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Calcium in PDB 5w7a: Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain)

Enzymatic activity of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain)

All present enzymatic activity of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain):
3.1.1.77;

Protein crystallography data

The structure of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain), PDB code: 5w7a 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) 34.69 / 2.30
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 89.578, 123.199, 125.918, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain) (pdb code 5w7a). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain), PDB code: 5w7a:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5w7a

Go back to Calcium Binding Sites List in 5w7a
Calcium binding site 1 out of 3 in the Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:17.0
occ:1.00
 OD1 B:ASP207 2.2 37.5 1.0
O B:TYR189 2.2 20.4 1.0
OD1 B:ASP183 2.3 30.4 1.0
OD1 B:ASP187 2.3 15.8 1.0
OD2 B:ASP204 2.3 18.2 1.0
OD1 B:ASP185 2.3 33.4 1.0
CG B:ASP187 3.1 30.5 1.0
H B:ASP187 3.2 35.5 1.0
CG B:ASP185 3.2 35.0 1.0
H B:TYR189 3.2 24.6 1.0
HA B:ASP207 3.2 48.4 1.0
OD2 B:ASP187 3.3 31.6 1.0
CG B:ASP207 3.3 38.5 1.0
C B:TYR189 3.4 19.6 1.0
CG B:ASP183 3.4 29.9 1.0
CG B:ASP204 3.4 19.5 1.0
OD2 B:ASP185 3.5 20.0 1.0
HB2 B:ASP204 3.6 25.0 1.0
HA B:ASP183 3.7 35.0 1.0
HB2 B:TYR189 3.7 24.4 1.0
H B:ASP185 3.9 40.1 1.0
N B:TYR189 3.9 20.5 1.0
CB B:ASP204 3.9 20.9 1.0
CA B:CA602 4.0 17.8 1.0
HB3 B:ASP204 4.0 25.0 1.0
N B:ASP187 4.1 29.6 1.0
CA B:ASP207 4.1 40.4 1.0
CA B:TYR189 4.1 19.9 1.0
HA B:SER190 4.1 25.6 1.0
CB B:ASP207 4.1 40.2 1.0
OD2 B:ASP183 4.1 29.6 1.0
H B:LYS188 4.2 29.4 1.0
HB2 B:ASP207 4.2 48.2 1.0
H B:SER186 4.2 40.2 1.0
OD2 B:ASP207 4.2 38.3 1.0
CB B:ASP187 4.3 27.2 1.0
CA B:ASP183 4.3 29.2 1.0
CB B:TYR189 4.3 20.4 1.0
CB B:ASP183 4.3 29.6 1.0
N B:SER190 4.4 19.2 1.0
OD1 B:ASP204 4.5 18.2 1.0
N B:SER186 4.5 33.5 1.0
N B:LYS188 4.5 24.5 1.0
N B:ASP185 4.5 33.4 1.0
HB2 B:ASP183 4.6 35.5 1.0
H B:VAL184 4.6 38.2 1.0
CA B:ASP187 4.6 26.2 1.0
C B:ASP183 4.6 28.3 1.0
CB B:ASP185 4.6 35.9 1.0
O B:ASP207 4.6 36.9 1.0
HB3 B:ASP187 4.7 32.6 1.0
C B:ASP187 4.8 23.8 1.0
HB3 B:TYR189 4.8 24.4 1.0
N B:VAL184 4.8 31.8 1.0
C B:ASP207 4.8 38.5 1.0
CA B:SER190 4.8 21.4 1.0
C B:ASP185 4.8 31.1 1.0
CA B:ASP185 4.9 33.9 1.0
O B:HOH702 4.9 36.8 1.0
C B:LYS188 5.0 21.7 1.0
HA B:TYR189 5.0 23.9 1.0

Calcium binding site 2 out of 3 in 5w7a

Go back to Calcium Binding Sites List in 5w7a
Calcium binding site 2 out of 3 in the Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:17.8
occ:1.00
 OD2 B:ASP187 2.3 31.6 1.0
O B:ASN206 2.3 52.0 1.0
O B:VAL212 2.3 26.6 1.0
OD2 B:ASP185 2.4 20.0 1.0
OD2 B:ASP204 2.5 18.2 1.0
O B:ASP209 2.5 30.3 1.0
OD1 B:ASP204 2.7 18.2 1.0
CG B:ASP204 2.9 19.5 1.0
HA B:ASP207 3.2 48.4 1.0
CG B:ASP185 3.4 35.0 1.0
C B:ASN206 3.4 50.6 1.0
H B:ASP209 3.4 44.0 1.0
CG B:ASP187 3.4 30.5 1.0
C B:VAL212 3.5 19.6 1.0
HB B:VAL212 3.6 27.1 1.0
C B:ASP209 3.6 33.4 1.0
H B:VAL212 3.7 26.3 1.0
OD1 B:ASP185 3.8 33.4 1.0
HB3 B:TYR213 3.8 19.6 1.0
HA B:LYS210 3.9 43.7 1.0
H B:ASN206 3.9 55.0 1.0
CA B:ASP207 4.0 40.4 1.0
CA B:CA601 4.0 17.0 1.0
OD1 B:ASP187 4.0 15.8 1.0
HB3 B:ASN206 4.1 75.6 1.0
N B:ASP207 4.1 45.5 1.0
N B:ASP209 4.2 36.7 1.0
CA B:VAL212 4.3 21.5 1.0
CB B:VAL212 4.3 22.6 1.0
HB3 B:ASP209 4.3 44.1 1.0
N B:VAL212 4.3 21.9 1.0
HA B:TYR213 4.4 20.7 1.0
HG12 B:VAL212 4.4 38.0 1.0
CA B:ASP209 4.4 36.6 1.0
CB B:ASP204 4.4 20.9 1.0
HB3 B:ASP187 4.4 32.6 1.0
N B:LYS210 4.4 35.4 1.0
CA B:ASN206 4.4 54.6 1.0
C B:ASP207 4.5 38.5 1.0
CA B:LYS210 4.5 36.5 1.0
CB B:ASP187 4.5 27.2 1.0
N B:TYR213 4.6 18.8 1.0
CB B:ASP185 4.6 35.9 1.0
N B:ASN206 4.6 45.9 1.0
HB2 B:ASP185 4.6 43.1 1.0
HD2 B:TYR213 4.6 27.6 1.0
CB B:TYR213 4.7 16.4 1.0
H B:SER208 4.7 46.2 1.0
HB2 B:ASP204 4.7 25.0 1.0
CB B:ASN206 4.7 63.0 1.0
CA B:TYR213 4.7 17.2 1.0
HB3 B:ASP185 4.7 43.1 1.0
N B:SER208 4.8 38.5 1.0
C B:LYS210 4.8 36.4 1.0
OD1 B:ASP207 4.8 37.5 1.0
HB2 B:TYR189 4.8 24.4 1.0
HB3 B:ASP204 4.8 25.0 1.0
HB2 B:ASP187 4.9 32.6 1.0
CG1 B:VAL212 4.9 31.7 1.0
H B:ASP207 4.9 54.6 1.0
CB B:ASP209 4.9 36.8 1.0

Calcium binding site 3 out of 3 in 5w7a

Go back to Calcium Binding Sites List in 5w7a
Calcium binding site 3 out of 3 in the Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Rabbit Acyloxyacyl Hydrolase (Aoah), Proteolytically Processed, S262A Mutant, with Lps (Low Quality Saposin Domain) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:28.4
occ:1.00
 OD2 B:ASP226 2.1 27.1 1.0
OE2 B:GLU244 2.3 39.4 1.0
O B:ILE232 2.3 38.3 1.0
OD2 B:ASP222 2.4 34.5 1.0
OD1 B:ASN228 2.5 24.6 1.0
OD1 B:ASN230 2.5 26.8 1.0
CG B:ASP226 3.3 34.9 1.0
CG B:ASP222 3.4 36.4 1.0
H B:ILE232 3.4 44.5 1.0
CD B:GLU244 3.4 39.6 1.0
CG B:ASN228 3.4 32.8 1.0
HA B:ASP226 3.4 38.4 1.0
CG B:ASN230 3.5 25.6 1.0
HD21 B:ASN228 3.5 30.2 1.0
C B:ILE232 3.5 40.2 1.0
H B:ASN228 3.5 31.9 1.0
HB B:ILE232 3.6 48.6 1.0
H B:ASN230 3.6 27.0 1.0
HD21 B:ASN230 3.6 31.5 1.0
HB2 B:ASP222 3.7 46.5 1.0
HB3 B:ASP222 3.8 46.5 1.0
ND2 B:ASN228 3.8 25.2 1.0
CB B:ASP222 3.9 38.8 1.0
ND2 B:ASN230 3.9 26.2 1.0
OE1 B:GLU244 3.9 37.7 1.0
HB3 B:TRP233 3.9 51.3 1.0
H B:SER227 3.9 35.8 1.0
N B:ILE232 4.0 37.1 1.0
OD1 B:ASP226 4.1 25.9 1.0
CA B:ILE232 4.1 40.1 1.0
HB2 B:GLU244 4.2 53.0 1.0
CA B:ASP226 4.2 32.0 1.0
CB B:ASP226 4.3 28.4 1.0
H B:CYS229 4.3 34.0 1.0
CB B:ILE232 4.3 40.5 1.0
OD1 B:ASP222 4.4 36.6 1.0
N B:ASN230 4.4 22.5 1.0
N B:ASN228 4.4 26.6 1.0
H B:GLY231 4.4 31.2 1.0
N B:SER227 4.5 29.8 1.0
HB2 B:ASP226 4.5 34.0 1.0
HA B:TRP233 4.5 52.3 1.0
N B:TRP233 4.6 42.5 1.0
HG3 B:PRO218 4.6 79.4 1.0
HB3 B:PRO218 4.6 38.9 1.0
N B:CYS229 4.6 28.3 1.0
CG B:GLU244 4.7 42.4 1.0
HD22 B:ASN228 4.7 30.2 1.0
CB B:ASN230 4.7 23.6 1.0
C B:ASP226 4.7 30.8 1.0
HD22 B:ASN230 4.7 31.5 1.0
N B:GLY231 4.7 26.0 1.0
CB B:ASN228 4.7 29.8 1.0
HG22 B:ILE232 4.7 43.6 1.0
CB B:TRP233 4.8 42.8 1.0
CA B:TRP233 4.9 43.6 1.0
CB B:GLU244 4.9 44.1 1.0
CA B:ASN230 4.9 23.2 1.0
CA B:ASN228 4.9 21.6 1.0
C B:ASN228 4.9 20.8 1.0
HG B:SER227 4.9 33.1 1.0
C B:ASN230 4.9 30.0 1.0
HB3 B:ASN230 5.0 28.4 1.0

Reference:

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
Page generated: Mon Jul 15 13:03:43 2024

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