Sodium in PDB 4xhq: Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains

The structure of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains, PDB code: 4xhq was solved by Q.Chen, Y.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 1.95
Space group	P 42 2 2
Cell size a, b, c (Å), α, β, γ (°)	99.172, 99.172, 163.991, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.3

The structure of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains (pdb code 4xhq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains, PDB code: 4xhq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na415 b:67.7 occ:1.00 CE2 A:PHE327 2.5 54.7 1.0 CD2 A:PHE327 2.7 55.9 1.0 O A:PRO314 2.8 49.4 1.0 NE2 A:GLN317 3.1 60.9 1.0 O A:GLU384 3.5 46.1 1.0 CB A:ALA383 3.5 45.2 1.0 CG A:GLN317 3.7 64.0 1.0 CD A:PRO314 3.7 61.0 1.0 CG A:PRO314 3.8 53.2 1.0 CZ A:PHE327 3.8 57.7 1.0 CD A:GLN317 3.9 73.9 1.0 C A:PRO314 3.9 56.3 1.0 N A:GLN317 4.0 53.8 1.0 CA A:THR316 4.0 57.0 1.0 CG A:PHE327 4.1 50.9 1.0 C A:THR316 4.1 59.5 1.0 N A:THR316 4.1 58.7 1.0 C A:GLU384 4.2 46.0 1.0 C A:PRO315 4.2 57.7 1.0 O A:PRO315 4.2 49.1 1.0 N A:GLU384 4.3 50.7 1.0 CB A:GLN317 4.3 54.2 1.0 N A:PRO314 4.4 60.1 1.0 C A:ALA383 4.6 45.5 1.0 CA A:ALA383 4.6 47.4 1.0 CA A:PRO314 4.6 64.5 1.0 CA A:GLN317 4.8 67.3 1.0 N A:PRO315 4.8 54.2 1.0 CB A:PRO314 4.8 60.5 1.0 O A:THR316 4.8 57.0 1.0 CE1 A:PHE327 4.9 63.2 1.0 CA A:GLU384 4.9 49.4 1.0 CA A:PRO315 4.9 48.2 1.0 CB A:PHE327 4.9 46.0 1.0 N A:LEU385 4.9 48.9 1.0 CD1 A:PHE327 4.9 60.4 1.0 CG2 A:ILE312 5.0 48.5 1.0

Sodium binding site 2 out of 4 in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na416 b:68.5 occ:1.00 NH1 A:ARG94 2.5 46.7 1.0 O A:HOH554 2.6 52.5 1.0 O A:SER378 2.8 36.0 1.0 CD A:ARG94 3.2 44.2 1.0 CZ A:ARG94 3.6 51.5 1.0 O A:HOH608 3.6 51.5 1.0 OD1 A:ASN12 3.8 59.0 1.0 O A:LEU308 3.8 38.3 1.0 NE A:ARG94 3.8 46.1 1.0 CB A:ALA379 3.8 33.1 1.0 CA A:ALA379 3.9 31.2 1.0 C A:SER378 3.9 38.3 1.0 O A:HOH649 4.0 39.9 1.0 N A:ALA379 4.3 30.9 1.0 CG A:ASN12 4.6 54.5 1.0 CG A:ARG94 4.6 36.2 1.0 NH2 A:ARG94 4.8 46.2 1.0 CB A:ARG94 4.8 29.9 1.0 C A:LEU308 4.8 49.0 1.0 ND2 A:ASN12 4.9 45.3 1.0 OE1 A:GLU377 5.0 57.0 1.0

Sodium binding site 3 out of 4 in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na417 b:65.6 occ:1.00 CD1 A:PHE88 2.7 76.0 1.0 OE2 A:GLU384 2.9 62.9 1.0 CG A:PHE88 2.9 66.0 1.0 CE1 A:PHE88 2.9 79.8 1.0 CD2 A:PHE88 3.3 69.0 1.0 CZ A:PHE88 3.3 86.0 1.0 CE2 A:PHE88 3.5 76.6 1.0 CB A:PHE88 3.7 55.9 1.0 CD A:GLU384 3.7 60.4 1.0 O A:HOH505 3.8 53.6 1.0 O A:GLN1 3.8 75.5 1.0 C A:GLN1 3.9 66.3 1.0 N A:LYS2 3.9 62.8 1.0 OE1 A:GLU384 3.9 47.7 1.0 N A:GLY3 4.0 57.8 1.0 CA A:LYS2 4.0 67.6 1.0 C A:LYS2 4.0 60.2 1.0 CD A:LYS386 4.1 65.5 1.0 N A:GLN1 4.4 64.4 1.0 NZ A:LYS386 4.4 67.1 1.0 CA A:GLN1 4.6 69.6 1.0 O A:LYS2 4.6 46.6 1.0 CG A:LYS386 4.7 61.7 1.0 CA A:GLY3 4.9 48.8 1.0 CE A:LYS386 4.9 66.1 1.0 O A:HOH726 5.0 54.0 1.0

Sodium binding site 4 out of 4 in the Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Re-Refinement the Crystal Structure of DSCAM1 Isoform 1.34, N-Terminal Four Ig Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na418 b:58.1 occ:1.00 O A:HOH657 2.4 37.5 1.0 O A:HOH526 2.5 34.3 1.0 O A:VAL259 2.8 36.0 1.0 O A:HOH607 3.2 47.2 1.0 O A:TRP246 3.9 28.3 1.0 C A:VAL259 3.9 31.7 1.0 CG A:LEU261 4.1 35.1 1.0 O A:HOH878 4.1 56.7 1.0 N A:VAL259 4.1 28.7 1.0 O A:HOH831 4.4 49.0 1.0 CA A:VAL259 4.4 31.5 1.0 CD2 A:LEU261 4.5 37.0 1.0 CB A:VAL259 4.5 29.2 1.0 CD1 A:LEU261 4.5 39.8 1.0 CB A:ALA258 4.5 34.5 1.0 OE1 A:GLN267 4.5 34.7 1.0 N A:TRP246 4.6 29.7 1.0 C A:ALA258 4.7 35.1 1.0 C A:TRP246 4.9 29.9 1.0 CA A:ALA258 5.0 35.2 1.0 N A:VAL260 5.0 31.7 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