Sodium in PDB 6z31: Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8

The structure of Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8, PDB code: 6z31 was solved by A.J.Bochel, C.Williams, M.P.Crump, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.02 / 2.56
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.555, 45.537, 70.275, 90.00, 116.36, 90.00
R / Rfree (%)	22.3 / 25.1

The structure of Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8 (pdb code 6z31). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8, PDB code: 6z31:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1302 b:33.5 occ:1.00 O A:HOH1443 3.7 31.4 1.0 OH A:TYR1130 3.8 39.8 1.0 O A:HOH1436 3.9 30.8 1.0 N A:GLY1133 4.0 36.2 1.0 CE1 A:TYR1130 4.3 32.9 1.0 CZ A:TYR1130 4.6 41.1 1.0 CA A:PRO1132 4.7 41.1 1.0 CA A:GLY1133 4.7 31.2 1.0 C A:PRO1132 4.8 46.5 1.0 OE1 A:GLN1135 4.9 64.0 1.0

Sodium binding site 2 out of 2 in the Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Cation-Independent Mannose 6-Phosphate/ IGF2 Receptor Domain 8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1302 b:44.8 occ:1.00 O B:HOH1416 2.5 40.3 1.0 NE2 B:GLN1135 2.6 43.9 1.0 OH B:TYR1130 2.6 49.2 1.0 CZ B:TYR1130 3.5 43.7 1.0 CE1 B:TYR1130 3.5 34.2 1.0 CD B:GLN1135 3.8 40.1 1.0 CG B:GLN1135 4.4 47.2 1.0 N B:GLY1133 4.5 34.4 1.0 CA B:PRO1132 4.6 34.8 1.0 OE1 B:GLN1135 4.7 41.6 1.0 CE2 B:TYR1130 4.8 36.0 1.0 CD1 B:TYR1130 4.9 34.5 1.0 CB B:PRO1132 5.0 30.4 1.0 O B:HOH1412 5.0 42.8 1.0

A.J.Bochel, C.Williams, A.J.Mccoy, H.J.Hoppe, A.J.Winter, R.D.Nicholls, K.Harlos, E.Y.Jones, I.Berger, A.B.Hassan, M.P.Crump. Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9. Structure V. 28 1300 2020.
ISSN: ISSN 0969-2126
PubMed: 32877646
DOI: 10.1016/J.STR.2020.08.002