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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

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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

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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

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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

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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

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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

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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

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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

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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

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