Atomistry » Zinc » PDB 2aqq-2b63 » 2b63
Atomistry »
  Zinc »
    PDB 2aqq-2b63 »
      2b63 »

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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Go back to Zinc Binding Sites List in 2b63
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy