Atomistry » Calcium » PDB 3hjb-3hz3 » 3hlh
Atomistry »
  Calcium »
    PDB 3hjb-3hz3 »
      3hlh »

Calcium in PDB 3hlh: 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: 3hlh 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) 47.77 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.110, 74.390, 118.640, 90.00, 99.90, 90.00
R / Rfree (%) 19.5 / 21.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Diisopropyl Fluorophosphatase (Dfpase), Active Site Mutants (pdb code 3hlh). 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: 3hlh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:3.1
occ:1.00
 OD1 A:ASN175 2.3 6.4 1.0
OE2 A:GLU21 2.3 5.3 1.0
O A:HOH319 2.4 2.1 1.0
OD1 A:ASP229 2.4 2.5 1.0
O A:HOH318 2.4 3.0 1.0
OD1 A:ASN120 2.4 3.7 1.0
CG A:ASN175 3.3 6.6 1.0
CD A:GLU21 3.4 4.8 1.0
CG A:ASN120 3.4 4.7 1.0
CG A:ASP229 3.6 4.4 1.0
ND2 A:ASN175 3.7 4.9 1.0
ND2 A:ASN120 3.8 3.3 1.0
OE1 A:GLU21 3.9 3.9 1.0
OD2 A:ASP229 4.1 3.8 1.0
ND2 A:ASN272 4.3 3.1 1.0
O A:SER271 4.5 3.7 1.0
CG A:GLU21 4.5 2.9 1.0
N A:GLY230 4.6 4.0 1.0
OD2 A:ASP121 4.6 3.8 1.0
CB A:ASP121 4.6 1.7 1.0
O A:ASN120 4.7 2.0 1.0
CB A:ASN175 4.7 5.0 1.0
C A:ASP229 4.8 4.1 1.0
CB A:ASP229 4.8 3.7 1.0
O A:ALA74 4.8 5.1 1.0
CB A:ASN120 4.8 2.5 1.0
CG A:ASP121 4.8 2.9 1.0
C A:ASN175 4.9 4.3 1.0
CA A:ASP229 4.9 3.8 1.0
C A:ASN120 4.9 2.4 1.0

Calcium binding site 2 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:3.0
occ:1.00
 OD2 A:ASP232 2.2 6.4 1.0
O A:HOH321 2.3 3.9 1.0
O A:LEU273 2.3 6.5 1.0
O A:HOH328 2.4 2.0 1.0
ND1 A:HIS274 2.4 5.0 1.0
O A:HOH325 2.4 3.8 1.0
CG A:ASP232 3.2 6.1 1.0
CE1 A:HIS274 3.4 6.1 1.0
CG A:HIS274 3.4 5.0 1.0
C A:LEU273 3.5 6.0 1.0
CB A:HIS274 3.7 4.1 1.0
OD1 A:ASP232 3.7 4.7 1.0
CA A:HIS274 3.8 4.3 1.0
OD1 A:ASN272 4.0 2.6 1.0
N A:HIS274 4.1 5.3 1.0
O A:PRO23 4.1 4.6 1.0
O A:MET231 4.2 4.8 1.0
O A:HOH324 4.3 5.5 1.0
O A:HOH346 4.3 6.7 1.0
CB A:ASP232 4.4 4.9 1.0
NE2 A:HIS274 4.5 7.2 1.0
O A:HOH323 4.5 2.4 1.0
CD2 A:HIS274 4.6 6.3 1.0
CA A:LEU273 4.7 5.6 1.0
N A:LEU273 4.7 5.6 1.0
CD1 A:LEU273 4.8 11.9 1.0
CG A:PRO23 4.8 3.0 1.0
CG A:ASN272 4.8 2.9 1.0

Calcium binding site 3 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:3.6
occ:1.00
 OD1 B:ASN175 2.3 3.1 1.0
OE2 B:GLU21 2.3 6.4 1.0
O A:PHE314 2.3 4.8 1.0
OD1 B:ASP229 2.4 3.4 1.0
O B:HOH369 2.4 3.2 1.0
OD1 B:ASN120 2.4 4.7 1.0
O B:HOH324 2.5 1.4 1.0
CG B:ASN175 3.3 3.7 1.0
CD B:GLU21 3.4 4.0 1.0
C A:PHE314 3.4 4.8 1.0
CG B:ASN120 3.5 5.5 1.0
CG B:ASP229 3.5 4.7 1.0
ND2 B:ASN175 3.8 1.0 1.0
ND2 B:ASN120 3.8 5.0 1.0
OXT A:PHE314 3.9 5.5 1.0
OE1 B:GLU21 3.9 3.5 1.0
OD2 B:ASP229 4.1 1.9 1.0
ND2 B:ASN272 4.4 2.6 1.0
OD2 B:ASP121 4.4 2.9 1.0
O B:SER271 4.5 3.5 1.0
CG B:GLU21 4.5 2.4 1.0
N B:GLY230 4.6 2.5 1.0
CB B:ASP121 4.6 2.8 1.0
CB B:ASN175 4.6 2.6 1.0
O B:ASN120 4.6 2.6 1.0
CA A:PHE314 4.7 5.3 1.0
C B:ASP229 4.7 2.7 1.0
O B:ALA74 4.7 4.2 1.0
CB B:ASP229 4.7 3.8 1.0
CB B:ASN120 4.8 4.0 1.0
CG B:ASP121 4.8 1.0 1.0
C B:ASN175 4.8 2.8 1.0
CA B:ASP229 4.9 3.4 1.0
C B:ASN120 4.9 3.2 1.0
N B:GLY176 5.0 2.4 1.0

Calcium binding site 4 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:2.2
occ:1.00
 OD2 B:ASP232 2.2 3.5 1.0
O B:HOH378 2.3 1.0 1.0
O B:LEU273 2.3 3.8 1.0
O B:HOH338 2.4 2.7 1.0
O B:HOH367 2.4 2.4 1.0
ND1 B:HIS274 2.5 3.2 1.0
CG B:ASP232 3.2 4.2 1.0
CE1 B:HIS274 3.4 3.4 1.0
CG B:HIS274 3.5 4.4 1.0
C B:LEU273 3.5 3.9 1.0
OD1 B:ASP232 3.7 3.7 1.0
CB B:HIS274 3.7 3.7 1.0
CA B:HIS274 3.8 4.5 1.0
OD1 B:ASN272 3.9 4.1 1.0
O B:PRO23 4.1 2.2 1.0
N B:HIS274 4.1 3.6 1.0
O B:MET231 4.2 5.0 1.0
O B:HOH384 4.3 3.5 1.0
O B:HOH374 4.4 3.4 1.0
CB B:ASP232 4.4 3.6 1.0
NE2 B:HIS274 4.5 4.2 1.0
O B:HOH371 4.6 2.2 1.0
CD2 B:HIS274 4.6 3.5 1.0
CD1 B:LEU273 4.6 14.8 1.0
N B:LEU273 4.7 3.9 1.0
CA B:LEU273 4.7 5.1 1.0
CG B:ASN272 4.8 3.1 1.0
CG B:PRO23 4.8 1.8 1.0

Calcium binding site 5 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:2.8
occ:1.00
 OD1 C:ASN175 2.3 3.0 1.0
OE2 C:GLU21 2.3 3.4 1.0
O B:PHE314 2.3 6.2 1.0
OD1 C:ASP229 2.4 3.6 1.0
OD1 C:ASN120 2.4 4.7 1.0
O C:HOH320 2.4 1.8 1.0
O C:HOH317 2.5 3.4 1.0
CD C:GLU21 3.4 2.3 1.0
CG C:ASN175 3.4 3.5 1.0
C B:PHE314 3.4 6.1 1.0
CG C:ASN120 3.4 3.7 1.0
CG C:ASP229 3.5 2.9 1.0
ND2 C:ASN175 3.8 4.3 1.0
ND2 C:ASN120 3.8 4.7 1.0
OXT B:PHE314 3.8 5.9 1.0
OE1 C:GLU21 3.9 3.0 1.0
OD2 C:ASP229 4.1 3.1 1.0
ND2 C:ASN272 4.4 2.3 1.0
OD2 C:ASP121 4.5 3.6 1.0
CG C:GLU21 4.5 4.1 1.0
O C:SER271 4.6 4.9 1.0
O C:ASN120 4.6 2.8 1.0
CA B:PHE314 4.6 6.4 1.0
N C:GLY230 4.6 4.2 1.0
CB C:ASP121 4.7 3.4 1.0
CB C:ASN175 4.7 3.8 1.0
O C:ALA74 4.7 2.8 1.0
C C:ASP229 4.7 3.9 1.0
CB C:ASP229 4.7 3.8 1.0
CB C:ASN120 4.8 3.8 1.0
CG C:ASP121 4.9 1.4 1.0
C C:ASN175 4.9 1.7 1.0
CA C:ASP229 4.9 3.3 1.0
C C:ASN120 4.9 3.2 1.0

Calcium binding site 6 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:2.1
occ:1.00
 OD2 C:ASP232 2.2 2.6 1.0
O C:LEU273 2.3 1.5 1.0
O C:HOH330 2.3 2.9 1.0
O C:HOH318 2.4 1.3 1.0
ND1 C:HIS274 2.4 1.9 1.0
O C:HOH319 2.4 1.0 1.0
CG C:ASP232 3.2 2.9 1.0
CE1 C:HIS274 3.3 2.9 1.0
CG C:HIS274 3.4 2.1 1.0
C C:LEU273 3.5 3.2 1.0
CB C:HIS274 3.7 1.8 1.0
OD1 C:ASP232 3.7 1.0 1.0
CA C:HIS274 3.8 2.7 1.0
OD1 C:ASN272 3.9 4.5 1.0
N C:HIS274 4.1 3.4 1.0
O C:PRO23 4.1 3.5 1.0
O C:MET231 4.2 3.7 1.0
O C:HOH323 4.3 5.3 1.0
O C:HOH334 4.3 2.6 1.0
NE2 C:HIS274 4.5 2.4 1.0
CB C:ASP232 4.5 2.8 1.0
CD2 C:HIS274 4.5 2.4 1.0
O C:HOH324 4.6 3.3 1.0
CA C:LEU273 4.7 4.1 1.0
N C:LEU273 4.7 2.6 1.0
CG C:ASN272 4.8 1.6 1.0
CD1 C:LEU273 4.8 11.2 1.0
CG C:PRO23 4.9 2.2 1.0

Calcium binding site 7 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:2.8
occ:1.00
 OE2 D:GLU21 2.3 6.1 1.0
OD1 D:ASN175 2.3 3.9 1.0
OD1 D:ASP229 2.4 2.4 1.0
ND2 D:ASN120 2.4 1.0 1.0
O D:HOH326 2.4 1.0 1.0
O D:HOH317 2.5 5.5 1.0
CD D:GLU21 3.3 4.7 1.0
CG D:ASN175 3.4 3.6 1.0
CG D:ASN120 3.5 4.5 1.0
CG D:ASP229 3.5 5.4 1.0
OE1 D:GLU21 3.8 3.3 1.0
ND2 D:ASN175 3.8 2.1 1.0
OD1 D:ASN120 3.8 6.0 1.0
OD2 D:ASP229 4.1 3.7 1.0
ND2 D:ASN272 4.4 3.3 1.0
OD2 D:ASP121 4.5 4.7 1.0
CG D:GLU21 4.5 5.1 1.0
O D:ASN120 4.6 1.8 1.0
N D:GLY230 4.6 3.9 1.0
O D:SER271 4.6 3.6 1.0
CB D:ASP121 4.6 2.5 1.0
CB D:ASN175 4.7 2.4 1.0
O D:ALA74 4.7 4.8 1.0
C D:ASP229 4.7 3.5 1.0
CB D:ASP229 4.8 5.1 1.0
CB D:ASN120 4.8 3.4 1.0
C D:ASN175 4.8 4.0 1.0
CG D:ASP121 4.9 3.8 1.0
CA D:ASP229 4.9 3.8 1.0
C D:ASN120 4.9 2.7 1.0
O D:ASN175 5.0 4.2 1.0

Calcium binding site 8 out of 8 in 3hlh

Go back to Calcium Binding Sites List in 3hlh
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:2.0
occ:1.00
 OD2 D:ASP232 2.2 3.6 1.0
O D:LEU273 2.3 3.0 1.0
O D:HOH329 2.3 4.2 1.0
O D:HOH318 2.4 2.2 1.0
O D:HOH321 2.4 1.0 1.0
ND1 D:HIS274 2.5 3.8 1.0
CG D:ASP232 3.2 5.0 1.0
CG D:HIS274 3.4 4.2 1.0
CE1 D:HIS274 3.4 4.5 1.0
C D:LEU273 3.5 4.6 1.0
CB D:HIS274 3.6 4.2 1.0
OD1 D:ASP232 3.7 4.5 1.0
CA D:HIS274 3.8 4.8 1.0
OD1 D:ASN272 3.9 4.8 1.0
O D:PRO23 4.1 4.3 1.0
N D:HIS274 4.1 4.6 1.0
O D:MET231 4.2 5.5 1.0
O D:HOH344 4.3 7.7 1.0
O D:HOH323 4.4 8.1 1.0
CB D:ASP232 4.5 4.2 1.0
O D:HOH331 4.6 3.3 1.0
NE2 D:HIS274 4.6 6.1 1.0
CD2 D:HIS274 4.6 5.9 1.0
CA D:LEU273 4.7 4.8 1.0
N D:LEU273 4.7 3.1 1.0
CG D:ASN272 4.8 4.8 1.0
CD1 D:LEU273 4.9 7.4 1.0
CG D:PRO23 4.9 3.2 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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy