Calcium in PDB 6iie: Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+

All present enzymatic activity of Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+:
2.7.1.107;

The structure of Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+, PDB code: 6iie was solved by D.Takahashi, K.Suzuki, T.Sakamoto, T.Iwamoto, T.Murata, F.Sakane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.88 / 2.14
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	58.190, 58.190, 61.120, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 23.8

The binding sites of Calcium atom in the Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+ (pdb code 6iie). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+, PDB code: 6iie:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+


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 Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:39.6 occ:1.00 OD1 A:ASP123 2.2 41.0 1.0 OD2 A:ASP125 2.3 42.7 1.0 O A:ILE129 2.3 42.5 1.0 OD1 A:ASN127 2.3 41.5 1.0 O A:HOH301 2.4 43.8 1.0 OE2 A:GLU134 2.6 41.9 1.0 OE1 A:GLU134 2.6 50.1 1.0 CD A:GLU134 2.9 45.5 1.0 CG A:ASN127 3.3 45.1 1.0 CG A:ASP125 3.4 42.5 1.0 CG A:ASP123 3.4 39.1 1.0 C A:ILE129 3.5 44.6 1.0 OD1 A:ASP125 3.8 50.4 1.0 ND2 A:ASN127 3.8 43.5 1.0 N A:ILE129 4.1 45.5 1.0 CA A:ASP123 4.2 37.7 1.0 OD2 A:ASP123 4.2 45.3 1.0 OD2 A:ASP131 4.2 77.7 1.0 N A:ASN127 4.2 50.0 1.0 CB A:ASP123 4.3 36.2 1.0 CG1 A:ILE129 4.3 55.0 1.0 N A:LEU130 4.4 39.2 1.0 CA A:LEU130 4.4 44.1 1.0 CA A:ILE129 4.4 44.2 1.0 N A:ASP131 4.4 40.6 1.0 CG A:GLU134 4.4 40.3 1.0 C A:ASP123 4.5 39.4 1.0 N A:ASP125 4.5 37.9 1.0 CB A:ASN127 4.5 43.4 1.0 CB A:ASP125 4.6 51.0 1.0 N A:ARG126 4.6 42.2 1.0 N A:GLY128 4.7 49.1 1.0 CA A:ASN127 4.7 51.5 1.0 N A:THR124 4.8 33.2 1.0 C A:ASN127 4.9 49.5 1.0 C A:ASP125 4.9 47.8 1.0 CA A:ASP125 4.9 47.3 1.0 CG A:ASP131 4.9 61.9 1.0 C A:LEU130 4.9 42.8 1.0 O A:ASP123 5.0 43.6 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+


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 Human Diacylglycerol Kinase Alpha Ef-Hand Domains Bound to CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:73.9 occ:1.00 OD2 A:ASP168 2.4 65.4 1.0 OD2 A:ASP170 2.4 0.6 1.0 O A:HOH309 2.5 74.8 1.0 OE2 A:GLU179 2.6 71.5 1.0 O A:SER174 2.6 61.2 1.0 OG A:SER172 2.8 72.9 1.0 OE1 A:GLU179 2.9 88.9 1.0 CD A:GLU179 3.0 75.0 1.0 CG A:ASP170 3.2 0.5 1.0 OD1 A:ASP170 3.3 0.4 1.0 CB A:SER172 3.5 88.0 1.0 CG A:ASP168 3.6 78.3 1.0 C A:SER174 3.7 56.0 1.0 N A:SER176 4.2 57.3 1.0 N A:SER172 4.2 0.8 1.0 OG A:SER174 4.3 68.9 1.0 CA A:VAL175 4.3 52.2 1.0 OD1 A:ASP168 4.4 70.5 1.0 N A:VAL175 4.4 49.2 1.0 CG A:GLU179 4.4 66.2 1.0 CA A:SER172 4.5 98.0 1.0 CA A:ASP168 4.5 65.7 1.0 N A:ASP170 4.5 84.9 1.0 CB A:ASP168 4.5 58.8 1.0 CB A:ASP170 4.5 95.0 1.0 C A:VAL175 4.7 48.3 1.0 N A:SER174 4.7 67.8 1.0 CA A:SER174 4.7 61.2 1.0 C A:ASP168 4.8 75.4 1.0 N A:TYR169 4.9 80.2 1.0 N A:GLY171 4.9 91.4 1.0 CB A:SER176 4.9 53.1 1.0 CA A:ASP170 4.9 91.4 1.0 OG A:SER176 4.9 55.2 1.0

D.Takahashi, K.Suzuki, T.Sakamoto, T.Iwamoto, T.Murata, F.Sakane. Crystal Structure and Calcium-Induced Conformational Changes of Diacylglycerol Kinase Alpha Ef-Hand Domains. Protein Sci. V. 28 694 2019.
ISSN: ESSN 1469-896X
PubMed: 30653270
DOI: 10.1002/PRO.3572