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Calcium in PDB 3hli: Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants

Enzymatic activity of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants

All present enzymatic activity of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants:
3.1.8.2;

Protein crystallography data

The structure of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants, PDB code: 3hli was solved by J.C.-H.Chen, M.-M.Blum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.82 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.950, 74.490, 118.950, 90.00, 100.00, 90.00
R / Rfree (%) 20.5 / 22.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants (pdb code 3hli). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants, PDB code: 3hli:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3hli

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Calcium binding site 1 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca315

b:4.5
occ:1.00
 OE2 A:GLU21 2.3 7.0 1.0
OD1 A:ASN175 2.3 6.3 1.0
OD1 A:ASP229 2.4 5.2 1.0
O A:HOH319 2.4 4.7 1.0
OD1 A:ASN120 2.4 5.5 1.0
O A:HOH318 2.4 6.1 1.0
CD A:GLU21 3.3 5.8 1.0
CG A:ASN175 3.4 5.0 1.0
CG A:ASN120 3.4 3.8 1.0
CG A:ASP229 3.5 5.4 1.0
ND2 A:ASN120 3.8 6.0 1.0
ND2 A:ASN175 3.8 6.5 1.0
OE1 A:GLU21 3.8 5.6 1.0
OD2 A:ASP229 4.1 4.7 1.0
ND2 A:ASN272 4.4 4.8 1.0
CG A:GLU21 4.5 6.2 1.0
O A:SER271 4.5 5.2 1.0
OD2 A:ASP121 4.6 4.1 1.0
N A:GLY230 4.6 4.5 1.0
O A:ASN120 4.7 4.0 1.0
CB A:ASP121 4.7 4.3 1.0
CB A:ASN175 4.7 6.1 1.0
CB A:ASP229 4.7 5.4 1.0
C A:ASP229 4.7 4.8 1.0
O A:ALA74 4.8 5.5 1.0
CB A:ASN120 4.8 4.0 1.0
C A:ASN175 4.9 5.7 1.0
CA A:ASP229 4.9 4.8 1.0
CG A:ASP121 4.9 3.7 1.0
C A:ASN120 5.0 4.5 1.0

Calcium binding site 2 out of 8 in 3hli

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Calcium binding site 2 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca316

b:4.5
occ:1.00
 OD2 A:ASP232 2.2 6.8 1.0
O A:HOH325 2.3 4.8 1.0
O A:LEU273 2.3 5.8 1.0
O A:HOH321 2.3 5.7 1.0
O A:HOH328 2.4 5.9 1.0
ND1 A:HIS274 2.5 5.0 1.0
CG A:ASP232 3.2 6.2 1.0
CE1 A:HIS274 3.4 4.4 1.0
CG A:HIS274 3.5 4.1 1.0
C A:LEU273 3.5 6.0 1.0
OD1 A:ASP232 3.7 6.5 1.0
CB A:HIS274 3.7 5.4 1.0
CA A:HIS274 3.8 5.4 1.0
OD1 A:ASN272 4.0 4.3 1.0
N A:HIS274 4.1 5.6 1.0
O A:PRO23 4.1 6.2 1.0
O A:MET231 4.2 5.6 1.0
O A:HOH324 4.2 7.6 1.0
O A:HOH346 4.3 7.5 1.0
CB A:ASP232 4.4 6.8 1.0
O A:HOH323 4.5 5.8 1.0
NE2 A:HIS274 4.6 6.7 1.0
CD2 A:HIS274 4.6 5.3 1.0
N A:LEU273 4.7 5.8 1.0
CA A:LEU273 4.7 6.2 1.0
CD1 A:LEU273 4.7 14.9 1.0
CG A:PRO23 4.8 6.1 1.0
CG A:ASN272 4.8 3.5 1.0

Calcium binding site 3 out of 8 in 3hli

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Calcium binding site 3 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca315

b:3.7
occ:1.00
 OD1 B:ASN175 2.3 6.3 1.0
OE2 B:GLU21 2.3 6.1 1.0
O A:PHE314 2.4 6.0 1.0
OD1 B:ASP229 2.4 4.8 1.0
O B:HOH369 2.4 4.3 1.0
O B:HOH324 2.5 5.2 1.0
OD1 B:ASN120 2.5 4.7 1.0
CD B:GLU21 3.3 4.7 1.0
CG B:ASN175 3.3 5.0 1.0
C A:PHE314 3.4 5.5 1.0
CG B:ASN120 3.5 4.2 1.0
CG B:ASP229 3.5 4.6 1.0
ND2 B:ASN175 3.8 6.8 1.0
OE1 B:GLU21 3.8 4.0 1.0
ND2 B:ASN120 3.8 5.7 1.0
OXT A:PHE314 3.8 4.8 1.0
OD2 B:ASP229 4.1 4.6 1.0
ND2 B:ASN272 4.4 3.3 1.0
CG B:GLU21 4.5 3.7 1.0
OD2 B:ASP121 4.6 3.9 1.0
O B:SER271 4.6 4.0 1.0
N B:GLY230 4.6 4.9 1.0
CB B:ASP121 4.6 4.3 1.0
O B:ASN120 4.6 4.1 1.0
CA A:PHE314 4.7 5.7 1.0
CB B:ASN175 4.7 4.7 1.0
C B:ASP229 4.7 4.7 1.0
CB B:ASP229 4.7 4.6 1.0
O B:ALA74 4.8 4.8 1.0
CB B:ASN120 4.8 4.0 1.0
CG B:ASP121 4.9 3.2 1.0
C B:ASN175 4.9 4.6 1.0
CA B:ASP229 4.9 5.1 1.0
C B:ASN120 5.0 4.1 1.0

Calcium binding site 4 out of 8 in 3hli

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Calcium binding site 4 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca316

b:4.0
occ:1.00
 OD2 B:ASP232 2.2 6.4 1.0
O B:HOH338 2.3 4.9 1.0
O B:HOH378 2.3 6.4 1.0
O B:LEU273 2.3 5.2 1.0
O B:HOH367 2.4 4.9 1.0
ND1 B:HIS274 2.5 5.2 1.0
CG B:ASP232 3.2 4.7 1.0
CE1 B:HIS274 3.4 5.7 1.0
CG B:HIS274 3.5 4.3 1.0
C B:LEU273 3.5 5.5 1.0
OD1 B:ASP232 3.7 6.0 1.0
CB B:HIS274 3.7 4.8 1.0
CA B:HIS274 3.8 4.2 1.0
OD1 B:ASN272 4.0 3.7 1.0
N B:HIS274 4.1 5.0 1.0
O B:PRO23 4.1 4.5 1.0
O B:MET231 4.2 5.9 1.0
O B:HOH384 4.3 6.6 1.0
O B:HOH374 4.3 7.1 1.0
CB B:ASP232 4.4 5.3 1.0
O B:HOH371 4.5 5.3 1.0
NE2 B:HIS274 4.5 5.8 1.0
CD2 B:HIS274 4.6 5.5 1.0
N B:LEU273 4.7 4.5 1.0
CA B:LEU273 4.7 6.0 1.0
CD1 B:LEU273 4.8 14.4 1.0
CG B:ASN272 4.8 2.1 1.0
CG B:PRO23 4.9 4.1 1.0

Calcium binding site 5 out of 8 in 3hli

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Calcium binding site 5 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca315

b:4.3
occ:1.00
 OE2 C:GLU21 2.3 7.8 1.0
O B:PHE314 2.3 6.5 1.0
OD1 C:ASN175 2.4 5.4 1.0
OD1 C:ASP229 2.4 4.2 1.0
O C:HOH320 2.4 3.9 1.0
OD1 C:ASN120 2.4 5.9 1.0
O C:HOH317 2.4 4.3 1.0
CD C:GLU21 3.3 5.2 1.0
C B:PHE314 3.4 7.4 1.0
CG C:ASN175 3.4 4.2 1.0
CG C:ASN120 3.4 4.9 1.0
CG C:ASP229 3.5 4.6 1.0
ND2 C:ASN120 3.8 5.5 1.0
OXT B:PHE314 3.8 6.8 1.0
ND2 C:ASN175 3.8 6.3 1.0
OE1 C:GLU21 3.9 5.8 1.0
OD2 C:ASP229 4.0 4.5 1.0
ND2 C:ASN272 4.4 5.1 1.0
CG C:GLU21 4.5 5.4 1.0
OD2 C:ASP121 4.5 3.5 1.0
O C:SER271 4.5 4.2 1.0
CA B:PHE314 4.6 7.2 1.0
O C:ASN120 4.6 4.3 1.0
N C:GLY230 4.6 4.0 1.0
CB C:ASP121 4.6 4.0 1.0
CB C:ASN175 4.7 5.2 1.0
O C:ALA74 4.7 4.6 1.0
CB C:ASP229 4.7 4.9 1.0
C C:ASP229 4.7 4.3 1.0
CB C:ASN120 4.8 4.8 1.0
CG C:ASP121 4.9 4.3 1.0
C C:ASN175 4.9 4.8 1.0
CA C:ASP229 4.9 4.2 1.0
C C:ASN120 4.9 3.9 1.0

Calcium binding site 6 out of 8 in 3hli

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Calcium binding site 6 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca316

b:4.6
occ:1.00
 OD2 C:ASP232 2.2 7.0 1.0
O C:HOH318 2.3 4.2 1.0
O C:HOH330 2.3 5.2 1.0
O C:LEU273 2.3 4.5 1.0
O C:HOH319 2.4 6.4 1.0
ND1 C:HIS274 2.5 4.2 1.0
CG C:ASP232 3.2 5.0 1.0
CE1 C:HIS274 3.4 4.4 1.0
CG C:HIS274 3.5 4.0 1.0
C C:LEU273 3.5 4.8 1.0
OD1 C:ASP232 3.7 6.0 1.0
CB C:HIS274 3.7 5.1 1.0
CA C:HIS274 3.8 3.8 1.0
OD1 C:ASN272 4.0 4.3 1.0
N C:HIS274 4.1 4.4 1.0
O C:PRO23 4.2 6.3 1.0
O C:MET231 4.2 4.2 1.0
O C:HOH323 4.2 7.0 1.0
O C:HOH334 4.3 6.3 1.0
CB C:ASP232 4.4 4.9 1.0
O C:HOH324 4.5 5.6 1.0
NE2 C:HIS274 4.6 4.9 1.0
CD2 C:HIS274 4.6 6.1 1.0
N C:LEU273 4.7 4.0 1.0
CA C:LEU273 4.7 4.3 1.0
CG C:ASN272 4.8 4.1 1.0
CD1 C:LEU273 4.8 13.7 1.0
CG C:PRO23 4.9 6.0 1.0

Calcium binding site 7 out of 8 in 3hli

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Calcium binding site 7 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca315

b:3.1
occ:1.00
 OE2 D:GLU21 2.3 6.1 1.0
OD1 D:ASN175 2.3 4.9 1.0
OD1 D:ASP229 2.4 2.9 1.0
O D:HOH326 2.4 4.0 1.0
OD1 D:ASN120 2.5 4.3 1.0
O D:HOH317 2.5 5.0 1.0
CD D:GLU21 3.3 5.2 1.0
CG D:ASN175 3.4 4.5 1.0
CG D:ASN120 3.5 3.9 1.0
CG D:ASP229 3.5 3.0 1.0
ND2 D:ASN175 3.8 5.8 1.0
OE1 D:GLU21 3.8 4.2 1.0
ND2 D:ASN120 3.8 5.8 1.0
OD2 D:ASP229 4.0 3.9 1.0
ND2 D:ASN272 4.4 4.2 1.0
CG D:GLU21 4.5 5.0 1.0
O D:SER271 4.5 3.2 1.0
OD2 D:ASP121 4.5 4.2 1.0
N D:GLY230 4.6 3.7 1.0
O D:ASN120 4.7 2.9 1.0
CB D:ASP121 4.7 3.7 1.0
CB D:ASN175 4.7 4.3 1.0
C D:ASP229 4.7 3.9 1.0
CB D:ASP229 4.7 5.0 1.0
O D:ALA74 4.8 4.8 1.0
CB D:ASN120 4.8 3.9 1.0
C D:ASN175 4.9 3.1 1.0
CA D:ASP229 4.9 3.9 1.0
CG D:ASP121 4.9 4.7 1.0
C D:ASN120 5.0 3.1 1.0

Calcium binding site 8 out of 8 in 3hli

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Calcium binding site 8 out of 8 in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca316

b:5.0
occ:1.00
 OD2 D:ASP232 2.2 6.9 1.0
O D:HOH318 2.2 3.9 1.0
O D:HOH329 2.3 5.7 1.0
O D:LEU273 2.3 5.1 1.0
O D:HOH321 2.4 6.0 1.0
ND1 D:HIS274 2.5 5.6 1.0
CG D:ASP232 3.2 3.9 1.0
CE1 D:HIS274 3.4 6.6 1.0
CG D:HIS274 3.5 5.5 1.0
C D:LEU273 3.5 5.0 1.0
CB D:HIS274 3.7 5.2 1.0
OD1 D:ASP232 3.7 5.7 1.0
CA D:HIS274 3.8 4.7 1.0
OD1 D:ASN272 4.0 3.4 1.0
O D:PRO23 4.1 5.1 1.0
N D:HIS274 4.1 5.0 1.0
O D:MET231 4.2 5.6 1.0
O D:HOH344 4.2 7.5 1.0
O D:HOH323 4.3 7.1 1.0
CB D:ASP232 4.4 5.2 1.0
O D:HOH331 4.5 6.0 1.0
NE2 D:HIS274 4.5 6.1 1.0
CD2 D:HIS274 4.6 6.2 1.0
N D:LEU273 4.7 4.6 1.0
CA D:LEU273 4.7 4.8 1.0
CG D:ASN272 4.8 2.7 1.0
CG D:PRO23 4.9 4.7 1.0
CD1 D:LEU273 4.9 11.8 1.0

Reference:

M.Melzer, J.C.Chen, A.Heidenreich, J.Gab, M.Koller, K.Kehe, M.M.Blum. Reversed Enantioselectivity of Diisopropyl Fluorophosphatase Against Organophosphorus Nerve Agents By Rational Design J.Am.Chem.Soc. V. 131 17226 2009.
ISSN: ISSN 0002-7863
PubMed: 19894712
DOI: 10.1021/JA905444G
Page generated: Sat Jul 13 11:04:49 2024

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