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Chlorine in PDB 4few: Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2

Enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2

All present enzymatic activity of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2:
2.7.1.95;

Protein crystallography data

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2, PDB code: 4few was solved by P.J.Stogios, E.Evdokimova, Z.Wawrzak, G.Minasov, O.Egorova, R.Di Leo, T.Shakya, P.Spanogiannopoulos, G.D.Wright, A.Savchenko, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.90 / 1.98
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.280, 93.579, 96.399, 61.22, 73.18, 87.35
R / Rfree (%) 15.7 / 21.6

Other elements in 4few:

The structure of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 also contains other interesting chemical elements:

Sodium (Na) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 (pdb code 4few). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2, PDB code: 4few:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4few

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:70.8
occ:0.87
 CL A:PP2302 0.0 70.8 0.9
C14 A:PP2302 1.7 46.6 0.9
C13 A:PP2302 2.7 85.2 0.9
C15 A:PP2302 2.7 0.2 0.9
OE1 A:GLN108 3.1 46.1 1.0
NE2 A:GLN108 3.4 40.2 1.0
CD A:GLN108 3.5 46.6 1.0
NE2 B:GLN5 3.7 0.9 1.0
C12 A:PP2302 4.0 81.8 0.9
C16 A:PP2302 4.0 73.5 0.9
CG2 A:THR105 4.4 28.8 1.0
O B:HOH416 4.5 42.2 1.0
C11 A:PP2302 4.5 31.5 0.9
CD B:GLN5 4.7 98.2 1.0
CG A:GLN108 4.8 32.4 1.0
CG B:GLN5 4.8 96.4 1.0

Chlorine binding site 2 out of 8 in 4few

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:45.7
occ:1.00
 N A:LYS58 3.3 30.4 1.0
O A:HIS56 3.6 30.0 1.0
O A:GLY37 3.8 46.8 1.0
CA A:GLY57 3.9 34.5 1.0
CG1 A:VAL61 4.0 43.7 1.0
CB A:VAL61 4.0 26.4 1.0
C A:GLY57 4.1 41.7 1.0
CB A:LYS58 4.2 33.0 1.0
CA A:ALA38 4.2 32.6 1.0
CG2 A:VAL61 4.2 26.9 1.0
CA A:LYS58 4.3 30.6 1.0
N A:THR39 4.3 33.6 1.0
O A:LYS58 4.3 30.6 1.0
OG1 A:THR39 4.4 49.3 1.0
C A:HIS56 4.5 35.0 1.0
C A:GLY37 4.6 39.0 1.0
C A:ALA38 4.6 46.0 1.0
N A:GLY57 4.7 27.4 1.0
N A:ALA38 4.8 26.8 1.0
C A:LYS58 4.8 29.8 1.0

Chlorine binding site 3 out of 8 in 4few

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:53.2
occ:0.79
 CL B:PP2302 0.0 53.2 0.8
C14 B:PP2302 1.7 64.4 0.8
C13 B:PP2302 2.7 57.5 0.8
C15 B:PP2302 2.7 63.9 0.8
OE1 B:GLN108 3.1 60.8 1.0
NE2 B:GLN108 3.3 64.6 1.0
CD B:GLN108 3.5 57.9 1.0
CG2 B:THR105 3.8 48.5 1.0
C12 B:PP2302 4.0 0.3 0.8
C16 B:PP2302 4.0 47.6 0.8
C11 B:PP2302 4.5 37.5 0.8
N B:THR105 4.6 39.6 1.0
CG B:GLN108 4.8 66.4 1.0
CA B:LYS104 4.9 50.8 1.0
O B:GLY103 4.9 48.4 1.0
CB B:THR105 5.0 49.8 1.0

Chlorine binding site 4 out of 8 in 4few

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:22.9
occ:0.54
 CL C:PP2302 0.0 22.9 0.5
C14 C:PP2302 1.7 34.8 0.5
C15 C:PP2302 2.7 22.0 0.5
C13 C:PP2302 2.7 37.2 0.5
OE1 C:GLN108 2.9 46.7 1.0
NE2 C:GLN108 3.1 46.9 1.0
NE2 D:GLN5 3.2 87.3 1.0
OE1 D:GLN5 3.2 78.2 1.0
CD C:GLN108 3.4 76.4 1.0
CD D:GLN5 3.6 98.1 1.0
CG2 C:THR105 3.9 18.5 1.0
C12 C:PP2302 4.0 48.6 0.5
C16 C:PP2302 4.0 37.5 0.5
N C:THR105 4.1 20.0 1.0
C24 C:PP2302 4.1 6.6 0.5
C23 C:PP2302 4.2 53.8 0.5
CA C:LYS104 4.3 29.3 1.0
C11 C:PP2302 4.5 21.7 0.5
O C:GLY103 4.6 24.1 1.0
C C:LYS104 4.7 20.5 1.0
O C:HOH511 4.7 59.1 1.0
CB C:LYS104 4.8 36.9 1.0
C22 C:PP2302 4.9 20.8 0.5
CG C:GLN108 4.9 25.7 1.0
CB C:THR105 4.9 18.6 1.0
OG1 C:THR105 4.9 19.4 1.0
O D:HOH548 4.9 48.2 1.0

Chlorine binding site 5 out of 8 in 4few

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl302

b:21.0
occ:0.46
 CL C:PP2302 0.0 21.0 0.5
C14 C:PP2302 1.7 33.4 0.5
C13 C:PP2302 2.7 16.7 0.5
C15 C:PP2302 2.7 58.3 0.5
OE2 C:GLU68 3.5 46.4 1.0
CD2 C:LEU96 3.5 19.7 1.0
CE C:LYS55 3.5 38.8 1.0
CB C:LYS55 3.8 19.1 1.0
CG C:LEU96 3.8 18.7 1.0
CD C:LYS55 3.9 56.9 1.0
C12 C:PP2302 4.0 0.1 0.5
CD C:GLU68 4.0 51.5 1.0
C16 C:PP2302 4.0 46.6 0.5
CG2 C:THR98 4.0 19.7 1.0
OE1 C:GLU68 4.1 46.0 1.0
C24 C:PP2302 4.1 5.6 0.5
OG1 C:THR98 4.2 25.8 1.0
O C:LEU96 4.3 26.6 1.0
C23 C:PP2302 4.4 46.4 0.5
CG C:LYS55 4.5 35.0 1.0
C11 C:PP2302 4.5 23.0 0.5
CB C:LEU96 4.5 18.6 1.0
NZ C:LYS55 4.6 31.4 1.0
O C:HOH579 4.6 36.3 1.0
CB C:THR98 4.8 22.7 1.0
N C:LYS55 4.8 19.1 1.0
C22 C:PP2302 4.9 27.1 0.5
CA C:LYS55 5.0 17.6 1.0
CD1 C:LEU72 5.0 32.0 1.0

Chlorine binding site 6 out of 8 in 4few

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl302

b:37.2
occ:0.71
 CL D:PP2302 0.0 37.2 0.7
C14 D:PP2302 1.7 51.3 0.7
C13 D:PP2302 2.7 40.4 0.7
C15 D:PP2302 2.8 45.2 0.7
OE1 D:GLN108 3.0 33.8 1.0
NE2 D:GLN108 3.4 60.1 1.0
CD D:GLN108 3.5 17.6 1.0
C12 D:PP2302 4.0 82.5 0.7
C16 D:PP2302 4.0 80.3 0.7
CG2 D:THR105 4.1 18.1 1.0
N D:THR105 4.5 17.6 1.0
C11 D:PP2302 4.6 22.8 0.7
CA D:LYS104 4.7 29.4 1.0
O D:GLY103 4.7 24.3 1.0
CG D:GLN108 4.9 22.2 1.0

Chlorine binding site 7 out of 8 in 4few

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl302

b:28.1
occ:0.80
 CL E:PP2302 0.0 28.1 0.8
C14 E:PP2302 1.7 56.7 0.8
C13 E:PP2302 2.7 32.0 0.8
C15 E:PP2302 2.8 39.8 0.8
OE1 E:GLN108 3.1 40.9 1.0
NE2 F:GLN5 3.3 66.6 1.0
O F:HOH477 3.3 52.3 1.0
CD F:GLN5 3.5 94.6 1.0
OE1 F:GLN5 3.6 81.6 1.0
NE2 E:GLN108 3.7 56.9 1.0
CD E:GLN108 3.8 42.8 1.0
CG2 E:THR105 3.8 31.0 1.0
C12 E:PP2302 4.0 60.5 0.8
C16 E:PP2302 4.0 38.1 0.8
O E:HOH487 4.1 47.2 1.0
N E:THR105 4.2 25.4 1.0
CG F:GLN5 4.3 48.0 1.0
CA E:LYS104 4.4 28.6 1.0
O F:HOH585 4.5 49.5 1.0
C11 E:PP2302 4.6 22.1 0.8
O E:GLY103 4.6 40.1 1.0
C E:LYS104 4.8 25.5 1.0
CB E:THR105 4.9 25.7 1.0

Chlorine binding site 8 out of 8 in 4few

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Aminoglycoside Phosphotransferase Aph(3')-Ia, with Substrate Kanamycin and Small Molecule Inhibitor Pyrazolopyrimidine PP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl302

b:43.4
occ:0.72
 CL F:PP2302 0.0 43.4 0.7
C14 F:PP2302 1.7 45.6 0.7
C13 F:PP2302 2.7 69.6 0.7
C15 F:PP2302 2.8 60.1 0.7
O F:HOH540 2.8 52.2 1.0
OE1 F:GLN108 3.2 22.7 1.0
NE2 F:GLN108 3.5 51.4 1.0
CD F:GLN108 3.7 48.0 1.0
CG2 F:THR105 3.8 24.8 1.0
C12 F:PP2302 4.0 87.0 0.7
C16 F:PP2302 4.0 39.0 0.7
N F:THR105 4.5 23.6 1.0
C11 F:PP2302 4.5 30.2 0.7
O F:GLY103 4.6 36.1 1.0
O F:HOH426 4.7 28.3 1.0
CA F:LYS104 4.8 32.4 1.0

Reference:

P.J.Stogios, P.Spanogiannopoulos, E.Evdokimova, O.Egorova, T.Shakya, N.Todorovic, A.Capretta, G.D.Wright, A.Savchenko. Structure-Guided Optimization of Protein Kinase Inhibitors Reverses Aminoglycoside Antibiotic Resistance. Biochem.J. V. 454 191 2013.
ISSN: ISSN 0264-6021
PubMed: 23758273
DOI: 10.1042/BJ20130317
Page generated: Sun Jul 21 13:42:08 2024

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