Magnesium in PDB 5o79: Klebsiella Pneumoniae OMPK36

The structure of Klebsiella Pneumoniae OMPK36, PDB code: 5o79 was solved by B.Van Den Berg, M.Pathania, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	107.57 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	232.316, 74.511, 90.814, 90.00, 112.18, 90.00
R / Rfree (%)	14.6 / 19

The binding sites of Magnesium atom in the Klebsiella Pneumoniae OMPK36 (pdb code 5o79). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Klebsiella Pneumoniae OMPK36, PDB code: 5o79:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Klebsiella Pneumoniae OMPK36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Klebsiella Pneumoniae OMPK36 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:34.6 occ:1.00 O A:ARG212 2.3 32.7 1.0 OD1 A:ASN252 2.3 28.7 1.0 OD1 A:ASN241 2.4 30.9 1.0 O A:HOH681 2.4 38.5 1.0 O A:HOH547 2.5 32.9 1.0 O A:HOH636 2.6 37.4 1.0 CG A:ASN252 3.2 29.6 1.0 CG A:ASN241 3.2 31.7 1.0 C A:ARG212 3.4 26.2 1.0 ND2 A:ASN241 3.4 44.7 1.0 CB A:ASN252 3.6 26.9 1.0 CA A:ASN252 3.9 27.6 1.0 N A:ARG212 4.0 27.8 1.0 ND2 A:ASN252 4.2 32.7 1.0 O A:ASN252 4.2 29.8 1.0 CA A:ARG212 4.3 29.1 1.0 N A:GLY213 4.3 30.2 1.0 CA A:GLY213 4.4 30.5 1.0 C A:ASN252 4.5 27.6 1.0 CB A:ASN241 4.7 28.9 1.0 CB A:ARG212 4.9 29.0 1.0

Magnesium binding site 2 out of 3 in the Klebsiella Pneumoniae OMPK36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Klebsiella Pneumoniae OMPK36 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:29.8 occ:1.00 O B:ARG212 2.3 28.9 1.0 O B:HOH684 2.4 35.9 1.0 O B:HOH656 2.4 31.4 1.0 OD1 B:ASN241 2.4 30.1 1.0 O B:HOH593 2.4 30.6 1.0 OD1 B:ASN252 2.5 24.5 1.0 CG B:ASN241 3.2 26.8 1.0 CG B:ASN252 3.3 26.8 1.0 ND2 B:ASN241 3.4 26.4 1.0 C B:ARG212 3.4 25.7 1.0 CB B:ASN252 3.6 25.5 1.0 CA B:ASN252 4.0 23.7 1.0 N B:ARG212 4.1 23.2 1.0 O B:ASN252 4.2 27.1 1.0 O B:HOH691 4.3 51.9 1.0 ND2 B:ASN252 4.3 26.0 1.0 N B:GLY213 4.3 28.3 1.0 CA B:ARG212 4.3 25.1 1.0 CA B:GLY213 4.4 27.5 1.0 C B:ASN252 4.5 25.1 1.0 CB B:ASN241 4.7 25.2 1.0 CB B:ARG212 4.9 26.6 1.0

Magnesium binding site 3 out of 3 in the Klebsiella Pneumoniae OMPK36


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Klebsiella Pneumoniae OMPK36 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:35.3 occ:1.00 O C:ARG212 2.3 29.2 1.0 O C:HOH706 2.3 42.8 1.0 OD1 C:ASN241 2.4 30.9 1.0 O C:HOH565 2.4 35.3 1.0 OD1 C:ASN252 2.5 28.9 1.0 O C:HOH672 2.5 42.1 1.0 CG C:ASN241 3.2 30.8 1.0 CG C:ASN252 3.2 31.2 1.0 ND2 C:ASN241 3.4 35.4 1.0 C C:ARG212 3.5 30.6 1.0 CB C:ASN252 3.6 27.9 1.0 CA C:ASN252 3.9 29.8 1.0 N C:ARG212 4.0 29.4 1.0 O C:ASN252 4.3 30.6 1.0 ND2 C:ASN252 4.3 32.3 1.0 CA C:ARG212 4.3 27.9 1.0 N C:GLY213 4.3 30.3 1.0 CA C:GLY213 4.4 30.5 1.0 C C:ASN252 4.5 28.7 1.0 CB C:ASN241 4.7 27.4 1.0 CB C:ARG212 5.0 30.7 1.0

S.Acosta-Gutierrez, L.Ferrara, M.Pathania, M.Masi, J.Wang, I.Bodrenko, M.Zahn, M.Winterhalter, R.A.Stavenger, J.M.Pages, J.H.Naismith, B.Van Den Berg, M.G.P.Page, M.Ceccarelli. Getting Drugs Into Gram-Negative Bacteria: Rational Rules For Permeation Through General Porins. Acs Infect Dis. V. 4 1487 2018.
ISSN: ESSN 2373-8227
PubMed: 29962203
DOI: 10.1021/ACSINFECDIS.8B00108