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Chlorine in PDB 5qk7: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193

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 Z1918536193:
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 Z1918536193, PDB code: 5qk7 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) 78.68 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.577, 59.461, 80.404, 79.39, 82.31, 76.19
R / Rfree (%) 21.7 / 25.5

Other elements in 5qk7:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193 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 Z1918536193 (pdb code 5qk7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 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 Z1918536193, PDB code: 5qk7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5qk7

Go back to Chlorine Binding Sites List in 5qk7
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:67.8
occ:1.00
 CG2 B:THR145 4.0 30.5 1.0
CG2 B:VAL67 4.2 32.9 1.0
ND1 A:HIS206 4.3 35.9 1.0
CG A:HIS206 4.3 33.0 1.0
CE1 A:HIS206 4.4 37.5 1.0
CG2 B:THR147 4.4 40.5 1.0
CD2 A:HIS206 4.5 30.9 1.0
NE2 A:HIS206 4.5 35.2 1.0
CB B:VAL67 4.7 34.1 1.0
CG1 B:VAL67 4.8 35.9 1.0
CB A:HIS206 4.8 29.2 1.0

Chlorine binding site 2 out of 5 in 5qk7

Go back to Chlorine Binding Sites List in 5qk7
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:49.6
occ:0.96
 CL B:K3P304 0.0 49.6 1.0
C6 B:K3P304 1.7 43.7 1.0
C5 B:K3P304 2.7 40.6 1.0
C3 B:K3P304 2.7 45.3 1.0
O B:K3P304 3.1 52.7 1.0
NH1 B:ARG51 3.1 31.0 1.0
O B:HOH458 3.6 38.7 1.0
CG2 B:VAL29 3.6 35.7 1.0
O A:GLY135 3.7 32.5 1.0
CZ B:ARG51 3.8 34.9 1.0
O B:HOH442 3.8 37.9 1.0
CD1 A:LEU136 3.9 38.7 1.0
N2 B:K3P304 4.0 40.9 1.0
N1 B:K3P304 4.0 41.9 1.0
NH2 B:ARG51 4.1 32.5 1.0
CB B:TRP28 4.2 45.9 1.0
NE1 A:TRP46 4.3 33.1 1.0
CA A:LEU136 4.4 34.0 1.0
C4 B:K3P304 4.4 38.8 1.0
O A:GLU47 4.4 36.2 1.0
C2 B:K3P304 4.4 57.5 1.0
C A:GLY135 4.5 31.4 1.0
O B:TRP28 4.7 33.9 1.0
CB A:LEU136 4.7 33.4 1.0
NE B:ARG51 4.8 31.7 1.0
CE2 A:TRP46 4.8 32.2 1.0
CZ2 A:TRP46 4.9 34.6 1.0
N A:LEU136 4.9 32.8 1.0
CG A:LEU136 5.0 36.8 1.0
C B:TRP28 5.0 36.0 1.0
CG B:ARG51 5.0 31.7 1.0
CG B:TRP28 5.0 53.8 1.0

Chlorine binding site 3 out of 5 in 5qk7

Go back to Chlorine Binding Sites List in 5qk7
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:38.5
occ:0.78
 CL B:K3P305 0.0 38.5 0.8
C6 B:K3P305 1.7 35.1 0.8
C5 B:K3P305 2.7 33.5 0.8
C3 B:K3P305 2.7 37.1 0.8
O B:K3P305 3.0 43.1 0.8
NH1 A:ARG51 3.3 29.0 1.0
CG2 A:VAL29 3.5 39.1 1.0
O B:GLY135 3.7 31.9 1.0
O A:HOH453 3.9 30.9 0.8
CD1 B:LEU136 3.9 32.6 1.0
CZ A:ARG51 3.9 32.9 1.0
N2 B:K3P305 4.0 34.8 0.8
N1 B:K3P305 4.0 36.9 0.8
O A:HOH439 4.1 32.3 1.0
O B:GLU47 4.1 35.5 1.0
CB A:TRP28 4.1 40.9 0.8
NH2 A:ARG51 4.2 37.9 1.0
NE1 B:TRP46 4.3 28.4 1.0
C4 B:K3P305 4.4 35.5 0.8
C2 B:K3P305 4.4 49.0 0.8
CA B:LEU136 4.5 28.5 1.0
C B:GLY135 4.6 27.7 1.0
O A:TRP28 4.7 30.7 0.8
CE2 B:TRP46 4.7 31.4 1.0
CB B:LEU136 4.8 29.3 1.0
CZ2 B:TRP46 4.8 30.9 1.0
NE A:ARG51 4.9 31.7 1.0
C A:TRP28 4.9 33.6 0.8
CG B:LEU136 5.0 28.9 1.0
N B:LEU136 5.0 26.2 1.0
CG A:TRP28 5.0 43.4 0.8

Chlorine binding site 4 out of 5 in 5qk7

Go back to Chlorine Binding Sites List in 5qk7
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193


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 Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl304

b:60.4
occ:0.96
 CL C:K3P304 0.0 60.4 1.0
C6 C:K3P304 1.7 56.2 1.0
C5 C:K3P304 2.6 53.0 1.0
C3 C:K3P304 2.8 57.1 1.0
O C:K3P304 3.2 67.8 1.0
NH1 C:ARG51 3.3 44.4 1.0
O D:HOH425 3.5 40.5 1.0
O D:GLY135 3.7 40.4 1.0
CD1 D:LEU136 3.8 40.6 1.0
N2 C:K3P304 3.9 52.4 1.0
CZ C:ARG51 3.9 48.3 1.0
N1 C:K3P304 4.0 55.5 1.0
CB C:TRP28 4.1 63.1 1.0
NH2 C:ARG51 4.2 52.5 1.0
O D:GLU47 4.4 38.6 1.0
C4 C:K3P304 4.4 55.3 1.0
NE1 D:TRP46 4.5 47.1 1.0
CA D:LEU136 4.5 33.1 1.0
C2 C:K3P304 4.5 67.9 1.0
CB D:LEU136 4.6 36.3 1.0
O C:TRP28 4.6 48.7 1.0
C D:GLY135 4.7 32.6 1.0
CB C:VAL29 4.8 48.6 1.0
C C:TRP28 4.8 55.7 1.0
CG D:LEU136 4.8 40.5 1.0
NE C:ARG51 4.8 43.3 1.0
CG1 C:VAL29 4.8 47.2 1.0
CG C:TRP28 4.9 68.3 1.0
CE2 D:TRP46 5.0 48.7 1.0

Chlorine binding site 5 out of 5 in 5qk7

Go back to Chlorine Binding Sites List in 5qk7
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1918536193 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl305

b:49.8
occ:0.83
 CL C:K3P305 0.0 49.8 0.8
C6 C:K3P305 1.7 42.0 0.8
C5 C:K3P305 2.6 40.1 0.8
C3 C:K3P305 2.7 41.9 0.8
NH2 D:ARG51 3.0 45.6 0.8
O C:K3P305 3.2 44.6 0.8
CZ D:ARG51 3.5 43.3 0.8
O C:GLY135 3.7 39.8 1.0
CG2 D:VAL29 3.8 40.2 0.8
CD2 C:LEU136 3.8 40.6 1.0
NH1 D:ARG51 3.9 44.2 0.8
N2 C:K3P305 3.9 37.8 0.8
N1 C:K3P305 4.0 39.9 0.8
CB D:TRP28 4.1 45.2 0.8
NE D:ARG51 4.4 49.8 0.8
NE1 C:TRP46 4.4 35.1 1.0
C4 C:K3P305 4.4 39.2 0.8
O C:GLU47 4.4 37.0 0.8
CA C:LEU136 4.4 34.4 1.0
C C:GLY135 4.5 38.3 1.0
C2 C:K3P305 4.6 49.5 0.8
CG C:LEU136 4.6 44.0 1.0
O D:TRP28 4.7 38.1 0.8
CB C:LEU136 4.7 39.1 1.0
CZ2 C:TRP46 4.8 33.9 1.0
CE2 C:TRP46 4.8 34.2 1.0
N C:LEU136 4.9 33.8 1.0
CG D:TRP28 4.9 45.0 0.8

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 15:51:11 2024

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