Calcium in PDB 5w7d: Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant

All present enzymatic activity of Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant:
3.1.1.77;

The structure of Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant, PDB code: 5w7d was solved by A.Gorelik, K.Illes, B.Nagar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.70 / 1.75
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.527, 98.590, 73.488, 90.00, 99.68, 90.00
R / Rfree (%)	15.2 / 18.2

The binding sites of Calcium atom in the Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant (pdb code 5w7d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant, PDB code: 5w7d:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:12.9 occ:1.00 OD2 A:ASP204 2.3 11.1 1.0 O A:HIS189 2.3 12.0 1.0 OD1 A:ASP183 2.3 15.8 1.0 OD1 A:ASP207 2.3 18.6 1.0 OD1 A:ASP187 2.4 13.1 1.0 OD1 A:ASP185 2.4 17.9 1.0 CG A:ASP187 3.2 13.5 1.0 H A:ASP187 3.3 18.8 1.0 CG A:ASP185 3.3 18.3 1.0 H A:HIS189 3.3 13.5 1.0 HA A:ASP207 3.4 19.8 1.0 CG A:ASP204 3.4 12.4 1.0 CG A:ASP183 3.4 14.6 1.0 C A:HIS189 3.5 12.0 1.0 CG A:ASP207 3.5 18.3 1.0 OD2 A:ASP187 3.6 14.5 1.0 HB2 A:ASP204 3.6 14.0 1.0 HA A:ASP183 3.6 19.4 1.0 OD2 A:ASP185 3.6 16.0 1.0 H A:ASP185 3.7 24.3 1.0 HB2 A:HIS189 3.9 11.8 1.0 CB A:ASP204 4.0 11.7 1.0 N A:HIS189 4.0 11.3 1.0 CA A:CA602 4.1 14.8 1.0 N A:ASP187 4.1 15.7 1.0 HB3 A:ASP204 4.1 14.0 1.0 HA A:SER190 4.1 13.8 1.0 H A:SER186 4.2 21.1 1.0 CA A:HIS189 4.2 10.7 1.0 CA A:ASP207 4.2 16.5 1.0 OD2 A:ASP183 4.2 15.7 1.0 CA A:ASP183 4.3 16.2 1.0 CB A:ASP207 4.3 16.9 1.0 H A:LYS188 4.3 13.3 1.0 CB A:ASP183 4.3 14.4 1.0 N A:ASP185 4.4 20.2 1.0 HB2 A:ASP207 4.4 20.2 1.0 CB A:ASP187 4.4 13.9 1.0 OD2 A:ASP207 4.4 19.1 1.0 H A:VAL184 4.5 24.0 1.0 OD1 A:ASP204 4.5 13.2 1.0 N A:SER190 4.5 11.9 1.0 CB A:HIS189 4.5 9.9 1.0 N A:SER186 4.5 17.6 1.0 C A:ASP183 4.5 19.4 1.0 HB2 A:ASP183 4.6 17.2 1.0 N A:LYS188 4.6 11.1 1.0 CA A:ASP187 4.6 14.7 1.0 CB A:ASP185 4.6 19.5 1.0 N A:VAL184 4.7 20.0 1.0 O A:ASP207 4.7 20.0 1.0 C A:ASP187 4.8 12.9 1.0 HB3 A:ASP187 4.8 16.7 1.0 CA A:SER190 4.8 11.5 1.0 C A:ASP185 4.8 17.5 1.0 CA A:ASP185 4.8 19.1 1.0 C A:ASP207 4.9 19.2 1.0 HB3 A:HIS189 4.9 11.8 1.0

Calcium binding site 2 out of 3 in the Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:14.8 occ:1.00 OD2 A:ASP187 2.3 14.5 1.0 O A:VAL212 2.3 12.1 1.0 O A:ASN206 2.3 14.3 1.0 OD2 A:ASP185 2.4 16.0 1.0 OD2 A:ASP204 2.6 11.1 1.0 O A:ASP209 2.6 14.2 1.0 OD1 A:ASP204 2.6 13.2 1.0 CG A:ASP204 2.9 12.4 1.0 HA A:ASP207 3.3 19.8 1.0 CG A:ASP185 3.4 18.3 1.0 CG A:ASP187 3.4 13.5 1.0 C A:ASN206 3.4 14.2 1.0 H A:ASP209 3.5 22.6 1.0 C A:ASP209 3.5 16.7 1.0 C A:VAL212 3.5 13.1 1.0 HB A:VAL212 3.6 22.7 1.0 HA A:LYS210 3.7 22.1 1.0 H A:VAL212 3.7 22.7 1.0 HB3 A:TYR213 3.7 14.3 1.0 OD1 A:ASP185 3.8 17.9 1.0 OD1 A:ASP187 3.9 13.1 1.0 H A:ASN206 3.9 19.1 1.0 CA A:ASP207 4.0 16.5 1.0 CA A:CA601 4.1 12.9 1.0 N A:ASP207 4.1 15.6 1.0 HG12 A:VAL212 4.2 23.7 1.0 HB3 A:ASN206 4.2 21.7 1.0 N A:ASP209 4.2 18.8 1.0 CA A:VAL212 4.3 17.1 1.0 HB3 A:ASP209 4.3 26.5 1.0 CB A:VAL212 4.3 18.9 1.0 N A:VAL212 4.3 18.9 1.0 N A:LYS210 4.3 18.5 1.0 CA A:LYS210 4.4 18.4 1.0 HD2 A:TYR213 4.4 18.3 1.0 CB A:ASP204 4.4 11.7 1.0 CA A:ASP209 4.4 18.6 1.0 HB3 A:ASP187 4.5 16.7 1.0 CA A:ASN206 4.5 15.7 1.0 HA A:TYR213 4.5 13.0 1.0 N A:ASN206 4.5 15.9 1.0 CB A:ASP187 4.6 13.9 1.0 N A:TYR213 4.6 12.7 1.0 C A:ASP207 4.6 19.2 1.0 CB A:TYR213 4.6 11.9 1.0 CB A:ASP185 4.7 19.5 1.0 CG1 A:VAL212 4.7 19.7 1.0 C A:LYS210 4.8 16.9 1.0 HB2 A:ASP204 4.8 14.0 1.0 CA A:TYR213 4.8 10.8 1.0 HB2 A:ASP185 4.8 23.4 1.0 CB A:ASN206 4.8 18.1 1.0 HB3 A:ASP204 4.8 14.0 1.0 HB3 A:ASP185 4.9 23.4 1.0 HB2 A:HIS189 4.9 11.8 1.0 HB2 A:ASP187 4.9 16.7 1.0 CB A:ASP209 4.9 22.1 1.0 HA A:ASP204 4.9 15.8 1.0 N A:SER208 4.9 19.6 1.0 H A:ASP207 5.0 18.7 1.0 H A:SER208 5.0 23.5 1.0 OD1 A:ASP207 5.0 18.6 1.0

Calcium binding site 3 out of 3 in the Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Murine Acyloxyacyl Hydrolase (Aoah), S262A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:13.2 occ:1.00 OE2 A:GLU244 2.2 22.1 1.0 O A:ILE232 2.3 16.0 1.0 OD2 A:ASP222 2.3 19.4 1.0 OD2 A:ASP226 2.3 14.2 1.0 OD1 A:ASN228 2.4 14.6 1.0 OD1 A:ASN230 2.4 14.4 1.0 H A:ILE232 3.3 17.8 1.0 CG A:ASN230 3.3 14.4 1.0 CD A:GLU244 3.3 23.1 1.0 HD21 A:ASN230 3.4 19.3 1.0 HB A:ILE232 3.4 20.6 1.0 CG A:ASP222 3.4 19.2 1.0 C A:ILE232 3.4 17.3 1.0 H A:ASN228 3.5 18.8 1.0 CG A:ASN228 3.5 14.8 1.0 CG A:ASP226 3.5 15.2 1.0 HA A:ASP226 3.5 21.1 1.0 H A:ASN230 3.6 15.8 1.0 HD21 A:ASN228 3.7 18.2 1.0 ND2 A:ASN230 3.7 16.1 1.0 HB2 A:ASP222 3.8 22.3 1.0 N A:ILE232 3.9 14.9 1.0 HB3 A:ASP222 3.9 22.3 1.0 OE1 A:GLU244 3.9 25.0 1.0 CB A:ASP222 4.0 18.6 1.0 ND2 A:ASN228 4.0 15.2 1.0 CA A:ILE232 4.0 17.1 1.0 HB2 A:GLU244 4.1 24.4 1.0 HB3 A:TRP233 4.1 23.6 1.0 CB A:ILE232 4.2 17.1 1.0 CA A:ASP226 4.2 17.6 1.0 H A:SER227 4.2 21.3 1.0 N A:ASN228 4.3 15.7 1.0 CB A:ASP226 4.3 16.3 1.0 N A:ASN230 4.3 13.1 1.0 OD1 A:ASP226 4.4 15.8 1.0 HB3 A:PRO218 4.4 21.8 1.0 HG22 A:ILE232 4.5 21.8 1.0 OD1 A:ASP222 4.5 18.5 1.0 H A:CYS229 4.5 17.0 1.0 HB2 A:ASP226 4.5 19.6 1.0 C A:ASP226 4.5 19.8 1.0 CG A:GLU244 4.5 22.7 1.0 N A:SER227 4.5 17.8 1.0 HA A:TRP233 4.5 21.9 1.0 HD22 A:ASN230 4.5 19.3 1.0 N A:TRP233 4.5 18.1 1.0 H A:GLY231 4.6 15.2 1.0 CB A:ASN230 4.6 13.2 1.0 HG2 A:GLU244 4.7 27.2 1.0 CB A:ASN228 4.7 13.0 1.0 N A:CYS229 4.7 14.2 1.0 N A:GLY231 4.7 12.6 1.0 C A:ASN228 4.8 13.5 1.0 CA A:ASN230 4.8 12.9 1.0 CB A:GLU244 4.8 20.3 1.0 CA A:ASN228 4.8 13.8 1.0 HD22 A:ASN228 4.8 18.2 1.0 CA A:TRP233 4.9 18.2 1.0 HG A:SER227 4.9 24.5 1.0 CG2 A:ILE232 4.9 18.2 1.0 C A:ASN230 4.9 13.7 1.0 CB A:TRP233 4.9 19.7 1.0 C A:GLY231 4.9 16.6 1.0 HA A:ILE232 5.0 20.6 1.0 HB3 A:ASN230 5.0 15.8 1.0

A.Gorelik, K.Illes, B.Nagar. Crystal Structure of the Mammalian Lipopolysaccharide Detoxifier. Proc. Natl. Acad. Sci. V. 115 E896 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29343645
DOI: 10.1073/PNAS.1719834115