Sodium in PDB 5yby: Structure of Human Gliomedin

The structure of Structure of Human Gliomedin, PDB code: 5yby was solved by H.Liu, Z.Lin, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.26 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.880, 81.573, 66.194, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 16.9

The structure of Structure of Human Gliomedin also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of Human Gliomedin (pdb code 5yby). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Human Gliomedin, PDB code: 5yby:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:15.0 occ:1.00 OD1 A:ASN302 2.3 15.5 1.0 O A:ALA351 2.3 14.9 1.0 OD1 A:ASN350 2.3 15.3 1.0 O A:LEU396 2.4 14.9 1.0 O A:HOH800 2.4 15.1 1.0 H A:ALA351 3.0 16.6 1.0 H A:LEU396 3.1 18.2 1.0 HB3 A:LEU396 3.2 19.6 1.0 CG A:ASN302 3.3 15.2 1.0 HD21 A:ASN302 3.4 24.2 1.0 O A:HOH773 3.4 16.0 1.0 C A:ALA351 3.5 14.4 1.0 CG A:ASN350 3.5 15.8 1.0 C A:LEU396 3.5 14.8 1.0 ND2 A:ASN302 3.7 20.2 1.0 N A:ALA351 3.8 13.8 1.0 HE2 A:PHE294 3.8 18.2 1.0 N A:LEU396 3.8 15.2 1.0 HD21 A:ASN350 3.9 26.0 1.0 CA A:LEU396 4.0 14.6 1.0 CB A:LEU396 4.0 16.3 1.0 ND2 A:ASN350 4.2 21.7 1.0 HA A:PHE352 4.2 16.6 1.0 CA A:ALA351 4.2 14.0 1.0 O A:HOH862 4.3 20.0 1.0 HA A:ALA397 4.4 18.4 1.0 HB3 A:PHE352 4.4 17.1 1.0 CE2 A:PHE294 4.5 15.2 1.0 HB3 A:ALA351 4.5 19.4 1.0 O A:HOH714 4.5 18.9 1.0 N A:PHE352 4.5 15.3 1.0 HD22 A:ASN302 4.6 24.2 1.0 HB2 A:ASN302 4.6 16.9 1.0 CB A:ASN302 4.6 14.1 1.0 CB A:ASN350 4.6 13.7 1.0 N A:ALA397 4.6 13.8 1.0 HB3 A:ASN350 4.6 16.5 1.0 HB2 A:LEU396 4.7 19.6 1.0 HG A:LEU396 4.7 20.4 1.0 HD23 A:LEU396 4.7 21.8 1.0 HA A:MET395 4.8 22.4 0.6 HA A:MET395 4.8 21.2 0.4 CA A:PHE352 4.8 13.8 1.0 HB2 A:ALA397 4.8 19.1 1.0 HD2 A:PHE294 4.9 18.4 1.0 C A:ASN350 4.9 13.9 1.0 CG A:LEU396 4.9 17.0 1.0 HD12 A:ILE313 4.9 19.3 1.0 HA A:ASN350 4.9 16.3 1.0 HA A:LEU396 4.9 17.5 1.0 CB A:ALA351 5.0 16.2 1.0 CA A:ALA397 5.0 15.4 1.0 HB3 A:ASN302 5.0 16.9 1.0

Sodium binding site 2 out of 4 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:56.8 occ:1.00 OD1 A:ASP385 2.3 54.6 1.0 O A:ARG387 2.7 26.2 1.0 HA A:THR388 3.1 32.8 1.0 HB3 A:MET366 3.1 35.1 1.0 HE3 A:MET366 3.1 50.0 1.0 CG A:ASP385 3.3 55.0 1.0 HG22 A:THR388 3.4 46.4 1.0 C A:ARG387 3.6 28.2 1.0 OD2 A:ASP385 3.6 56.1 1.0 O A:MET366 3.8 21.8 1.0 CA A:THR388 3.9 27.3 1.0 CB A:MET366 4.0 29.2 1.0 H A:ARG387 4.1 25.6 1.0 CE A:MET366 4.1 41.7 1.0 HG23 A:THR388 4.1 46.4 1.0 CG2 A:THR388 4.1 38.7 1.0 N A:THR388 4.1 28.5 1.0 O A:HOH852 4.3 61.5 1.0 HB2 A:MET366 4.3 35.1 1.0 HG2 A:ARG367 4.3 30.3 1.0 HE2 A:MET366 4.4 50.0 1.0 HG3 A:ARG367 4.4 30.3 1.0 C A:MET366 4.5 23.8 1.0 HE1 A:MET366 4.5 50.0 1.0 O A:HOH612 4.5 45.8 1.0 HA A:MET366 4.6 23.7 1.0 N A:ARG387 4.6 21.3 1.0 CB A:THR388 4.6 36.2 1.0 HH11 A:ARG367 4.6 46.0 1.0 H A:LEU386 4.7 26.1 1.0 CB A:ASP385 4.7 43.5 1.0 CA A:MET366 4.7 19.7 1.0 CA A:ARG387 4.7 22.9 1.0 HB2 A:ASP385 4.8 52.2 1.0 CG A:ARG367 4.8 25.3 1.0 HA A:ASP385 4.9 25.3 1.0 HG21 A:THR388 4.9 46.4 1.0 H A:THR388 4.9 34.2 1.0 HB A:THR388 4.9 43.5 1.0 HG3 A:MET366 4.9 49.4 1.0 CG A:MET366 4.9 41.2 1.0 C A:THR388 5.0 30.8 1.0

Sodium binding site 3 out of 4 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:46.3 occ:1.00 O A:HOH908 2.1 36.4 1.0 HZ2 A:LYS223 2.6 39.8 1.0 O A:HOH764 2.7 48.1 1.0 HZ3 A:LYS223 2.8 39.8 1.0 OE1 A:GLU215 2.9 39.8 1.0 HD2 A:LYS223 3.1 29.1 1.0 NZ A:LYS223 3.1 33.1 1.0 HZ A:PHE225 3.2 22.7 1.0 O A:HOH820 3.3 42.0 1.0 HD3 A:LYS223 3.5 29.1 1.0 HG11 A:VAL213 3.6 22.3 1.0 CD A:LYS223 3.6 24.2 1.0 HZ1 A:LYS223 3.8 39.8 1.0 HG11 A:VAL192 3.8 32.3 1.0 CE A:LYS223 3.9 31.4 1.0 CZ A:PHE225 4.1 18.9 1.0 CD A:GLU215 4.1 34.4 1.0 O A:HOH656 4.3 32.4 1.0 HE1 A:PHE225 4.3 24.4 1.0 HE3 A:LYS223 4.5 37.7 1.0 CG1 A:VAL213 4.5 18.6 1.0 HE2 A:LYS223 4.6 37.7 1.0 CE1 A:PHE225 4.6 20.3 1.0 HG12 A:VAL213 4.7 22.3 1.0 CG1 A:VAL192 4.7 26.9 1.0 HG21 A:VAL213 4.7 21.9 1.0 HH2 A:TRP408 4.8 22.6 1.0 HG3 A:GLU215 4.8 33.0 1.0 HG12 A:VAL192 4.8 32.3 1.0 HG21 A:VAL192 4.8 27.1 1.0 HG2 A:GLU215 4.8 33.0 1.0 HB A:VAL213 4.9 20.4 1.0 OE1 A:GLU194 4.9 32.6 1.0 CG A:GLU215 4.9 27.5 1.0 OE2 A:GLU215 4.9 38.0 1.0 HB A:VAL192 5.0 30.9 1.0

Sodium binding site 4 out of 4 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:50.4 occ:1.00 HH22 A:ARG387 2.1 29.2 1.0 O A:HOH715 2.3 44.5 1.0 HH21 A:ARG387 2.4 29.2 1.0 NH2 A:ARG387 2.5 24.4 1.0 O A:HOH687 2.8 24.3 1.0 O A:LYS364 2.9 21.9 1.0 HB2 A:ASP365 3.0 24.2 1.0 O A:SER391 3.2 26.0 1.0 O A:GLN390 3.4 36.9 1.0 HA A:VAL392 3.4 26.1 1.0 HA A:GLN390 3.7 53.7 1.0 CZ A:ARG387 3.8 25.5 1.0 C A:LYS364 3.9 21.2 1.0 C A:GLN390 3.9 35.9 1.0 C A:SER391 3.9 23.0 1.0 CB A:ASP365 3.9 20.1 1.0 H A:LEU393 4.0 23.2 1.0 O A:HOH877 4.0 39.9 1.0 HB3 A:ASP365 4.2 24.2 1.0 CA A:VAL392 4.3 21.7 1.0 HH12 A:ARG387 4.3 27.3 1.0 HA A:LYS364 4.3 25.2 1.0 CA A:GLN390 4.3 44.8 1.0 HB2 A:LEU393 4.4 22.6 1.0 N A:VAL392 4.4 23.3 1.0 N A:LEU393 4.5 19.3 1.0 NH1 A:ARG387 4.5 22.8 1.0 OD2 A:ASP365 4.5 19.0 1.0 HE A:ARG387 4.5 31.9 1.0 HB3 A:LEU393 4.6 22.6 1.0 N A:SER391 4.6 30.8 1.0 N A:ASP365 4.7 18.3 1.0 CA A:LYS364 4.7 21.0 1.0 NE A:ARG387 4.7 26.6 1.0 HB3 A:LYS364 4.7 31.2 1.0 CA A:ASP365 4.7 17.5 1.0 SD A:MET366 4.7 38.7 1.0 C A:VAL392 4.7 22.6 1.0 O A:HOH766 4.8 39.2 1.0 CG A:ASP365 4.8 16.6 1.0 O A:SER389 4.9 32.3 1.0 HB3 A:GLN390 4.9 63.1 1.0 O A:ASP365 4.9 21.6 1.0 C A:ASP365 4.9 18.6 1.0 CA A:SER391 4.9 28.1 1.0 CB A:LEU393 4.9 18.9 1.0

H.Liu, Z.Lin, F.Xu. High Resolution Structure of Human Gliomedin To Be Published.