Manganese in PDB 5u7x: Crystal Structure of A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese

The structure of Crystal Structure of A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese, PDB code: 5u7x was solved by M.H.Cumming, E.L.Summers, T.Oulavallickal, N.Roberts, V.L.Arcus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.62 / 2.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	120.090, 71.110, 93.270, 90.00, 139.45, 90.00
R / Rfree (%)	16.8 / 24.8

The binding sites of Manganese atom in the Crystal Structure of A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese (pdb code 5u7x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Crystal Structure of A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese, PDB code: 5u7x:

Manganese binding site 1 out of 1 in the Crystal Structure of A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese


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 A Nucleoside Triphosphate Diphosphohydrolase (Ntpdase) From the Legume Vigna Unguiculata Subsp. Cylindrica (Dolichos Biflorus) in Complex with Phosphate and Manganese within 5.0Å range: probe atom residue distance (Å) B Occ F:Mn503 b:20.2 occ:1.00 O F:HOH609 2.0 16.1 1.0 O F:HOH621 2.1 22.9 1.0 O F:HOH625 2.2 5.3 1.0 O1 F:PO4502 2.2 21.5 1.0 O F:HOH663 2.3 15.9 1.0 O F:HOH668 2.3 13.2 1.0 P F:PO4502 3.6 21.9 1.0 O4 F:PO4502 4.0 22.8 1.0 NE1 F:TRP393 4.1 19.9 1.0 OE2 F:GLU131 4.1 20.0 1.0 OD2 F:ASP12 4.1 24.0 1.0 O3 F:PO4502 4.1 23.4 1.0 O F:HOH634 4.2 13.1 1.0 OD2 F:ASP158 4.2 20.5 1.0 OD1 F:ASP158 4.3 20.6 1.0 CD1 F:TRP393 4.4 20.8 1.0 CA F:GLY160 4.6 19.0 1.0 OG1 F:THR88 4.6 21.8 1.0 OD1 F:ASP12 4.6 20.9 1.0 O F:HOH717 4.6 33.8 1.0 CG F:ASP158 4.7 20.7 1.0 O2 F:PO4502 4.7 23.0 1.0 O F:HOH619 4.8 24.3 1.0 CG F:ASP12 4.8 22.5 1.0 OG F:SER299 4.9 21.8 1.0

E.L.Summers, M.H.Cumming, T.Oulavallickal, N.J.Roberts, V.L.Arcus. Structures and Kinetics For Plant Nucleoside Triphosphate Diphosphohydrolases Support A Domain Motion Catalytic Mechanism. Protein Sci. V. 26 1627 2017.
ISSN: ESSN 1469-896X
PubMed: 28543850
DOI: 10.1002/PRO.3199