Sodium in PDB 4x5l: Crystal Structure of DSCAM1 IG7 Domain, Isoform 9

The structure of Crystal Structure of DSCAM1 IG7 Domain, Isoform 9, PDB code: 4x5l was solved by Q.Chen, Y.Yu, S.A.Li, L.Cheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.37
Space group	P 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	45.527, 117.370, 117.333, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 24.7

The binding sites of Sodium atom in the Crystal Structure of DSCAM1 IG7 Domain, Isoform 9 (pdb code 4x5l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of DSCAM1 IG7 Domain, Isoform 9, PDB code: 4x5l:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of DSCAM1 IG7 Domain, Isoform 9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of DSCAM1 IG7 Domain, Isoform 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na101 b:63.0 occ:1.00 HG1 B:THR82 2.1 71.4 1.0 HG21 B:THR87 2.4 83.5 1.0 OG1 B:THR82 2.6 59.5 1.0 HG22 B:THR87 2.8 83.5 1.0 CG2 B:THR87 3.0 69.6 1.0 HB B:THR87 3.1 67.5 1.0 HG21 B:ILE80 3.2 67.3 1.0 HG22 B:ILE80 3.6 67.3 1.0 CB B:THR87 3.6 56.3 1.0 CG2 B:ILE80 3.7 56.1 1.0 HH12 B:ARG37 3.7 93.0 1.0 HG21 B:THR82 3.8 71.2 1.0 HG23 B:THR87 3.8 83.5 1.0 CB B:THR82 3.8 46.9 1.0 HG23 B:ILE80 3.9 67.3 1.0 HG23 B:THR82 3.9 71.2 1.0 HG1 B:THR87 4.0 0.9 1.0 CG2 B:THR82 4.1 59.4 1.0 OG1 B:THR87 4.3 84.9 1.0 HB B:THR82 4.3 56.3 1.0 NH1 B:ARG37 4.4 77.5 1.0 HH11 B:ARG37 4.6 93.0 1.0 HA B:THR87 4.7 61.3 1.0 HA B:THR82 4.7 58.2 1.0 CA B:THR87 4.8 51.1 1.0 CA B:THR82 4.9 48.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of DSCAM1 IG7 Domain, Isoform 9


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of DSCAM1 IG7 Domain, Isoform 9 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:80.6 occ:1.00 HD2 D:PRO28 1.8 56.5 1.0 O D:GLN4 2.1 60.6 1.0 HG D:LEU6 2.1 47.4 1.0 H D:LEU6 2.2 49.4 1.0 HA D:VAL27 2.3 64.7 1.0 O D:VAL26 2.5 59.3 1.0 HA D:VAL5 2.5 69.8 1.0 N D:LEU6 2.6 41.1 1.0 CD D:PRO28 2.6 47.1 1.0 HD3 D:PRO28 2.6 56.5 1.0 CG D:LEU6 3.0 39.5 1.0 C D:VAL5 3.1 41.9 1.0 C D:GLN4 3.1 45.8 1.0 CA D:VAL5 3.1 58.1 1.0 CA D:VAL27 3.2 53.9 1.0 HB2 D:LEU6 3.4 34.9 1.0 C D:VAL26 3.4 43.8 1.0 CB D:LEU6 3.4 29.1 1.0 CA D:LEU6 3.5 27.2 1.0 N D:VAL5 3.6 49.7 1.0 N D:PRO28 3.6 59.5 1.0 HD23 D:LEU6 3.7 40.4 1.0 N D:VAL27 3.7 43.3 1.0 CG D:PRO28 3.7 54.6 1.0 HA D:LEU6 3.7 32.7 1.0 HG13 D:VAL27 3.8 69.3 1.0 HG2 D:PRO28 3.8 65.6 1.0 CD2 D:LEU6 3.8 33.7 1.0 HG3 D:PRO28 3.8 65.6 1.0 C D:VAL27 3.9 60.5 1.0 HD12 D:LEU6 4.0 40.6 1.0 HG22 D:VAL27 4.0 50.6 1.0 HD21 D:LEU6 4.1 40.4 1.0 CD1 D:LEU6 4.1 33.9 1.0 O D:VAL5 4.1 39.8 1.0 HB2 D:GLN4 4.2 78.9 1.0 CB D:VAL27 4.3 50.1 1.0 HD11 D:LEU6 4.3 40.6 1.0 HG12 D:VAL26 4.3 50.3 1.0 CG1 D:VAL27 4.4 57.7 1.0 HB3 D:LEU6 4.4 34.9 1.0 H D:VAL5 4.4 59.6 1.0 H D:LYS29 4.4 54.3 1.0 HB D:VAL26 4.4 52.5 1.0 CA D:GLN4 4.5 50.0 1.0 H D:VAL27 4.5 51.9 1.0 H D:GLN4 4.5 57.5 1.0 HG13 D:VAL5 4.5 40.4 1.0 CB D:VAL5 4.5 47.5 1.0 HG12 D:VAL27 4.6 69.3 1.0 CG2 D:VAL27 4.6 42.2 1.0 CA D:VAL26 4.7 40.5 1.0 HD22 D:LEU6 4.7 40.4 1.0 CB D:GLN4 4.8 65.8 1.0 HG12 D:VAL5 4.8 40.4 1.0 C D:LEU6 4.8 38.2 1.0 HG22 D:VAL5 4.9 54.1 1.0 CG1 D:VAL5 4.9 33.6 1.0 CA D:PRO28 4.9 66.5 1.0 HD13 D:LEU6 4.9 40.6 1.0 HG B:SER13 4.9 48.0 1.0 CB D:PRO28 4.9 56.1 1.0 CB D:VAL26 4.9 43.7 1.0 HG23 D:VAL27 4.9 50.6 1.0 N D:GLN4 4.9 47.9 1.0 H D:VAL26 4.9 66.8 1.0

S.A.Li, L.Cheng, Y.Yu, Q.Chen. Structural Basis of DSCAM1 Homodimerization: Insights Into Context Constraint For Protein Recognition Sci Adv V. 2 01118 2016.
ISSN: ESSN 2375-2548
PubMed: 27386517
DOI: 10.1126/SCIADV.1501118