Sodium in PDB 5l38: The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment

The structure of The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment, PDB code: 5l38 was solved by E.Mallette, M.S.Kimber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.14 / 2.20
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	93.600, 93.600, 192.540, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.3

The structure of The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment (pdb code 5l38). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment, PDB code: 5l38:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:45.7 occ:1.00 O A:HOH356 2.1 25.0 1.0 O A:VAL25 2.2 13.6 1.0 O A:ALA28 2.3 20.4 1.0 O A:HOH306 2.4 28.2 1.0 C A:ALA28 3.2 20.1 1.0 C A:VAL25 3.4 12.5 1.0 N A:ASN29 3.9 24.1 1.0 CA A:ASN29 3.9 23.6 1.0 N A:ALA28 4.0 13.9 1.0 CA A:ALA28 4.1 13.2 1.0 CA A:VAL25 4.2 12.2 1.0 N A:VAL30 4.3 16.6 1.0 ND2 A:ASN29 4.3 31.0 1.0 C A:LYS26 4.4 19.1 1.0 O A:LYS26 4.4 16.1 1.0 N A:LYS26 4.4 14.0 1.0 NE2 B:HIS81 4.5 44.1 1.0 CA A:LYS26 4.5 16.4 1.0 C A:ASN29 4.7 21.2 1.0 CB A:VAL25 4.8 12.3 1.0 O A:VAL30 4.8 19.2 1.0 N A:ALA27 4.8 19.4 1.0 C A:ALA27 5.0 16.2 1.0

Sodium binding site 2 out of 3 in the The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment within 5.0Å range: probe atom residue distance (Å) B Occ G:Na201 b:16.3 occ:1.00 O G:VAL25 2.3 16.2 1.0 O G:ALA28 2.4 19.0 1.0 O H:HOH225 2.6 14.8 1.0 C G:ALA28 3.4 18.8 1.0 C G:VAL25 3.4 18.2 1.0 CA G:ASN29 3.9 22.9 1.0 N G:ASN29 4.0 18.4 1.0 CA G:VAL25 4.1 19.3 1.0 NE2 H:HIS81 4.2 30.0 1.0 N G:VAL30 4.2 18.1 1.0 N G:ALA28 4.4 19.3 1.0 CA G:ALA28 4.5 19.4 1.0 O G:VAL30 4.5 28.0 1.0 N G:LYS26 4.5 18.1 1.0 CB G:VAL25 4.5 18.4 1.0 C G:ASN29 4.6 21.6 1.0 CA G:LYS26 4.7 16.6 1.0 C G:LYS26 4.8 22.0 1.0 CD2 H:HIS81 4.9 27.9 1.0 CE1 H:HIS81 4.9 34.7 1.0

Sodium binding site 3 out of 3 in the The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of the Hexagonal Shell Protein MSM0272 From the Rmm Microcompartment within 5.0Å range: probe atom residue distance (Å) B Occ I:Na201 b:30.6 occ:1.00 O I:VAL25 2.3 21.4 1.0 O J:HOH218 2.6 21.4 1.0 O I:ALA28 2.6 23.1 1.0 C I:VAL25 3.4 24.0 1.0 C I:ALA28 3.5 23.5 1.0 CA I:ASN29 4.0 38.2 1.0 CA I:VAL25 4.0 20.8 1.0 NE2 J:HIS81 4.1 34.4 1.0 N I:ASN29 4.2 21.5 1.0 N I:VAL30 4.3 31.3 1.0 N I:ALA28 4.4 19.8 1.0 N I:LYS26 4.4 24.3 1.0 CB I:VAL25 4.5 22.5 1.0 CA I:ALA28 4.5 20.4 1.0 O I:VAL30 4.6 29.2 1.0 CA I:LYS26 4.7 24.6 1.0 C I:ASN29 4.8 30.4 1.0 CE1 J:HIS81 4.8 37.3 1.0 CD2 J:HIS81 4.8 33.3 1.0 C I:LYS26 4.9 25.2 1.0

E.Mallette, M.S.Kimber. A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport. J. Biol. Chem. V. 292 1197 2017.
ISSN: ESSN 1083-351X
PubMed: 27927988
DOI: 10.1074/JBC.M116.754093