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Chlorine in PDB 5qjb: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869

All present enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869, PDB code: 5qjb was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.93 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.598, 60.134, 79.856, 79.31, 80.90, 75.37
R / Rfree (%) 25 / 29.2

Other elements in 5qjb:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 also contains other interesting chemical elements:

Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 (pdb code 5qjb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869, PDB code: 5qjb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5qjb

Go back to Chlorine Binding Sites List in 5qjb
Chlorine binding site 1 out of 4 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:67.9
occ:1.00
 CG2 B:VAL67 4.0 32.5 1.0
CG2 B:THR145 4.1 31.6 1.0
ND1 A:HIS206 4.3 33.4 1.0
CG A:HIS206 4.3 30.5 1.0
CE1 A:HIS206 4.5 29.0 1.0
CG2 B:THR147 4.5 38.6 1.0
CD2 A:HIS206 4.5 26.8 1.0
CG1 B:VAL67 4.6 31.5 1.0
CB B:VAL67 4.6 31.3 1.0
NE2 A:HIS206 4.7 30.5 1.0
CB A:HIS206 4.8 28.9 1.0

Chlorine binding site 2 out of 4 in 5qjb

Go back to Chlorine Binding Sites List in 5qjb
Chlorine binding site 2 out of 4 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:53.9
occ:0.80
 CL A:K07304 0.0 53.9 0.8
C9 A:K07304 1.7 49.3 0.8
C8 A:K07304 2.6 48.6 0.8
C6 A:K07304 2.9 49.8 0.8
NH1 B:ARG51 3.0 39.6 1.0
C A:K07304 3.3 48.4 0.8
N A:K07304 3.4 50.2 0.8
O B:HOH430 3.8 30.9 0.8
O A:GLY135 3.9 32.9 1.0
N2 A:K07304 3.9 49.2 0.8
CB B:TRP28 3.9 50.3 0.8
CZ B:ARG51 4.0 40.4 1.0
N1 A:K07304 4.1 49.7 0.8
CZ2 A:TRP46 4.1 36.7 0.8
NE1 A:TRP46 4.2 39.0 0.8
CG2 B:VAL29 4.2 47.6 1.0
NH2 B:ARG51 4.3 36.8 1.0
CE2 A:TRP46 4.3 38.1 0.8
C7 A:K07304 4.4 49.4 0.8
CG B:TRP28 4.7 56.5 0.8
CD1 A:LEU136 4.7 38.2 1.0
O B:TRP28 4.7 37.6 0.8
O A:GLU47 4.8 35.0 1.0
C1 A:K07304 4.9 49.3 0.8
C A:GLY135 4.9 30.5 1.0
C B:TRP28 5.0 43.4 0.8

Chlorine binding site 3 out of 4 in 5qjb

Go back to Chlorine Binding Sites List in 5qjb
Chlorine binding site 3 out of 4 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:47.3
occ:0.82
 CL A:K07305 0.0 47.3 0.8
C9 A:K07305 1.7 40.6 0.8
C8 A:K07305 2.6 40.3 0.8
C6 A:K07305 2.8 40.5 0.8
C A:K07305 3.1 41.7 0.8
NH1 A:ARG51 3.1 32.6 1.0
N A:K07305 3.4 40.5 0.8
O A:HOH466 3.4 38.3 0.8
O A:HOH442 3.5 31.9 1.0
CB A:TRP28 3.8 37.8 0.8
N2 A:K07305 3.9 38.3 0.8
N1 A:K07305 4.1 38.2 0.8
CZ A:ARG51 4.1 34.5 1.0
CG2 A:VAL29 4.1 39.7 0.8
O B:GLY135 4.1 31.3 1.0
NH2 A:ARG51 4.4 34.4 1.0
C7 A:K07305 4.4 38.7 0.8
CG A:TRP28 4.5 39.0 0.8
NE1 B:TRP46 4.5 32.4 1.0
CD1 B:LEU136 4.6 33.2 1.0
O B:GLU47 4.6 36.8 1.0
CZ2 B:TRP46 4.6 33.9 1.0
O A:TRP28 4.7 31.7 0.8
CE2 B:TRP46 4.7 31.8 1.0
C1 A:K07305 4.9 42.1 0.8
C A:TRP28 4.9 34.0 0.8
CA A:TRP28 5.0 35.6 0.8

Chlorine binding site 4 out of 4 in 5qjb

Go back to Chlorine Binding Sites List in 5qjb
Chlorine binding site 4 out of 4 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1787627869 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:70.5
occ:0.94
 CL C:K07304 0.0 70.5 0.9
C9 C:K07304 1.7 59.1 0.9
C8 C:K07304 2.5 57.1 0.9
C6 C:K07304 2.9 61.0 0.9
NH1 C:ARG51 3.0 48.3 1.0
C C:K07304 3.4 65.2 0.9
N C:K07304 3.5 64.7 0.9
O D:GLY135 3.6 42.2 1.0
N2 C:K07304 3.9 53.5 0.9
CZ C:ARG51 4.0 46.3 1.0
CB C:TRP28 4.0 51.9 1.0
N1 C:K07304 4.1 56.4 0.9
NE1 D:TRP46 4.1 45.6 1.0
CZ2 D:TRP46 4.2 42.6 1.0
NH2 C:ARG51 4.3 51.9 1.0
CE2 D:TRP46 4.3 44.5 1.0
C7 C:K07304 4.4 55.1 0.9
CG C:TRP28 4.5 46.5 1.0
O C:TRP28 4.8 52.0 1.0
C D:GLY135 4.8 35.4 1.0
O D:GLU47 4.8 55.6 1.0
C1 C:K07304 4.9 66.4 0.9
CD2 C:TRP28 5.0 49.1 1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) To Be Published.
Page generated: Fri Jul 26 15:48:08 2024

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