Sodium in PDB 5ew6: Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium

The structure of Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium, PDB code: 5ew6 was solved by C.Yuan, M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.19 / 2.29
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.110, 78.110, 252.770, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.7

The binding sites of Sodium atom in the Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium (pdb code 5ew6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium, PDB code: 5ew6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na601 b:64.8 occ:1.00 O A:HOH718 2.3 64.7 1.0 OD1 A:ASN472 2.4 85.1 1.0 OD1 A:ASP493 2.4 70.0 1.0 OD1 A:ASN473 2.4 68.7 1.0 O A:ASP493 2.4 62.2 1.0 OE2 A:GLU470 2.5 87.1 1.0 CD A:GLU470 3.3 83.8 1.0 CG A:ASN472 3.4 80.2 1.0 C A:ASP493 3.4 58.9 1.0 OE1 A:GLU470 3.5 83.5 1.0 CG A:ASN473 3.5 69.5 1.0 CG A:ASP493 3.5 60.6 1.0 N A:ASP493 3.8 63.2 1.0 ND2 A:ASN472 3.8 78.8 1.0 CA A:ASP493 4.1 60.5 1.0 CB A:ASN473 4.2 64.9 1.0 N A:ASN472 4.2 83.0 1.0 N A:ASN473 4.3 73.9 1.0 OD2 A:ASP493 4.4 65.0 1.0 CB A:ASP493 4.4 57.4 1.0 ND2 A:ASN473 4.5 66.0 1.0 N A:SER494 4.5 65.4 1.0 CB A:ASN472 4.6 83.8 1.0 CB A:ASN492 4.7 63.3 1.0 CA A:ASN472 4.7 79.6 1.0 CA A:SER494 4.8 67.4 1.0 CG A:GLU470 4.8 67.0 1.0 C A:ASN472 4.8 77.1 1.0 C A:ASN492 4.9 59.1 1.0 CA A:ASN473 4.9 72.1 1.0

Sodium binding site 2 out of 2 in the Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ligand Binding Region of Uparap at pH 7.4 Without Calcium within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:95.1 occ:1.00 O A:ASN348 2.5 77.3 1.0 OD1 A:ASP328 2.6 0.4 1.0 OE2 A:GLU333 2.9 91.2 1.0 OE1 A:GLN326 3.0 85.6 1.0 OD1 A:ASN348 3.4 85.0 1.0 CG A:ASP328 3.5 0.6 1.0 CD A:GLU333 3.5 95.0 1.0 OE1 A:GLU333 3.6 97.1 1.0 NE2 A:GLN326 3.7 78.3 1.0 OD2 A:ASP328 3.7 0.4 1.0 CD A:GLN326 3.7 76.3 1.0 C A:ASN348 3.7 77.7 1.0 CD A:ARG349 4.2 79.5 1.0 CG A:ASN348 4.2 80.5 1.0 N A:ASN348 4.2 72.7 1.0 CA A:ASN348 4.5 71.4 1.0 CB A:GLN347 4.5 65.8 1.0 N A:ARG349 4.7 79.7 1.0 NE2 A:GLN347 4.7 65.5 1.0 OD1 A:ASN329 4.8 0.5 1.0 CD A:GLN347 4.8 66.6 1.0 N A:ASP328 4.8 85.1 1.0 CG A:GLU333 4.8 93.2 1.0 CA A:ARG349 4.9 78.8 1.0 CB A:ASP328 4.9 95.9 1.0 CG A:GLN347 4.9 68.6 1.0 CB A:ASN348 5.0 69.5 1.0

C.Yuan, H.J.Jurgensen, L.H.Engelholm, R.Li, M.Liu, L.Jiang, Z.Luo, N.Behrendt, M.Huang. Crystal Structures of the Ligand-Binding Region of Uparap: Effect of Calcium Ion Binding Biochem.J. V. 473 2359 2016.
ISSN: ESSN 1470-8728
PubMed: 27247422
DOI: 10.1042/BCJ20160276