Magnesium in PDB 5nnw: Nlppya in Complex with Glucosamine

The structure of Nlppya in Complex with Glucosamine, PDB code: 5nnw was solved by M.Podobnik, G.Anderluh, T.Lenarcic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.62 / 1.54
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	114.996, 122.285, 121.099, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 19.4

The binding sites of Magnesium atom in the Nlppya in Complex with Glucosamine (pdb code 5nnw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Nlppya in Complex with Glucosamine, PDB code: 5nnw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Nlppya in Complex with Glucosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Nlppya in Complex with Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:19.1 occ:0.95 O A:HOH440 2.0 31.2 1.0 OE2 A:GLU106 2.0 25.8 1.0 O A:HIS159 2.1 24.5 1.0 OD2 A:ASP93 2.2 24.1 1.0 OD2 A:ASP104 2.3 15.7 1.0 OD1 A:ASP104 2.3 15.8 1.0 CG A:ASP104 2.6 15.9 1.0 CG A:ASP93 3.2 21.9 1.0 CD A:GLU106 3.3 23.0 1.0 C A:HIS159 3.3 23.6 1.0 CG A:GLU106 4.0 20.1 1.0 OD1 A:ASP93 4.0 19.5 1.0 CA A:HIS159 4.1 21.4 1.0 CB A:ASP93 4.1 16.9 1.0 N A:HIS159 4.1 21.5 1.0 CB A:ASP104 4.1 13.6 1.0 OE1 A:GLU106 4.2 22.6 1.0 O A:HOH432 4.2 34.9 1.0 CB A:HIS159 4.3 20.9 1.0 N A:GLU160 4.3 20.1 1.0 CB A:ASP158 4.4 29.3 1.0 CA A:GLU160 4.5 21.0 1.0 OH A:TYR151 4.5 16.0 1.0 CE1 A:TYR151 4.6 15.5 1.0 C A:ASP158 4.7 27.1 1.0 CA A:ASP104 5.0 14.2 1.0

Magnesium binding site 2 out of 4 in the Nlppya in Complex with Glucosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Nlppya in Complex with Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:26.6 occ:0.95 O B:HOH445 2.1 51.1 1.0 OE2 B:GLU106 2.1 28.5 0.8 O B:HIS159 2.1 31.1 1.0 OD2 B:ASP93 2.3 28.5 0.8 OD2 B:ASP104 2.4 22.2 1.0 OD1 B:ASP104 2.4 21.4 1.0 CG B:ASP104 2.7 21.1 1.0 CD B:GLU106 3.3 27.9 1.0 C B:HIS159 3.3 32.7 1.0 CG B:ASP93 3.3 24.7 1.0 CG B:GLU106 4.0 27.1 1.0 CA B:HIS159 4.1 29.6 1.0 CB B:ASP93 4.1 22.3 1.0 N B:HIS159 4.1 29.3 1.0 OD1 B:ASP93 4.2 27.2 0.8 CB B:HIS159 4.2 25.9 1.0 CB B:ASP104 4.2 18.4 1.0 O B:HOH441 4.2 36.8 1.0 OE1 B:GLU106 4.3 28.6 0.9 N B:GLU160 4.4 27.9 1.0 CE1 B:TYR151 4.5 18.7 1.0 OH B:TYR151 4.5 21.4 1.0 CA B:GLU160 4.6 28.8 1.0 CB B:ASP158 4.7 41.5 1.0 C B:ASP158 4.9 38.1 1.0 CZ B:TYR151 4.9 19.9 1.0

Magnesium binding site 3 out of 4 in the Nlppya in Complex with Glucosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Nlppya in Complex with Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:27.5 occ:0.90 OE2 C:GLU106 2.2 28.2 1.0 OD2 C:ASP104 2.4 18.2 1.0 OD2 C:ASP93 2.4 32.9 1.0 O C:HOH402 2.5 35.1 1.0 OD1 C:ASP104 2.7 22.8 1.0 O C:HIS159 2.7 34.2 1.0 O C:HOH408 2.8 51.4 1.0 CG C:ASP104 2.9 19.9 1.0 CG C:ASP93 3.4 23.5 1.0 CD C:GLU106 3.4 25.1 1.0 C C:HIS159 3.4 31.1 1.0 CB C:HIS159 3.9 27.1 1.0 O C:HOH451 3.9 31.2 1.0 CA C:HIS159 4.0 29.1 1.0 OD1 C:ASP93 4.1 24.6 1.0 N C:HIS159 4.1 28.4 1.0 CG C:GLU106 4.1 22.3 1.0 CB C:ASP93 4.2 22.6 1.0 OE1 C:GLU106 4.3 25.9 1.0 OH C:TYR151 4.3 20.2 1.0 N C:GLU160 4.3 26.4 1.0 OD1 C:ASP158 4.3 34.4 0.2 CB C:ASP104 4.4 17.2 1.0 CE1 C:TYR151 4.4 18.0 1.0 O C:HOH407 4.4 39.3 1.0 CA C:GLU160 4.6 23.2 1.0 CZ C:TYR151 4.8 18.8 1.0

Magnesium binding site 4 out of 4 in the Nlppya in Complex with Glucosamine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Nlppya in Complex with Glucosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:21.2 occ:0.90 O D:HOH401 1.9 20.7 1.0 O D:HOH403 1.9 26.4 1.0 OE2 D:GLU106 2.0 20.8 1.0 O D:HOH407 2.1 22.9 1.0 O D:HOH417 2.1 26.8 1.0 O D:HIS159 2.2 26.0 1.0 CD D:GLU106 3.0 22.4 1.0 C D:HIS159 3.2 23.6 1.0 OE1 D:GLU106 3.4 22.6 1.0 OD1 D:ASP104 3.9 20.0 1.0 CA D:GLU160 4.0 24.0 1.0 N D:GLU160 4.0 20.0 1.0 OD1 D:ASP158 4.0 34.9 0.3 OD2 D:ASP93 4.0 34.5 1.0 OD2 D:ASP104 4.0 17.6 1.0 O1 D:GCS302 4.1 51.7 0.7 O D:HOH554 4.2 43.3 1.0 CA D:HIS159 4.3 23.3 1.0 CG D:GLU106 4.3 17.7 1.0 OD2 D:ASP158 4.4 34.3 0.7 CG D:ASP104 4.4 18.6 1.0 N D:HIS159 4.5 23.8 1.0 CG D:ASP158 4.5 30.8 0.7 O D:ALA127 4.6 28.9 1.0 OD1 D:ASP158 4.6 34.9 0.7 CB D:HIS159 4.6 23.3 1.0 C1 D:GCS302 4.6 53.5 0.7 CG D:GLU160 4.7 27.8 1.0 CG D:ASP93 4.9 23.1 1.0 CB D:GLU160 4.9 23.8 1.0 C D:ALA127 4.9 25.0 1.0

T.Lenarcic, I.Albert, H.Bohm, V.Hodnik, K.Pirc, A.B.Zavec, M.Podobnik, D.Pahovnik, E.Zagar, R.Pruitt, P.Greimel, A.Yamaji-Hasegawa, T.Kobayashi, A.Zienkiewicz, J.Gomann, J.C.Mortimer, L.Fang, A.Mamode-Cassim, M.Deleu, L.Lins, C.Oecking, I.Feussner, S.Mongrand, G.Anderluh, T.Nurnberger. Eudicot Plant-Specific Sphingolipids Determine Host Selectivity of Microbial Nlp Cytolysins. Science V. 358 1431 2017.
ISSN: ESSN 1095-9203
PubMed: 29242345
DOI: 10.1126/SCIENCE.AAN6874