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Chlorine in PDB 5qtp: Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227, PDB code: 5qtp was solved by Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.67 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.246, 59.826, 80.052, 79.42, 81.55, 75.70
R / Rfree (%) 22.9 / 26.1

Other elements in 5qtp:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227 also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Magnesium (Mg) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227 (pdb code 5qtp). 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 -- Crystal Structure of NUDT5 in Complex with Ae-0227, PDB code: 5qtp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5qtp

Go back to Chlorine Binding Sites List in 5qtp
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:43.0
occ:0.83
 CL A:PWJ303 0.0 43.0 0.8
C A:PWJ303 1.7 41.1 0.8
C1 A:PWJ303 2.6 37.5 0.8
C7 A:PWJ303 2.7 42.0 0.8
C8 A:PWJ303 2.9 43.5 0.8
N A:PWJ303 3.0 36.0 0.8
O A:THR45 3.4 29.3 1.0
CE3 A:TRP46 3.5 30.3 0.8
N2 A:PWJ303 3.5 42.1 0.8
NE1 B:TRP28 3.6 42.1 0.8
O B:HOH455 3.6 36.2 0.8
CA A:TRP46 3.7 29.4 0.8
CD2 A:TRP46 3.8 32.8 0.8
CD1 B:TRP28 3.9 45.1 0.8
N1 A:PWJ303 3.9 37.0 0.8
CZ3 A:TRP46 4.0 29.9 0.8
C5 A:PWJ303 4.0 42.7 0.8
CE2 B:TRP28 4.2 43.5 0.8
C A:THR45 4.2 27.1 1.0
CG A:TRP46 4.2 30.2 0.8
C2 A:PWJ303 4.4 33.7 0.8
N A:GLU47 4.4 28.5 1.0
N A:TRP46 4.4 30.0 0.8
CB A:TRP46 4.4 30.0 0.8
CE2 A:TRP46 4.5 30.4 0.8
C4 A:PWJ303 4.5 40.8 0.8
C A:TRP46 4.5 28.2 0.8
CG B:TRP28 4.5 42.2 0.8
CH2 A:TRP46 4.6 31.7 0.8
CD2 B:TRP28 4.7 40.8 0.8
CZ2 B:TRP28 4.7 44.0 0.8
C3 A:PWJ303 4.8 37.9 0.8
CZ2 A:TRP46 4.8 29.5 0.8

Chlorine binding site 2 out of 5 in 5qtp

Go back to Chlorine Binding Sites List in 5qtp
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:69.6
occ:1.00
 CG2 B:THR145 3.9 29.2 1.0
CG2 B:THR147 4.1 33.8 1.0
CG2 B:VAL67 4.1 31.4 1.0
ND1 A:HIS206 4.4 27.9 1.0
CE1 A:HIS206 4.5 25.7 1.0
CG A:HIS206 4.6 25.7 1.0
NE2 A:HIS206 4.6 28.3 1.0
CB B:VAL67 4.6 28.8 1.0
CD2 A:HIS206 4.7 21.5 1.0
CG1 B:VAL67 4.8 28.4 1.0
CB B:ALA124 4.8 37.4 1.0

Chlorine binding site 3 out of 5 in 5qtp

Go back to Chlorine Binding Sites List in 5qtp
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:35.5
occ:0.70
 CL B:PWJ305 0.0 35.5 0.7
C B:PWJ305 1.7 33.1 0.7
C1 B:PWJ305 2.6 33.2 0.7
C7 B:PWJ305 2.7 38.6 0.7
C8 B:PWJ305 2.9 40.0 0.7
N B:PWJ305 3.1 31.3 0.7
O B:THR45 3.3 32.6 1.0
NE1 A:TRP28 3.5 31.9 0.7
CE3 B:TRP46 3.5 24.1 0.7
N2 B:PWJ305 3.6 45.8 0.7
CD1 A:TRP28 3.6 35.5 0.7
CA B:TRP46 3.7 30.9 0.7
CD2 B:TRP46 3.7 24.7 0.7
N1 B:PWJ305 4.0 33.1 0.7
CZ3 B:TRP46 4.0 24.1 0.7
C5 B:PWJ305 4.1 38.9 0.7
C B:THR45 4.1 31.6 1.0
CG B:TRP46 4.1 29.1 0.7
CE2 A:TRP28 4.2 34.2 0.7
N B:GLU47 4.2 29.4 1.0
CG A:TRP28 4.3 34.6 0.7
N B:TRP46 4.4 32.5 0.7
CB B:TRP46 4.4 28.8 0.7
C2 B:PWJ305 4.4 30.1 0.7
CE2 B:TRP46 4.4 25.1 0.7
C B:TRP46 4.5 29.7 0.7
C4 B:PWJ305 4.6 34.2 0.7
CH2 B:TRP46 4.6 25.7 0.7
CD2 A:TRP28 4.6 33.3 0.7
CZ2 B:TRP46 4.8 24.7 0.7
C3 B:PWJ305 4.8 32.7 0.7
CZ2 A:TRP28 4.9 34.8 0.7
CD1 B:TRP46 4.9 26.4 0.7

Chlorine binding site 4 out of 5 in 5qtp

Go back to Chlorine Binding Sites List in 5qtp
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl306

b:53.0
occ:0.87
 CL C:PWJ306 0.0 53.0 0.9
C C:PWJ306 1.7 48.7 0.9
C7 C:PWJ306 2.7 54.3 0.9
C1 C:PWJ306 2.7 46.4 0.9
C8 C:PWJ306 2.8 54.3 0.9
N C:PWJ306 3.2 43.8 0.9
NE1 C:TRP28 3.3 54.2 0.9
N2 C:PWJ306 3.4 56.9 0.9
CD1 C:TRP28 3.6 52.8 0.9
O D:THR45 3.7 39.9 1.0
CE3 D:TRP46 3.7 35.1 1.0
CE2 C:TRP28 3.9 50.0 0.9
CA D:TRP46 4.0 42.8 1.0
N1 C:PWJ306 4.0 45.9 0.9
C5 C:PWJ306 4.0 48.5 0.9
CD2 D:TRP46 4.0 36.8 1.0
CZ3 D:TRP46 4.1 38.8 1.0
CG C:TRP28 4.3 53.1 0.9
CD2 C:TRP28 4.4 54.1 0.9
C D:THR45 4.5 43.5 1.0
CZ2 C:TRP28 4.5 51.0 0.9
CG D:TRP46 4.5 37.0 1.0
C4 C:PWJ306 4.5 49.0 0.9
N D:GLU47 4.5 41.9 1.0
C2 C:PWJ306 4.6 44.0 0.9
N D:TRP46 4.6 44.7 1.0
CE2 D:TRP46 4.7 38.3 1.0
CB D:TRP46 4.7 43.2 1.0
C D:TRP46 4.8 39.8 1.0
CH2 D:TRP46 4.8 40.2 1.0
C3 C:PWJ306 5.0 46.4 0.9

Chlorine binding site 5 out of 5 in 5qtp

Go back to Chlorine Binding Sites List in 5qtp
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition -- Crystal Structure of NUDT5 in Complex with Ae-0227


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 -- Crystal Structure of NUDT5 in Complex with Ae-0227 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:56.1
occ:0.80
 CL D:PWJ501 0.0 56.1 0.8
C D:PWJ501 1.7 45.9 0.8
C7 D:PWJ501 2.6 47.0 0.8
C1 D:PWJ501 2.7 42.1 0.8
C8 D:PWJ501 2.9 46.4 0.8
N D:PWJ501 3.2 37.5 0.8
NE1 D:TRP28 3.2 48.4 0.8
O C:THR45 3.5 39.7 1.0
N2 D:PWJ501 3.5 45.1 0.8
CE3 C:TRP46 3.5 40.2 0.8
CE2 D:TRP28 3.7 47.5 0.8
CD1 D:TRP28 3.8 47.3 0.8
CZ3 C:TRP46 3.9 41.0 0.8
CD2 C:TRP46 3.9 36.5 0.8
N1 D:PWJ501 4.0 44.5 0.8
C5 D:PWJ501 4.0 52.2 0.8
CA C:TRP46 4.0 39.7 0.8
CZ2 D:TRP28 4.1 51.2 0.8
CD2 D:TRP28 4.4 47.4 0.8
CG D:TRP28 4.4 49.5 0.8
C C:THR45 4.4 38.7 1.0
CG C:TRP46 4.5 38.1 0.8
C4 D:PWJ501 4.5 47.8 0.8
CH2 C:TRP46 4.6 40.1 0.8
C2 D:PWJ501 4.6 40.1 0.8
CE2 C:TRP46 4.6 35.8 0.8
N C:TRP46 4.6 37.9 0.8
CB C:TRP46 4.7 41.1 0.8
N C:GLU47 4.8 39.3 0.8
CZ2 C:TRP46 4.9 37.3 0.8
C C:TRP46 4.9 39.6 0.8
C3 D:PWJ501 4.9 45.4 0.8

Reference:

Y.Dubianok, T.Krojer, H.Kovacs, F.Moriaud, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, F.Von Delft. Pandda Analysis Group Deposition To Be Published.
Page generated: Fri Jul 26 15:53:42 2024

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