Calcium in PDB 7ym0: Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+

The structure of Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+, PDB code: 7ym0 was solved by Y.Yasutake, S.Sakasegawa, D.Sugimori, K.Murayama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.29 / 2.91
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	142.952, 142.952, 126.134, 90, 90, 90
R / Rfree (%)	17.7 / 21.5

The binding sites of Calcium atom in the Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+ (pdb code 7ym0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+, PDB code: 7ym0:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:123.0 occ:1.00 OD1 A:ASP75 1.9 130.3 1.0 OE2 A:GLU73 2.2 106.9 1.0 OE2 A:GLU175 2.4 117.7 1.0 CG A:ASP75 3.0 96.8 1.0 CD A:GLU73 3.3 92.9 1.0 OD2 A:ASP75 3.5 105.5 1.0 CD A:GLU175 3.5 92.1 1.0 OE1 A:GLU73 3.7 87.3 1.0 CB A:GLU175 4.0 69.3 1.0 OE1 A:GLU175 4.3 86.8 1.0 CB A:ASP75 4.3 80.2 1.0 CG A:GLU175 4.4 81.2 1.0 CD2 A:HIS88 4.4 68.9 1.0 NE2 A:HIS46 4.4 70.5 1.0 CE A:LYS177 4.4 70.2 1.0 O A:LEU74 4.4 73.1 1.0 NZ A:LYS177 4.5 66.0 1.0 CG A:GLU73 4.6 87.2 1.0 C A:LEU74 4.7 75.2 1.0 CA A:ASP75 5.0 76.9 1.0 CD2 A:HIS46 5.0 71.7 1.0 N A:ASP75 5.0 68.6 1.0 NE2 A:HIS88 5.0 68.7 1.0

Calcium binding site 2 out of 2 in the Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lysoplasmalogen-Specific Phospholipase D (Lypls-Pld) with CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:136.2 occ:1.00 OD2 B:ASP75 1.9 163.9 1.0 OE2 B:GLU73 2.4 92.8 1.0 OE2 B:GLU175 2.6 100.7 1.0 CG B:ASP75 2.9 111.8 1.0 OD1 B:ASP75 3.2 106.0 1.0 CD B:GLU73 3.2 83.0 1.0 OE1 B:GLU73 3.3 85.4 1.0 CD B:GLU175 3.8 87.7 1.0 NE2 B:HIS46 4.1 84.0 1.0 CB B:GLU175 4.2 69.3 1.0 CB B:ASP75 4.3 86.5 1.0 NZ B:LYS177 4.4 82.3 1.0 CD2 B:HIS88 4.4 71.3 1.0 O B:LEU74 4.5 85.6 1.0 CE1 B:HIS46 4.6 83.1 1.0 CG B:GLU175 4.6 73.1 1.0 CE B:LYS177 4.7 72.4 1.0 CG B:GLU73 4.7 79.9 1.0 OE1 B:GLU175 4.7 98.1 1.0 C B:LEU74 4.7 70.3 1.0 CD2 B:HIS46 4.7 79.8 1.0 N B:ASP75 4.8 78.7 1.0 CA B:ASP75 5.0 79.6 1.0

H.Hamana, Y.Yasutake, M.Kato-Murayama, T.Hosaka, M.Shirouzu, S.I.Sakasegawa, D.Sugimori, K.Murayama. Structural Basis For the Substrate Specificity Switching of Lysoplasmalogen-Specific Phospholipase D From Thermocrispum Sp. RD004668. Biosci.Biotechnol.Biochem. V. 87 74 2022.
ISSN: ISSN 0916-8451
PubMed: 36307380
DOI: 10.1093/BBB/ZBAC169