Atomistry » Zinc » PDB 3zqz-4a3e » 4a3e
Atomistry »
  Zinc »
    PDB 3zqz-4a3e »
      4a3e »

Zinc in PDB 4a3e: Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp

Enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp

All present enzymatic activity of Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp, PDB code: 4a3e was solved by A.C.M.Cheung, S.Sainsbury, P.Cramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.61 / 3.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 223.680, 394.170, 283.290, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 18.8

Other elements in 4a3e:

The structure of Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp (pdb code 4a3e). 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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp, PDB code: 4a3e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 1 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2456

b:0.5
occ:1.00
 SG A:CYS148 2.3 0.1 1.0
SG A:CYS107 2.3 0.5 1.0
SG A:CYS110 2.4 0.3 1.0
SG A:CYS167 2.4 0.2 1.0
CB A:CYS167 2.7 0.8 1.0
CB A:CYS148 3.1 0.5 1.0
CB A:CYS110 3.2 0.0 1.0
CB A:CYS107 3.3 1.0 1.0
N A:CYS110 3.7 0.7 1.0
CA A:CYS110 4.0 0.6 1.0
O A:GLY166 4.0 0.4 1.0
CA A:CYS167 4.0 0.6 1.0
C A:CYS167 4.3 0.8 1.0
O A:CYS167 4.3 0.3 1.0
CA A:CYS148 4.5 0.7 1.0
CA A:CYS107 4.7 1.0 1.0
C A:GLY166 4.8 0.6 1.0
N A:CYS167 4.8 1.0 1.0
NE2 A:GLN171 4.8 0.7 1.0
C A:CYS110 4.9 0.5 1.0
C A:HIS109 4.9 0.2 1.0
N A:GLY111 4.9 0.1 1.0
CB A:HIS109 5.0 0.4 1.0
CD2 A:HIS109 5.0 0.3 1.0

Zinc binding site 2 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 2 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2457

b:85.4
occ:1.00
 NE2 A:HIS80 2.2 98.2 1.0
SG A:CYS77 2.4 90.0 1.0
SG A:CYS67 2.5 98.7 1.0
SG A:CYS70 2.5 93.5 1.0
CD2 A:HIS80 2.6 98.8 1.0
O A:THR69 3.2 97.2 1.0
CB A:CYS70 3.3 91.2 1.0
CE1 A:HIS80 3.4 98.1 1.0
CB A:CYS67 3.5 95.0 1.0
CB A:CYS77 3.7 85.6 1.0
CG A:HIS80 3.9 97.5 1.0
O A:CYS70 4.1 98.9 1.0
O A:PRO78 4.2 93.5 1.0
C A:THR69 4.2 97.3 1.0
ND1 A:HIS80 4.3 98.7 1.0
CA A:CYS70 4.4 92.0 1.0
CA A:CYS77 4.5 85.7 1.0
C A:CYS70 4.6 97.7 1.0
N A:CYS70 4.7 93.1 1.0
CA A:CYS67 4.9 96.0 1.0

Zinc binding site 3 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 3 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2225

b:95.6
occ:1.00
 SG B:CYS1182 2.3 96.3 1.0
SG B:CYS1166 2.3 99.1 1.0
SG B:CYS1185 2.3 0.1 1.0
SG B:CYS1163 2.3 94.8 1.0
CB B:CYS1163 3.0 89.3 1.0
CB B:CYS1185 3.1 97.8 1.0
CB B:CYS1166 3.7 95.1 1.0
CB B:CYS1182 3.7 93.4 1.0
O B:CYS1166 3.8 94.8 1.0
N B:CYS1166 3.9 94.2 1.0
CA B:CYS1166 4.3 93.7 1.0
CA B:CYS1185 4.4 99.4 1.0
C B:CYS1166 4.5 95.0 1.0
CA B:CYS1163 4.5 87.5 1.0
OG1 B:THR1170 4.6 1.0 1.0
O B:CYS1182 4.6 0.9 1.0
CB B:THR1170 4.6 0.2 1.0
N B:CYS1185 4.6 0.4 1.0
CG2 B:THR1170 4.7 0.8 1.0
CB B:ILE1165 4.9 90.9 1.0
CA B:CYS1182 5.0 94.3 1.0

Zinc binding site 4 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 4 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:96.5
occ:1.00
 SG C:CYS92 2.2 89.8 1.0
SG C:CYS95 2.2 90.0 1.0
SG C:CYS86 2.3 85.0 1.0
SG C:CYS88 2.3 87.5 1.0
CB C:CYS86 3.3 80.1 1.0
CB C:CYS95 3.4 87.1 1.0
CB C:CYS92 3.4 87.0 1.0
N C:CYS92 3.5 88.2 1.0
CB C:CYS88 3.7 83.7 1.0
C C:HIS91 3.9 93.1 1.0
CA C:CYS92 3.9 87.7 1.0
N C:CYS95 4.1 90.1 1.0
CA C:HIS91 4.1 88.7 1.0
CA C:CYS95 4.3 88.5 1.0
N C:CYS88 4.4 79.5 1.0
C C:CYS92 4.4 93.6 1.0
CB C:LYS94 4.6 90.4 1.0
O C:CYS92 4.6 92.0 1.0
O C:HIS91 4.6 93.9 1.0
CA C:CYS86 4.6 80.0 1.0
O C:ASP90 4.7 95.9 1.0
CA C:CYS88 4.7 82.6 1.0
C C:LYS94 4.9 94.8 1.0
C C:CYS86 4.9 81.9 1.0
N C:LYS94 4.9 90.3 1.0

Zinc binding site 5 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 5 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1121

b:0.7
occ:1.00
 SG I:CYS7 2.2 0.8 1.0
SG I:CYS32 2.3 1.0 1.0
SG I:CYS29 2.3 0.9 1.0
SG I:CYS10 2.3 0.3 1.0
CB I:CYS10 2.6 0.1 1.0
CB I:CYS29 3.3 0.7 1.0
CB I:CYS32 3.5 0.9 1.0
CB I:CYS7 3.5 0.4 1.0
CA I:CYS10 3.8 0.3 1.0
N I:CYS10 3.8 0.4 1.0
N I:CYS32 3.8 0.8 1.0
CA I:CYS32 4.2 0.1 1.0
OG1 I:THR31 4.2 0.3 1.0
CB I:TYR34 4.4 0.4 1.0
O I:ARG8 4.4 0.8 1.0
CB I:THR31 4.6 0.6 1.0
CA I:CYS29 4.7 0.3 1.0
C I:THR31 4.7 0.6 1.0
C I:CYS32 4.7 0.9 1.0
CA I:CYS7 4.8 0.3 1.0
C I:ASP9 4.8 0.6 1.0
O I:CYS7 4.9 0.9 1.0
C I:CYS10 4.9 0.8 1.0
C I:CYS7 4.9 0.7 1.0
O I:CYS32 4.9 1.0 1.0
CB I:ASP9 5.0 0.8 1.0
N I:ASN11 5.0 0.5 1.0

Zinc binding site 6 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 6 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1122

b:1.0
occ:1.00
 SG I:CYS106 2.3 0.1 1.0
SG I:CYS78 2.4 0.7 1.0
SG I:CYS75 2.4 0.7 1.0
SG I:CYS103 2.4 0.8 1.0
CB I:CYS75 3.1 0.3 1.0
CB I:CYS103 3.1 0.6 1.0
CB I:CYS78 3.5 0.9 1.0
CB I:CYS106 3.5 0.3 1.0
N I:CYS78 3.8 0.4 1.0
OG I:SER105 3.9 0.0 1.0
CA I:CYS78 4.1 0.8 1.0
N I:CYS106 4.2 0.9 1.0
CA I:CYS106 4.4 0.8 1.0
CB I:HIS108 4.5 0.2 1.0
CA I:CYS75 4.5 0.6 1.0
CA I:CYS103 4.6 0.6 1.0
CB I:SER80 4.6 0.9 1.0
C I:CYS78 4.7 0.2 1.0
N I:SER107 4.8 0.2 1.0
CB I:LYS77 4.8 0.2 1.0
N I:HIS79 4.8 0.7 1.0
N I:HIS108 4.8 0.1 1.0
N I:SER80 4.9 0.7 1.0
C I:LYS77 4.9 0.7 1.0
C I:CYS106 4.9 0.5 1.0

Zinc binding site 7 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 7 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1066

b:98.4
occ:1.00
 SG J:CYS10 2.2 99.5 1.0
SG J:CYS7 2.3 0.1 1.0
SG J:CYS45 2.3 97.3 1.0
SG J:CYS46 2.4 99.5 1.0
CB J:CYS7 3.1 99.3 1.0
N J:CYS46 3.2 94.7 1.0
CB J:CYS10 3.3 95.0 1.0
CB J:CYS45 3.4 92.9 1.0
CA J:CYS46 3.5 94.3 1.0
CB J:CYS46 3.5 95.4 1.0
C J:CYS45 3.6 98.2 1.0
N J:CYS10 3.8 92.0 1.0
CA J:CYS10 4.1 93.4 1.0
CA J:CYS45 4.1 93.3 1.0
NH2 J:ARG43 4.2 0.1 1.0
O J:CYS45 4.3 98.6 1.0
NE J:ARG43 4.4 0.9 1.0
CA J:CYS7 4.5 98.1 1.0
N J:GLY11 4.7 95.2 1.0
CZ J:ARG43 4.8 0.3 1.0
CB J:SER9 4.8 92.0 1.0
C J:CYS10 4.8 97.8 1.0
C J:SER9 4.8 93.3 1.0
N J:CYS45 4.8 94.7 1.0
CB J:LYS12 4.8 0.2 1.0
CB J:ARG43 4.9 0.2 1.0
C J:CYS7 4.9 97.5 1.0
N J:LYS12 4.9 96.1 1.0

Zinc binding site 8 out of 8 in 4a3e

Go back to Zinc Binding Sites List in 4a3e
Zinc binding site 8 out of 8 in the Rna Polymerase II Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp


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 Initial Transcribing Complex with A 5NT Dna-Rna Hybrid and Soaked with Ampcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1071

b:0.3
occ:1.00
 SG L:CYS51 2.3 0.5 1.0
SG L:CYS48 2.3 0.9 1.0
SG L:CYS34 2.4 0.7 1.0
SG L:CYS31 2.4 0.0 1.0
CB L:CYS48 3.2 0.7 1.0
CB L:CYS31 3.5 0.8 1.0
CB L:CYS34 3.7 0.6 1.0
CB L:CYS51 3.9 0.7 1.0
N L:CYS51 4.3 0.9 1.0
N L:CYS34 4.4 0.6 1.0
OG L:SER36 4.5 0.7 1.0
CA L:CYS51 4.6 0.4 1.0
OE2 L:GLU33 4.6 0.1 1.0
CA L:CYS34 4.6 0.0 1.0
CA L:CYS48 4.6 0.4 1.0
CG L:GLU33 4.7 0.1 1.0
C L:CYS51 4.8 0.6 1.0
CA L:CYS31 5.0 0.2 1.0
O L:CYS51 5.0 0.2 1.0

Reference:

A.C.Cheung, S.Sainsbury, P.Cramer. Structural Basis of Initial Rna Polymerase II Transcription. Embo J. V. 30 4755 2011.
ISSN: ESSN 1460-2075
PubMed: 22056778
DOI: 10.1038/EMBOJ.2011.396
Page generated: Sat Oct 26 18:52:08 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy