Atomistry » Zinc » PDB 5onh-5phf » 5ot2
Atomistry »
  Zinc »
    PDB 5onh-5phf »
      5ot2 »

Zinc in PDB 5ot2: Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A

Enzymatic activity of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A

All present enzymatic activity of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A:
2.7.7.6;

Protein crystallography data

The structure of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A, PDB code: 5ot2 was solved by S.Malvezzi, L.Farnung, C.Aloisi, T.Angelov, P.Cramer, S.J.Sturla, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.88 / 3.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 221.350, 394.930, 283.710, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 22.2

Other elements in 5ot2:

The structure of Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A 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 Elongation Complex in the Presence of 3D-Napht-A (pdb code 5ot2). 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 Elongation Complex in the Presence of 3D-Napht-A, PDB code: 5ot2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 1 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1801

b:0.7
occ:1.00
 CB A:CYS167 1.4 0.5 1.0
CB A:CYS110 2.2 0.0 1.0
SG A:CYS107 2.3 0.7 1.0
SG A:CYS148 2.3 0.2 1.0
SG A:CYS167 2.3 0.2 1.0
SG A:CYS110 2.3 0.7 1.0
CA A:CYS167 2.7 0.6 1.0
N A:CYS167 3.0 0.4 1.0
CB A:CYS107 3.3 0.8 1.0
CA A:CYS110 3.6 0.6 1.0
O A:CYS110 3.7 0.7 1.0
C A:CYS167 3.9 0.2 1.0
CB A:CYS148 3.9 0.5 1.0
N A:CYS110 4.1 0.3 1.0
C A:CYS110 4.1 0.2 1.0
C A:GLY166 4.3 0.6 1.0
O A:CYS167 4.4 0.1 1.0
O A:CYS148 4.6 0.9 1.0
N A:GLY168 4.7 0.9 1.0
CA A:CYS107 4.7 0.8 1.0
O A:MET108 4.7 0.3 1.0
CB A:LYS112 4.8 1.0 1.0

Zinc binding site 2 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 2 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1802

b:0.2
occ:1.00
 NE2 A:HIS80 2.1 0.4 1.0
CB A:CYS70 2.2 0.5 1.0
N A:CYS70 2.2 0.8 1.0
SG A:CYS77 2.3 85.1 1.0
SG A:CYS67 2.3 0.5 1.0
SG A:CYS70 2.3 0.5 1.0
O A:CYS67 2.4 1.0 1.0
CE1 A:HIS80 2.6 0.7 1.0
CA A:CYS70 2.7 95.7 1.0
CB A:CYS67 2.8 0.9 1.0
OG1 A:THR69 2.9 0.5 1.0
CD2 A:HIS80 3.1 0.8 1.0
C A:CYS67 3.3 0.3 1.0
C A:THR69 3.3 0.2 1.0
CA A:CYS67 3.5 0.6 1.0
ND1 A:HIS80 3.6 0.7 1.0
CG A:HIS80 3.8 0.9 1.0
CA A:THR69 3.8 0.4 1.0
N A:THR69 3.9 0.4 1.0
CB A:THR69 3.9 0.8 1.0
C A:CYS70 3.9 0.0 1.0
CB A:CYS77 4.0 0.7 1.0
N A:GLN71 4.2 0.6 1.0
O A:THR69 4.3 0.8 1.0
N A:GLN68 4.5 0.7 1.0
C A:GLN68 4.8 0.5 1.0
N A:CYS67 4.9 0.3 1.0
O A:LYS66 4.9 0.8 1.0
O A:CYS70 4.9 0.7 1.0
CA A:CYS77 4.9 0.5 1.0

Zinc binding site 3 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 3 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:0.8
occ:1.00
 SG B:CYS1185 2.3 0.6 1.0
CB B:CYS1166 2.3 82.5 1.0
SG B:CYS1182 2.3 89.2 1.0
SG B:CYS1166 2.3 0.1 1.0
SG B:CYS1163 2.3 0.6 1.0
CB B:CYS1185 2.4 83.9 1.0
N B:CYS1166 2.9 0.1 1.0
CB B:CYS1163 2.9 0.4 1.0
CA B:CYS1166 3.2 97.1 1.0
CB B:CYS1182 3.5 1.0 1.0
CA B:CYS1185 3.9 0.6 1.0
C B:ILE1165 4.2 0.3 1.0
N B:CYS1185 4.2 0.1 1.0
ND2 B:ASN1187 4.3 0.8 1.0
C B:CYS1166 4.3 0.9 1.0
CA B:CYS1163 4.4 1.0 1.0
O B:CYS1182 4.4 0.4 1.0
N B:GLY1167 4.5 0.9 1.0
N B:ILE1165 4.6 0.7 1.0
CB B:ILE1165 4.6 0.6 1.0
CA B:ILE1165 4.7 82.5 1.0
C B:CYS1163 4.7 0.2 1.0
CA B:CYS1182 4.8 0.7 1.0
C B:CYS1185 4.8 0.9 1.0
C B:CYS1182 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 4 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:0.3
occ:1.00
 CB C:CYS92 1.5 0.8 1.0
SG C:CYS88 2.3 98.0 1.0
SG C:CYS95 2.3 97.1 1.0
SG C:CYS86 2.3 0.8 1.0
SG C:CYS92 2.3 0.7 1.0
CA C:CYS92 2.9 0.2 1.0
N C:CYS92 3.0 0.8 1.0
CB C:CYS86 3.3 0.5 1.0
CB C:CYS88 3.5 0.7 1.0
CB C:CYS95 3.6 0.5 1.0
C C:CYS92 3.7 0.7 1.0
N C:CYS88 4.0 0.2 1.0
O C:CYS86 4.0 99.2 1.0
C C:CYS86 4.1 0.7 1.0
N C:CYS95 4.2 0.4 1.0
N C:ASP93 4.2 0.8 1.0
C C:HIS91 4.2 0.1 1.0
CA C:CYS86 4.3 0.7 1.0
CA C:CYS88 4.3 99.8 1.0
O C:CYS92 4.4 0.8 1.0
N C:LYS94 4.5 0.0 1.0
CA C:CYS95 4.6 0.1 1.0
C C:LYS94 4.7 0.0 1.0
N C:PHE87 4.7 0.2 1.0
CA C:HIS91 4.9 0.4 1.0
CB C:LYS94 4.9 1.0 1.0
CA C:LYS94 4.9 0.5 1.0
CG C:LYS94 5.0 0.2 1.0

Zinc binding site 5 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 5 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:0.3
occ:1.00
 CB I:CYS32 1.4 0.3 1.0
SG I:CYS29 2.3 0.5 1.0
SG I:CYS7 2.3 0.7 1.0
SG I:CYS10 2.3 0.5 1.0
SG I:CYS32 2.3 0.1 1.0
CA I:CYS32 2.8 0.1 1.0
CB I:CYS10 2.8 0.8 1.0
N I:CYS32 3.1 0.2 1.0
N I:CYS10 3.4 0.2 1.0
CB I:CYS29 3.6 0.6 1.0
CB I:CYS7 3.6 0.2 1.0
CA I:CYS10 3.7 0.9 1.0
C I:CYS32 3.8 0.1 1.0
CB I:TYR34 4.1 0.5 1.0
C I:THR31 4.2 0.9 1.0
N I:SER33 4.3 0.2 1.0
N I:TYR34 4.4 0.1 1.0
OG1 I:THR31 4.4 0.0 1.0
CB I:ASP9 4.4 0.7 1.0
O I:CYS32 4.5 0.5 1.0
C I:ASP9 4.6 0.3 1.0
C I:CYS10 4.8 0.3 1.0
CA I:ASP9 4.9 0.5 1.0
OD2 I:ASP9 4.9 0.7 1.0
N I:ASP9 4.9 0.9 1.0
CA I:CYS7 4.9 0.7 1.0
CA I:TYR34 4.9 0.2 1.0
O I:THR31 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 6 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:0.9
occ:1.00
 CB I:CYS78 1.7 0.5 1.0
SG I:CYS78 2.3 0.3 1.0
SG I:CYS106 2.3 0.3 1.0
SG I:CYS75 2.3 0.1 1.0
SG I:CYS103 2.3 0.2 1.0
CB I:CYS103 2.5 0.4 1.0
CA I:CYS78 3.2 0.4 1.0
OG I:SER105 3.4 0.7 1.0
CB I:CYS75 3.5 0.9 1.0
CB I:CYS106 3.5 0.8 1.0
N I:CYS106 3.6 0.7 1.0
N I:CYS78 3.7 0.2 1.0
CA I:CYS103 4.0 0.2 1.0
CA I:CYS106 4.1 0.1 1.0
C I:CYS78 4.2 0.8 1.0
N I:SER80 4.5 0.5 1.0
N I:HIS79 4.5 0.7 1.0
CB I:SER80 4.6 0.6 1.0
N I:SER107 4.6 0.8 1.0
C I:CYS103 4.6 0.9 1.0
CB I:SER105 4.7 1.0 1.0
N I:SER105 4.7 0.3 1.0
C I:SER105 4.7 0.7 1.0
C I:CYS106 4.8 0.7 1.0
N I:HIS108 4.8 0.7 1.0
CB I:HIS108 4.9 0.2 1.0
CA I:CYS75 4.9 0.6 1.0
N I:CYS103 4.9 0.8 1.0
O I:CYS103 5.0 0.9 1.0
O I:CYS78 5.0 0.3 1.0
CA I:SER105 5.0 0.9 1.0

Zinc binding site 7 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 7 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn101

b:0.3
occ:1.00
 CB J:CYS10 1.6 0.6 1.0
SG J:CYS10 2.3 0.9 1.0
SG J:CYS7 2.4 84.2 1.0
SG J:CYS45 2.4 0.7 1.0
SG J:CYS46 2.4 0.9 1.0
CB J:CYS46 2.6 0.2 1.0
N J:CYS46 2.7 0.5 1.0
CA J:CYS10 3.0 0.2 1.0
CA J:CYS46 3.1 0.8 1.0
C J:CYS45 3.4 0.7 1.0
CB J:CYS45 3.4 0.5 1.0
NH1 J:ARG43 3.4 0.3 1.0
N J:CYS10 3.5 0.1 1.0
CB J:CYS7 3.5 0.3 1.0
CA J:CYS45 3.9 0.3 1.0
O J:CYS45 4.1 0.9 1.0
C J:CYS10 4.1 0.2 1.0
N J:CYS45 4.4 0.2 1.0
N J:GLY11 4.5 1.0 1.0
C J:CYS46 4.6 0.8 1.0
CZ J:ARG43 4.6 0.3 1.0
CB J:ARG43 4.6 0.0 1.0
CB J:LYS12 4.7 0.9 1.0
C J:SER9 4.7 0.1 1.0
N J:LYS12 4.8 0.6 1.0
O J:ARG43 4.9 0.1 1.0

Zinc binding site 8 out of 8 in 5ot2

Go back to Zinc Binding Sites List in 5ot2
Zinc binding site 8 out of 8 in the Rna Polymerase II Elongation Complex in the Presence of 3D-Napht-A


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 Elongation Complex in the Presence of 3D-Napht-A within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn101

b:0.2
occ:1.01
 CB L:CYS51 2.2 0.2 1.0
SG L:CYS34 2.3 0.3 1.0
SG L:CYS48 2.3 0.5 1.0
SG L:CYS51 2.4 0.2 1.0
SG L:CYS31 2.4 0.2 1.0
CB L:CYS48 3.0 0.8 1.0
CB L:HIS53 3.0 0.2 1.0
N L:CYS34 3.3 0.4 1.0
CB L:GLU33 3.4 0.6 1.0
N L:HIS53 3.5 0.5 1.0
CB L:CYS34 3.5 98.1 1.0
CA L:CYS51 3.5 0.8 1.0
CA L:HIS53 3.8 0.9 1.0
N L:GLY52 3.8 0.0 1.0
CG L:GLU33 3.9 0.1 1.0
CA L:CYS34 3.9 0.7 1.0
C L:CYS51 4.0 0.8 1.0
N L:CYS51 4.1 0.9 1.0
CB L:CYS31 4.2 0.6 1.0
C L:GLU33 4.2 0.9 1.0
CG L:HIS53 4.2 0.1 1.0
CA L:GLU33 4.3 0.2 1.0
CA L:CYS48 4.4 0.1 1.0
O L:HIS53 4.4 0.4 1.0
C L:HIS53 4.5 0.7 1.0
ND1 L:HIS53 4.5 0.3 1.0
C L:GLY52 4.6 0.2 1.0
N L:GLU33 4.7 0.3 1.0
O L:CYS48 4.7 0.1 1.0
N L:CYS48 4.8 0.5 1.0
CA L:GLY52 4.8 0.7 1.0
O L:CYS51 4.9 0.9 1.0

Reference:

S.Malvezzi, L.Farnung, C.M.N.Aloisi, T.Angelov, P.Cramer, S.J.Sturla. Mechanism of Rna Polymerase II Stalling By Dna Alkylation. Proc. Natl. Acad. Sci. V. 114 12172 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29087308
DOI: 10.1073/PNAS.1706592114
Page generated: Sun Oct 27 23:47:36 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