Sodium in PDB 4mmz: Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin, PDB code: 4mmz was solved by J.Van Agthoven, J.Xiong, M.A.Arnaout, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.48 / 3.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	129.790, 129.790, 307.676, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 25.6

The structure of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin also contains other interesting chemical elements:

Manganese	(Mn)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin (pdb code 4mmz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin, PDB code: 4mmz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1023 b:89.3 occ:1.00 O A:SER546 2.4 0.2 1.0 OD1 A:ASP544 2.4 0.5 1.0 CA A:GLU547 2.9 0.6 1.0 C A:SER546 2.9 1.0 1.0 N A:GLU547 3.1 0.3 1.0 CG A:GLU547 3.3 0.8 1.0 CB A:GLU547 3.4 0.0 1.0 O A:GLU545 3.6 0.6 1.0 CG A:ASP544 3.7 0.7 1.0 OE2 A:GLU547 3.8 0.7 1.0 CD A:GLU547 4.1 0.3 1.0 CA A:SER546 4.2 0.1 1.0 C A:GLU547 4.2 0.7 1.0 C A:GLU545 4.4 0.9 1.0 OD2 A:ASP544 4.4 0.8 1.0 CB A:SER546 4.5 0.5 1.0 OD2 B:ASP477 4.5 0.8 1.0 CB A:ASP544 4.6 0.5 1.0 N A:SER546 4.7 0.1 1.0 O A:GLU547 4.8 0.1 1.0 O A:ASP544 4.8 0.6 1.0 N A:PHE548 5.0 0.2 1.0

Sodium binding site 2 out of 2 in the Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Integrin ALPHAVBETA3 Ectodomain Bound to An Antagonistic Tenth Domain of Fibronectin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na711 b:0.8 occ:1.00 CL B:CL712 2.4 0.9 1.0 CL B:CL713 2.4 0.6 1.0 OD1 B:ASN654 2.4 0.8 1.0 CG B:ASN654 3.4 0.9 1.0 CA B:ASP647 3.7 0.7 1.0 ND2 B:ASN654 3.7 0.7 1.0 O B:ASP647 3.9 0.8 1.0 O B:LYS646 4.0 0.8 1.0 C B:ASP647 4.1 1.0 1.0 OD1 B:ASP647 4.2 0.5 1.0 CD2 B:LEU645 4.2 0.2 1.0 O B:LEU645 4.4 0.9 1.0 N B:ASP647 4.4 0.5 1.0 C B:LYS646 4.4 0.2 1.0 CB B:ASP647 4.6 0.8 1.0 CB B:ASN654 4.8 0.1 1.0 CG B:ASP647 4.9 0.2 1.0 NE2 B:GLN668 4.9 0.4 1.0

J.F.Van Agthoven, J.P.Xiong, J.L.Alonso, X.Rui, B.D.Adair, S.L.Goodman, M.A.Arnaout. Structural Basis For Pure Antagonism of Integrin Alpha V Beta 3 By A High-Affinity Form of Fibronectin. Nat.Struct.Mol.Biol. V. 21 383 2014.
ISSN: ISSN 1545-9993
PubMed: 24658351
DOI: 10.1038/NSMB.2797