Calcium in PDB 6cmw: Crystal Structure of Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+

The structure of Crystal Structure of Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+, PDB code: 6cmw was solved by X.Zeng, D.Sui, J.Hu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.98 / 3.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.590, 88.590, 157.484, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 26

The binding sites of Calcium atom in the Crystal Structure of Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+ (pdb code 6cmw). 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 Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+, PDB code: 6cmw:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/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 Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:66.9 occ:1.00 O2G A:ATP501 2.4 76.3 1.0 O2A A:ATP501 2.5 57.3 1.0 OD2 A:ASP378 2.7 66.5 1.0 OG A:SER301 3.3 56.8 1.0 CG A:ASP378 3.4 63.0 1.0 PG A:ATP501 3.5 76.4 1.0 CB A:ASP378 3.5 57.8 1.0 NZ A:LYS238 3.6 53.5 1.0 O A:ASP299 3.6 0.2 1.0 O1G A:ATP501 3.6 79.7 1.0 PA A:ATP501 4.0 61.5 1.0 O3B A:ATP501 4.1 72.3 1.0 CE A:LYS238 4.4 52.8 1.0 OD1 A:ASP378 4.5 64.4 1.0 OD2 A:ASP236 4.5 79.1 1.0 CB A:SER301 4.6 57.8 1.0 C5' A:ATP501 4.6 62.8 1.0 OD1 A:ASP236 4.7 81.6 1.0 O1A A:ATP501 4.7 61.0 1.0 C A:ASP299 4.8 0.3 1.0 O3G A:ATP501 4.8 79.5 1.0 O5' A:ATP501 4.9 60.5 1.0 N A:SER301 4.9 59.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/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 Zebrafish Phosphatidylinositol-4-Phosphate 5- Kinase Alpha Isoform with Bound Atp/CA2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:75.5 occ:1.00 O1G A:ATP501 2.5 79.7 1.0 OD1 A:ASP378 2.5 64.4 1.0 O1B A:ATP501 2.6 68.5 1.0 OD2 A:ASP378 2.7 66.5 1.0 CG A:ASP378 3.0 63.0 1.0 PG A:ATP501 4.0 76.4 1.0 OE2 A:GLU177 4.0 78.1 1.0 PB A:ATP501 4.0 69.0 1.0 NZ A:LYS171 4.4 51.9 1.0 O3B A:ATP501 4.4 72.3 1.0 CB A:SER156 4.5 0.4 1.0 CB A:ASP378 4.5 57.8 1.0 O3G A:ATP501 4.8 79.5 1.0 O2G A:ATP501 4.9 76.3 1.0 O3A A:ATP501 4.9 62.6 1.0 O2A A:ATP501 5.0 57.3 1.0 CD A:GLU177 5.0 76.2 1.0

X.Zeng, A.Uyar, D.Sui, N.Donyapour, D.Wu, A.Dickson, J.Hu. Structural Insights Into Lethal Contractural Syndrome Type 3 (LCCS3) Caused By A Missense Mutation of PIP5K Gamma. Biochem. J. V. 475 2257 2018.
ISSN: ESSN 1470-8728
PubMed: 29959184
DOI: 10.1042/BCJ20180326