Calcium in PDB 1n28: Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2

All present enzymatic activity of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2:
3.1.1.4;

The structure of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2, PDB code: 1n28 was solved by S.H.Edwards, D.Thompson, S.F.Baker, S.P.Wood, D.C.Wilton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.580, 34.420, 73.900, 90.00, 126.56, 90.00
R / Rfree (%)	18.4 / 20.7

The binding sites of Calcium atom in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2 (pdb code 1n28). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2, PDB code: 1n28:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca125 b:24.8 occ:1.00 O B:HIS27 2.2 17.2 1.0 O B:GLY31 2.3 24.0 1.0 O B:GLY29 2.4 22.2 1.0 O B:HOH161 2.5 27.6 1.0 OD2 B:ASP48 2.5 25.0 1.0 OD1 B:ASP48 2.8 26.9 1.0 CG B:ASP48 3.0 22.4 1.0 C B:HIS27 3.4 18.4 1.0 C B:GLY31 3.5 21.3 1.0 C B:GLY29 3.6 20.0 1.0 N B:GLY31 3.8 21.0 1.0 N B:GLY29 4.0 20.0 1.0 C B:CYS28 4.1 19.9 1.0 O B:HOH160 4.1 30.1 1.0 CA B:CYS28 4.1 18.7 1.0 O B:HOH159 4.1 32.6 1.0 C B:VAL30 4.2 20.8 1.0 CA B:GLY31 4.2 20.6 1.0 N B:CYS28 4.3 18.8 1.0 CA B:HIS27 4.4 17.2 1.0 O B:HOH169 4.4 27.3 1.0 CA B:GLY29 4.5 20.8 1.0 N B:VAL30 4.5 21.1 1.0 CA B:VAL30 4.5 20.8 1.0 CB B:ASP48 4.5 21.2 1.0 O B:CYS28 4.6 21.0 1.0 N B:GLY32 4.6 22.1 1.0 O B:CYS44 4.7 15.8 1.0 O B:HOH162 4.7 25.6 1.0 CA B:GLY32 4.8 22.0 1.0 O B:VAL30 4.8 23.9 1.0 CB B:HIS27 5.0 17.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca127 b:27.7 occ:1.00 O B:GLY25 2.2 16.8 1.0 O B:TYR112 2.2 25.4 1.0 O B:HOH171 2.4 21.8 1.0 O B:PHE23 2.6 22.8 1.0 OD1 B:ASN114 2.9 29.0 1.0 C B:TYR112 3.4 25.1 1.0 C B:GLY25 3.4 16.4 1.0 C B:PHE23 3.5 21.2 1.0 CG B:ASN114 3.9 30.8 1.0 CB B:TYR112 4.1 25.8 1.0 O B:TYR24 4.1 18.8 1.0 C B:TYR24 4.1 18.7 1.0 CA B:PHE23 4.1 21.9 1.0 CA B:TYR112 4.2 25.3 1.0 N B:GLY25 4.2 17.9 1.0 N B:ASN114 4.3 28.9 1.0 N B:TYR112 4.3 24.0 1.0 N B:CYS26 4.3 16.5 1.0 CA B:GLY25 4.3 16.9 1.0 CA B:CYS26 4.4 18.8 1.0 CB B:PHE23 4.4 23.4 1.0 C B:SER113 4.4 27.8 1.0 N B:SER113 4.5 26.2 1.0 N B:TYR24 4.5 19.8 1.0 O B:HOH134 4.5 38.8 1.0 ND2 B:ASN114 4.6 33.5 1.0 CA B:SER113 4.6 27.3 1.0 CD2 B:TYR112 4.7 26.7 1.0 C B:CYS26 4.8 17.9 1.0 CA B:TYR24 4.8 19.0 1.0 O B:HOH169 4.8 27.3 1.0 CG B:TYR112 4.9 26.3 1.0 O B:CYS28 5.0 21.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca126 b:27.0 occ:1.00 O A:HIS27 2.2 17.5 1.0 OD2 A:ASP48 2.2 28.8 1.0 O A:GLY29 2.4 22.5 1.0 O A:GLY31 2.5 28.3 1.0 O A:HOH140 2.5 22.8 1.0 OD1 A:ASP48 2.9 30.3 1.0 CG A:ASP48 2.9 27.1 1.0 C A:HIS27 3.4 18.9 1.0 C A:GLY29 3.5 22.1 1.0 C A:GLY31 3.5 28.9 1.0 N A:GLY31 3.7 29.1 1.0 N A:GLY29 4.0 19.3 1.0 C A:CYS28 4.1 19.2 1.0 C A:VAL30 4.1 27.7 1.0 CA A:GLY31 4.1 29.4 1.0 CA A:CYS28 4.2 19.1 1.0 O A:HOH167 4.2 25.7 1.0 CB A:ASP48 4.4 22.6 1.0 N A:CYS28 4.4 18.4 1.0 N A:VAL30 4.4 23.7 1.0 CA A:HIS27 4.4 19.2 1.0 CA A:VAL30 4.4 26.4 1.0 CA A:GLY29 4.4 19.6 1.0 O A:CYS28 4.5 20.1 1.0 O A:HOH148 4.5 23.8 1.0 O A:CYS44 4.6 18.5 1.0 N A:GLY32 4.6 28.9 1.0 O A:HOH131 4.8 30.2 1.0 O A:VAL30 4.8 29.7 1.0 CB A:HIS27 4.9 21.4 1.0 CB A:CYS44 4.9 16.5 1.0 CA A:GLY32 4.9 28.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the H48Q Mutant of Human Group Iia Phospholipase A2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca128 b:82.0 occ:1.00 O A:GLY25 2.1 18.2 1.0 O A:TYR112 2.3 20.9 1.0 O A:HOH165 2.4 22.4 1.0 O A:PHE23 2.5 19.1 1.0 O A:HOH166 2.6 22.1 1.0 ND2 A:ASN114 2.6 24.2 1.0 C A:GLY25 3.3 18.6 1.0 C A:PHE23 3.4 17.5 1.0 C A:TYR112 3.4 23.0 1.0 CG A:ASN114 3.9 27.9 1.0 O A:TYR24 3.9 17.5 1.0 C A:TYR24 3.9 17.6 1.0 CB A:TYR112 4.0 23.9 1.0 N A:GLY25 4.0 17.1 1.0 CA A:TYR112 4.1 22.8 1.0 CA A:PHE23 4.1 17.4 1.0 CA A:GLY25 4.2 18.1 1.0 N A:TYR112 4.2 22.5 1.0 N A:CYS26 4.2 18.5 1.0 N A:ASN114 4.3 24.6 1.0 N A:TYR24 4.3 17.4 1.0 O A:HOH131 4.4 30.2 1.0 CA A:CYS26 4.4 20.4 1.0 OD1 A:ASN114 4.4 29.4 1.0 N A:SER113 4.5 22.1 1.0 CB A:PHE23 4.5 17.7 1.0 CA A:TYR24 4.6 15.8 1.0 C A:SER113 4.7 24.5 1.0 CA A:SER113 4.7 24.4 1.0 C A:CYS26 4.8 18.1 1.0 CA A:ASN114 4.8 25.4 1.0 CD2 A:TYR112 4.9 28.0 1.0 CG A:TYR112 4.9 26.8 1.0 CB A:ASN114 5.0 26.3 1.0

S.H.Edwards, D.Thompson, S.F.Baker, S.P.Wood, D.C.Wilton. The Crystal Structure of the H48Q Active Site Mutant of Human Group Iia Secreted Phospholipase A2 at 1.5 A Resolution Provides An Insight Into the Catalytic Mechanism Biochemistry V. 41 15468 2002.
ISSN: ISSN 0006-2960
PubMed: 12501175
DOI: 10.1021/BI020485Z