Sodium in PDB 4g1m: Re-Refinement of Alpha V Beta 3 Structure

The structure of Re-Refinement of Alpha V Beta 3 Structure, PDB code: 4g1m was solved by T.A.Springer, L.Mi, J.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.00 / 2.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.870, 129.870, 305.900, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 23.3

The structure of Re-Refinement of Alpha V Beta 3 Structure also contains other interesting chemical elements:

Calcium

(Ca)

7 atoms

The binding sites of Sodium atom in the Re-Refinement of Alpha V Beta 3 Structure (pdb code 4g1m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Re-Refinement of Alpha V Beta 3 Structure, PDB code: 4g1m:

Sodium binding site 1 out of 1 in the Re-Refinement of Alpha V Beta 3 Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Re-Refinement of Alpha V Beta 3 Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na3000 b:0.3 occ:1.00 O A:SER705 2.3 1.0 1.0 O A:MET707 2.6 0.1 1.0 OD1 A:ASP708 2.7 0.3 1.0 CG A:ASP708 3.1 0.3 1.0 C A:MET707 3.2 0.9 1.0 C A:SER705 3.5 0.8 1.0 C A:GLU706 3.5 0.3 1.0 N A:MET707 3.5 0.0 1.0 O A:GLU706 3.6 0.2 1.0 OD2 A:ASP708 3.6 0.7 1.0 CA A:MET707 3.9 0.4 1.0 CB A:ASP708 4.0 0.7 1.0 N A:ASP708 4.0 0.0 1.0 CA A:GLU706 4.1 0.3 1.0 OG A:SER705 4.2 0.3 1.0 N A:GLU706 4.2 0.2 1.0 CB A:GLU706 4.3 0.6 1.0 CB A:SER705 4.3 0.1 1.0 CA A:ASP708 4.5 0.8 1.0 CA A:SER705 4.5 0.8 1.0 CB A:MET707 4.7 0.4 1.0

X.Dong, L.Z.Mi, J.Zhu, W.Wang, P.Hu, B.H.Luo, T.A.Springer. Alpha V Beta 3 Integrin Crystal Structures and Their Functional Implications Biochemistry V. 51 8814 2012.
ISSN: ISSN 0006-2960
PubMed: 23106217
DOI: 10.1021/BI300734N