Sodium in PDB 5mdq: Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi

The structure of Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi, PDB code: 5mdq was solved by M.Zahn, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	128.39 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	255.730, 148.639, 54.364, 90.00, 94.94, 90.00
R / Rfree (%)	23 / 24.1

The binding sites of Sodium atom in the Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi (pdb code 5mdq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi, PDB code: 5mdq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.0 occ:1.00 O A:HOH505 2.3 22.6 1.0 OD1 A:ASP174 2.4 31.8 1.0 O A:HOH511 2.4 48.7 1.0 OD2 A:ASP174 2.4 33.3 1.0 OE1 A:GLN146 2.4 37.4 1.0 OE1 A:GLN149 2.5 25.7 1.0 CG A:ASP174 2.8 32.5 1.0 CD A:GLN149 3.6 26.0 1.0 CD A:GLN146 3.6 34.6 1.0 NE2 A:GLN149 4.1 26.3 1.0 CB A:GLN146 4.3 33.4 1.0 CB A:ASP174 4.4 33.5 1.0 CG A:GLN146 4.4 33.8 1.0 O A:ARG148 4.4 27.7 1.0 CA A:GLN146 4.5 34.1 1.0 NE2 A:GLN146 4.6 35.3 1.0 OD1 A:ASP147 4.7 32.0 1.0 N A:ASP147 4.7 33.6 1.0 CG A:GLN149 4.9 26.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:26.9 occ:1.00 OE1 B:GLN146 2.4 38.4 1.0 OD2 B:ASP174 2.5 36.6 1.0 OD1 B:ASP174 2.5 35.7 1.0 O B:HOH505 2.5 47.3 1.0 OE1 B:GLN149 2.5 32.0 1.0 CG B:ASP174 2.9 35.7 1.0 CD B:GLN146 3.6 35.3 1.0 CD B:GLN149 3.7 32.4 1.0 NE2 B:GLN149 4.1 33.1 1.0 CB B:GLN146 4.2 33.8 1.0 CG B:GLN146 4.3 34.6 1.0 O B:ARG148 4.4 34.4 1.0 CA B:GLN146 4.4 34.4 1.0 CB B:ASP174 4.5 36.0 1.0 OD1 B:ASP147 4.5 30.0 1.0 NE2 B:GLN146 4.6 36.2 1.0 N B:ASP147 4.6 33.0 1.0 OD2 B:ASP147 4.9 31.6 1.0 CG B:ASP147 5.0 30.8 1.0 CG B:GLN149 5.0 32.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Outer Membrane Expressed Chitoporin Vhchip From Vibrio Harveyi within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:32.2 occ:1.00 OE1 C:GLN149 2.3 55.8 1.0 O C:HOH504 2.4 52.7 1.0 OE1 C:GLN146 2.6 62.0 1.0 OD1 C:ASP174 2.7 60.2 1.0 OD2 C:ASP174 2.9 57.9 1.0 CG C:ASP174 3.2 59.7 1.0 CD C:GLN149 3.4 57.5 1.0 CD C:GLN146 3.7 63.8 1.0 O C:ARG148 4.0 54.0 1.0 NE2 C:GLN149 4.0 58.2 1.0 CB C:GLN146 4.0 64.0 1.0 OD1 C:ASP147 4.3 58.6 1.0 CA C:GLN146 4.3 65.3 1.0 CG C:GLN146 4.3 64.8 1.0 N C:ASP147 4.3 62.4 1.0 CG C:GLN149 4.7 57.8 1.0 CG C:ASP147 4.8 58.4 1.0 CB C:ASP174 4.8 59.9 1.0 NE2 C:GLN146 4.8 65.1 1.0 C C:GLN146 4.9 65.0 1.0 OD2 C:ASP147 4.9 57.4 1.0 CB C:GLN149 4.9 57.5 1.0

A.Aunkham, M.Zahn, A.Kesireddy, K.R.Pothula, A.Schulte, A.Basle, U.Kleinekathofer, W.Suginta, B.Van Den Berg. Structural Basis For Chitin Acquisition By Marine Vibrio Species. Nat Commun V. 9 220 2018.
ISSN: ESSN 2041-1723
PubMed: 29335469
DOI: 10.1038/S41467-017-02523-Y