Magnesium in PDB 5no9: Nlppya in Complex with Mannosamine

The structure of Nlppya in Complex with Mannosamine, PDB code: 5no9 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)	36.59 / 1.75
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	115.026, 122.284, 121.138, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.3

The binding sites of Magnesium atom in the Nlppya in Complex with Mannosamine (pdb code 5no9). 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 Mannosamine, PDB code: 5no9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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


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 Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:35.8 occ:1.00 O A:HOH450 2.1 48.2 1.0 O A:HIS159 2.1 35.2 1.0 OE2 A:GLU106 2.2 36.0 1.0 OD2 A:ASP93 2.2 35.7 1.0 OD1 A:ASP104 2.5 22.1 1.0 OD2 A:ASP104 2.5 21.1 1.0 CG A:ASP104 2.9 21.5 1.0 CG A:ASP93 3.3 30.9 1.0 C A:HIS159 3.3 32.2 1.0 CD A:GLU106 3.4 34.6 1.0 CA A:HIS159 4.0 32.4 1.0 N A:HIS159 4.1 33.4 1.0 CG A:GLU106 4.1 30.1 1.0 OD1 A:ASP93 4.1 32.4 1.0 CB A:ASP93 4.1 26.7 1.0 CB A:HIS159 4.1 28.3 1.0 OE1 A:GLU106 4.3 32.6 1.0 N A:GLU160 4.3 29.1 1.0 CB A:ASP104 4.4 18.4 1.0 OH A:TYR151 4.5 23.2 1.0 CE1 A:TYR151 4.6 20.3 1.0 CB A:ASP158 4.6 49.3 1.0 CA A:GLU160 4.6 30.8 1.0 C A:ASP158 4.7 44.0 1.0

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


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 Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:25.4 occ:1.00 O B:HOH441 2.0 33.5 1.0 O B:HIS159 2.1 29.5 1.0 OE2 B:GLU106 2.1 31.8 1.0 OD2 B:ASP93 2.2 27.9 1.0 OD2 B:ASP104 2.3 19.0 1.0 OD1 B:ASP104 2.4 19.2 1.0 CG B:ASP104 2.7 18.6 1.0 C B:HIS159 3.3 28.1 1.0 CD B:GLU106 3.3 26.4 1.0 CG B:ASP93 3.3 28.0 1.0 CG B:GLU106 4.0 22.8 1.0 CA B:HIS159 4.1 26.2 1.0 OD1 B:ASP93 4.1 26.4 1.0 N B:HIS159 4.1 26.0 1.0 CB B:ASP93 4.1 21.3 1.0 CB B:ASP104 4.2 16.4 1.0 CB B:HIS159 4.2 24.3 1.0 OE1 B:GLU106 4.2 26.6 1.0 N B:GLU160 4.3 25.6 1.0 O B:HOH485 4.3 34.4 1.0 CB B:ASP158 4.4 35.6 1.0 CA B:GLU160 4.5 26.1 1.0 OH B:TYR151 4.5 20.2 1.0 CE1 B:TYR151 4.6 20.4 1.0 C B:ASP158 4.6 31.1 1.0

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


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 Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg301 b:38.6 occ:1.00 OE2 C:GLU106 2.2 30.8 1.0 O C:HOH404 2.4 42.5 1.0 OD2 C:ASP93 2.4 33.2 1.0 O C:HIS159 2.5 35.0 1.0 OD2 C:ASP104 2.7 24.9 1.0 OD1 C:ASP104 2.9 25.8 1.0 CG C:ASP104 3.2 24.8 1.0 C C:HIS159 3.3 34.0 1.0 CG C:ASP93 3.3 28.4 1.0 CD C:GLU106 3.4 27.2 1.0 O C:HOH425 3.8 37.0 1.0 CA C:HIS159 3.9 30.1 1.0 OD1 C:ASP93 4.0 30.1 1.0 CB C:HIS159 4.0 27.0 1.0 N C:HIS159 4.0 31.7 1.0 OE1 C:GLU106 4.2 27.5 1.0 N C:GLU160 4.2 26.8 1.0 CB C:ASP93 4.3 24.8 1.0 O C:HOH434 4.4 39.7 1.0 CG C:GLU106 4.4 24.7 1.0 CA C:GLU160 4.5 26.6 1.0 OH C:TYR151 4.6 21.9 1.0 CE1 C:TYR151 4.6 20.9 1.0 CB C:ASP104 4.7 21.7 1.0 CG C:ASP158 4.7 42.3 1.0 OD1 C:ASP158 4.8 44.6 1.0 C C:ASP158 4.9 32.8 1.0 OD2 C:ASP158 5.0 46.2 1.0

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


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 Mannosamine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg301 b:29.6 occ:1.00 O D:HOH404 1.9 24.4 1.0 O D:HOH401 2.0 24.7 1.0 OE2 D:GLU106 2.0 24.5 1.0 O D:HOH407 2.0 32.0 1.0 O D:HOH405 2.1 23.8 1.0 O D:HIS159 2.2 29.0 1.0 CD D:GLU106 3.0 23.6 1.0 C D:HIS159 3.3 28.7 1.0 O1 D:95Z302 3.3 70.3 0.9 OE1 D:GLU106 3.4 22.8 1.0 CA D:GLU160 3.7 25.8 1.0 OD2 D:ASP158 3.8 35.5 0.6 N D:GLU160 3.9 23.7 1.0 OD1 D:ASP104 3.9 25.0 1.0 OD2 D:ASP93 4.0 38.5 1.0 OD2 D:ASP104 4.1 18.6 1.0 CB D:GLU160 4.1 27.2 1.0 CG D:GLU106 4.3 20.7 1.0 CA D:HIS159 4.3 27.6 1.0 CG D:ASP104 4.5 22.5 1.0 O D:ALA127 4.5 30.1 1.0 OD1 D:ASP158 4.5 35.5 0.4 CG D:ASP158 4.5 32.5 0.6 N D:HIS159 4.6 27.5 1.0 C1 D:95Z302 4.6 70.4 0.9 CB D:HIS159 4.7 27.4 1.0 N2 D:95Z302 4.9 70.6 0.9 C D:ALA127 4.9 28.2 1.0 CG D:ASP93 4.9 28.6 1.0 C D:GLU160 5.0 22.1 1.0 OD1 D:ASP158 5.0 39.4 0.6

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