Manganese in PDB 5e3t: Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase

The structure of Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase, PDB code: 5e3t was solved by Y.Muftuoglu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.30
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	87.928, 87.928, 156.462, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 27.2

The binding sites of Manganese atom in the Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase (pdb code 5e3t). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase, PDB code: 5e3t:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn502 b:0.5 occ:1.00 OD2 A:ASP378 1.7 0.9 1.0 O1G A:ANP501 2.1 0.7 1.0 O1B A:ANP501 2.1 87.5 1.0 O A:HOH602 2.3 62.1 1.0 CG A:ASP378 2.3 92.0 1.0 OD1 A:ASP378 2.5 86.7 1.0 OD1 A:ASP299 3.0 0.2 1.0 OD2 A:ASP299 3.0 0.8 1.0 PG A:ANP501 3.2 0.8 1.0 PB A:ANP501 3.3 96.3 1.0 CG A:ASP299 3.3 0.3 1.0 MN A:MN503 3.6 95.5 1.0 O3G A:ANP501 3.6 0.6 1.0 N3B A:ANP501 3.7 92.6 1.0 CB A:ASP378 3.7 86.9 1.0 O3A A:ANP501 3.8 0.1 1.0 O2A A:ANP501 4.1 79.9 1.0 PA A:ANP501 4.5 89.8 1.0 O2G A:ANP501 4.5 0.8 1.0 O2B A:ANP501 4.6 93.5 1.0 CA A:ASP378 4.7 83.4 1.0 CB A:ASP299 4.8 0.0 1.0 NZ A:LYS171 4.9 87.0 1.0 O A:ASP299 5.0 0.6 1.0

Manganese binding site 2 out of 2 in the Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn503 b:95.5 occ:1.00 O3G A:ANP501 1.9 0.6 1.0 O A:HOH601 1.9 95.2 1.0 O2A A:ANP501 1.9 79.9 1.0 OD2 A:ASP378 2.2 0.9 1.0 PG A:ANP501 3.0 0.8 1.0 CG A:ASP378 3.1 92.0 1.0 N3B A:ANP501 3.3 92.6 1.0 OG A:SER301 3.3 73.5 1.0 OD1 A:ASP299 3.3 0.2 1.0 PA A:ANP501 3.4 89.8 1.0 CB A:ASP378 3.4 86.9 1.0 O1G A:ANP501 3.5 0.7 1.0 MN A:MN502 3.6 0.5 1.0 O A:ASP299 3.9 0.6 1.0 O3A A:ANP501 4.0 0.1 1.0 PB A:ANP501 4.1 96.3 1.0 NZ A:LYS238 4.2 0.4 1.0 O1A A:ANP501 4.3 85.5 1.0 OD1 A:ASP378 4.3 86.7 1.0 O1B A:ANP501 4.3 87.5 1.0 CE A:LYS238 4.3 95.8 1.0 O2G A:ANP501 4.3 0.8 1.0 OD2 A:ASP236 4.3 76.6 1.0 O5' A:ANP501 4.4 85.3 1.0 CG A:ASP299 4.4 0.3 1.0 C5' A:ANP501 4.5 88.7 1.0 CB A:SER301 4.6 75.2 1.0 OD2 A:ASP299 4.9 0.8 1.0 CA A:ASP378 4.9 83.4 1.0

Y.Muftuoglu, Y.Xue, X.Gao, D.Wu, Y.Ha. Mechanism of Substrate Specificity of Phosphatidylinositol Phosphate Kinases. Proc.Natl.Acad.Sci.Usa V. 113 8711 2016.
ISSN: ESSN 1091-6490
PubMed: 27439870
DOI: 10.1073/PNAS.1522112113