Calcium in PDB 6pmp: Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1

All present enzymatic activity of Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1:
3.1.4.11;

The structure of Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1, PDB code: 6pmp was solved by N.Y.Rugema, A.M.Lyon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.73
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.572, 127.755, 139.337, 90.00, 101.12, 90.00
R / Rfree (%)	23.4 / 27.3

The binding sites of Calcium atom in the Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1 (pdb code 6pmp). 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 A Fragment of Rat Phospholipase Cepsilon EF3-RA1, PDB code: 6pmp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1


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 A Fragment of Rat Phospholipase Cepsilon EF3-RA1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2100 b:83.2 occ:1.00 ND2 A:ASN1389 2.4 41.7 1.0 OD2 A:ASP1420 2.8 51.7 1.0 OD1 A:ASN1389 2.9 42.7 1.0 OE2 A:GLU1467 3.0 47.6 1.0 CG A:ASN1389 3.0 42.0 1.0 OD1 A:ASP1420 3.3 50.1 1.0 CG A:ASP1420 3.4 50.9 1.0 CD A:GLU1467 3.7 47.6 1.0 OE2 A:GLU1418 3.8 47.7 1.0 OE1 A:GLU1467 3.8 48.5 1.0 CE1 A:HIS1388 4.1 41.7 1.0 OH A:TYR1391 4.2 46.4 1.0 CD A:GLU1418 4.2 45.5 1.0 CD2 A:HIS1433 4.5 58.2 1.0 OE1 A:GLU1418 4.5 45.5 1.0 CB A:ASN1389 4.5 41.7 1.0 NE2 A:HIS1433 4.5 57.5 1.0 ND1 A:HIS1388 4.8 41.0 1.0 NE2 A:HIS1388 4.8 41.9 1.0 CB A:ASP1420 4.9 50.5 1.0 CG A:GLU1467 4.9 46.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1


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 A Fragment of Rat Phospholipase Cepsilon EF3-RA1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca2100 b:0.9 occ:1.00 ND2 B:ASN1389 2.6 48.7 1.0 OE2 B:GLU1467 2.6 70.7 1.0 OD2 B:ASP1420 3.1 59.5 1.0 OE2 B:GLU1418 3.1 55.4 1.0 OD1 B:ASP1420 3.2 58.5 1.0 CD B:GLU1467 3.4 69.2 1.0 CG B:ASN1389 3.4 48.6 1.0 OD1 B:ASN1389 3.5 49.9 1.0 CG B:ASP1420 3.6 59.1 1.0 CD B:GLU1418 3.7 53.7 1.0 OE1 B:GLU1467 3.8 71.0 1.0 CE1 B:HIS1388 4.0 45.0 1.0 OE1 B:GLU1418 4.1 54.5 1.0 ND1 B:HIS1388 4.6 43.6 1.0 CG B:GLU1467 4.6 65.4 1.0 CG B:GLU1418 4.7 51.4 1.0 OH B:TYR1391 4.8 56.3 1.0 CB B:ASN1389 4.8 47.5 1.0 NE2 B:HIS1388 5.0 45.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1


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 A Fragment of Rat Phospholipase Cepsilon EF3-RA1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca2100 b:0.1 occ:1.00 OE1 C:GLU1467 2.4 72.1 1.0 ND2 C:ASN1389 2.6 49.8 1.0 OD2 C:ASP1420 2.9 57.7 1.0 OD1 C:ASN1389 3.3 49.6 1.0 OD1 C:ASP1420 3.3 57.7 1.0 CG C:ASN1389 3.3 48.7 1.0 CG C:ASP1420 3.5 57.7 1.0 CD C:GLU1467 3.5 72.1 1.0 OE2 C:GLU1418 3.6 57.0 1.0 OE2 C:GLU1467 4.0 76.8 1.0 CE1 C:HIS1388 4.1 45.1 1.0 CD C:GLU1418 4.1 56.0 1.0 OE1 C:GLU1418 4.4 54.5 1.0 OH C:TYR1391 4.5 53.2 1.0 CD2 C:HIS1433 4.7 59.6 1.0 NE2 C:HIS1433 4.7 59.9 1.0 ND1 C:HIS1388 4.8 44.0 1.0 CG C:GLU1467 4.8 68.3 1.0 CB C:ASN1389 4.8 48.0 1.0 NE2 C:HIS1388 5.0 45.2 1.0 CG C:GLU1418 5.0 55.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of A Fragment of Rat Phospholipase Cepsilon EF3-RA1


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 A Fragment of Rat Phospholipase Cepsilon EF3-RA1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca2100 b:0.3 occ:1.00 ND2 D:ASN1389 2.5 55.9 1.0 OE2 D:GLU1467 2.6 64.9 1.0 OE2 D:GLU1418 3.0 57.8 1.0 OD2 D:ASP1420 3.0 76.6 1.0 OD1 D:ASP1420 3.1 71.8 1.0 CD D:GLU1467 3.4 62.6 1.0 CG D:ASN1389 3.4 55.0 1.0 CG D:ASP1420 3.4 71.6 1.0 OD1 D:ASN1389 3.5 56.6 1.0 CD D:GLU1418 3.6 57.9 1.0 OE1 D:GLU1467 3.7 63.3 1.0 OE1 D:GLU1418 4.0 56.1 1.0 CE1 D:HIS1388 4.0 50.9 1.0 CG D:GLU1418 4.5 55.6 1.0 CG D:GLU1467 4.5 60.9 1.0 ND1 D:HIS1388 4.6 50.2 1.0 OH D:TYR1391 4.8 58.8 1.0 CB D:ASN1389 4.8 53.4 1.0 CB D:GLU1467 4.9 58.2 1.0 CB D:ASP1420 5.0 69.0 1.0 NE2 D:HIS1388 5.0 51.5 1.0

N.Y.Rugema, E.E.Garland-Kuntz, M.Sieng, K.Muralidharan, M.M.Van Camp, H.O'neill, W.Mbongo, A.F.Selvia, A.T.Marti, A.Everly, E.Mckenzie, A.M.Lyon. Structure of Phospholipase C Epsilon Reveals An Integrated RA1 Domain and Previously Unidentified Regulatory Elements. Commun Biol V. 3 445 2020.
ISSN: ESSN 2399-3642
PubMed: 32796910
DOI: 10.1038/S42003-020-01178-8