Atomistry » Magnesium » PDB 5n96-5nol » 5no9
Atomistry »
  Magnesium »
    PDB 5n96-5nol »
      5no9 »

Magnesium in PDB 5no9: Nlppya in Complex with Mannosamine

Protein crystallography data

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

Magnesium Binding Sites:

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 5no9

Go back to Magnesium Binding Sites List in 5no9
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 5no9

Go back to Magnesium Binding Sites List in 5no9
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 5no9

Go back to Magnesium Binding Sites List in 5no9
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 5no9

Go back to Magnesium Binding Sites List in 5no9
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

Reference:

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
Page generated: Sun Sep 29 23:22:55 2024

Last articles

Cl in 2V19
Cl in 2V1Q
Cl in 2V1P
Cl in 2UZC
Cl in 2V0Y
Cl in 2V0N
Cl in 2UXP
Cl in 2V08
Cl in 2V0D
Cl in 2V06
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy