS31 2.9 0.0 1.0
CB L:CYS48 3.0 0.9 1.0
CB L:CYS31 3.1 0.4 1.0
CB L:CYS51 3.5 0.5 1.0
C L:CYS51 3.8 0.2 1.0
CB L:CYS34 4.0 0.3 1.0
CA L:CYS31 4.1 0.2 1.0
CA L:CYS51 4.1 0.7 1.0
N L:CYS51 4.4 0.1 1.0
CA L:CYS48 4.4 0.1 1.0
O L:GLY52 4.6 0.2 1.0
O L:CYS34 4.7 0.7 1.0
N L:LYS49 4.8 0.3 1.0
C L:CYS48 4.8 0.4 1.0
CA L:CYS34 4.9 0.4 1.0
C L:CYS34 5.0 0.6 1.0

Reference:

H.Kettenberger, A.Eisenfuehr, F.Brueckner, M.Theis, M.Famulok, P.Cramer. Structure of An Rna Polymerase II-Rna Inhibitor Complex Elucidates Transcription Regulation By Noncoding Rnas Nat.Struct.Mol.Biol. V. 13 44 2006.
ISSN: ISSN 1545-9993
PubMed: 16341226
DOI: 10.1038/NSMB1032
Page generated: Wed Oct 16 21:54:46 2024

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