Manganese in PDB 5e3u: Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase

The structure of Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase, PDB code: 5e3u 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 / 3.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.134, 88.134, 155.757, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.1

The binding sites of Manganese atom in the Crystal Structure of Phosphatidylinositol-4-Phosphate 5-Kinase (pdb code 5e3u). 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: 5e3u:
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:97.0 occ:1.00 OD2 A:ASP378 1.9 80.7 1.0 O A:HOH602 1.9 39.9 1.0 O2G A:ANP501 2.0 89.5 1.0 OD1 A:ASP378 2.4 71.5 1.0 CG A:ASP378 2.4 74.0 1.0 O1B A:ANP501 2.5 71.8 1.0 OD2 A:ASP299 2.8 0.2 1.0 PG A:ANP501 3.3 85.8 1.0 MN A:MN503 3.4 0.3 1.0 O1G A:ANP501 3.6 97.8 1.0 CG A:ASP299 3.7 0.1 1.0 PB A:ANP501 3.7 83.4 1.0 OD1 A:ASP299 3.7 0.6 1.0 CB A:ASP378 3.9 72.6 1.0 N3B A:ANP501 3.9 81.5 1.0 CD A:GLN381 4.2 74.0 1.0 O3A A:ANP501 4.2 84.5 1.0 O3G A:ANP501 4.5 83.5 1.0 O2A A:ANP501 4.7 72.7 1.0 NZ A:LYS171 4.8 96.1 1.0 CA A:ASP378 4.9 71.2 1.0 CG A:GLN381 4.9 77.7 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:0.3 occ:1.00 O1G A:ANP501 1.7 97.8 1.0 O A:HOH601 1.8 22.4 1.0 OD2 A:ASP378 1.9 80.7 1.0 O2A A:ANP501 2.2 72.7 1.0 PG A:ANP501 2.7 85.8 1.0 CG A:ASP378 2.8 74.0 1.0 N3B A:ANP501 3.0 81.5 1.0 O2G A:ANP501 3.2 89.5 1.0 CB A:ASP378 3.2 72.6 1.0 MN A:MN502 3.4 97.0 1.0 OD2 A:ASP299 3.5 0.2 1.0 PA A:ANP501 3.5 75.6 1.0 O3A A:ANP501 3.8 84.5 1.0 PB A:ANP501 3.9 83.4 1.0 OD1 A:ASP378 3.9 71.5 1.0 O3G A:ANP501 4.0 83.5 1.0 OG A:SER301 4.0 54.4 1.0 O1B A:ANP501 4.0 71.8 1.0 O A:ASP299 4.1 81.6 1.0 NZ A:LYS238 4.2 85.7 1.0 O5' A:ANP501 4.4 72.6 1.0 O1A A:ANP501 4.5 76.5 1.0 CE A:LYS238 4.6 80.5 1.0 C5' A:ANP501 4.6 74.4 1.0 CG A:ASP299 4.6 0.1 1.0 CA A:ASP378 4.7 71.2 1.0 OD2 A:ASP236 5.0 65.8 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