Sodium in PDB 6nyq: Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment

The structure of Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment, PDB code: 6nyq was solved by C.S.Huang, G.Boenig, S.G.Hymowitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.924, 55.238, 99.639, 90.00, 99.35, 90.00
R / Rfree (%)	16.4 / 20.4

The binding sites of Sodium atom in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment (pdb code 6nyq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment, PDB code: 6nyq:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment


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 Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:38.8 occ:1.00 O H:HOH548 2.5 41.8 1.0 OG H:SER7 2.6 20.7 1.0 O H:GLY8 2.7 25.8 1.0 OD1 H:ASP10 3.0 66.0 1.0 CB H:SER7 3.1 24.9 1.0 N H:GLY8 3.6 24.3 1.0 C H:SER7 3.7 26.5 1.0 CG2 H:THR113 3.7 23.7 1.0 CD2 H:LEU20 3.7 24.9 1.0 C H:GLY8 3.8 24.0 1.0 CG H:ASP10 3.8 55.0 1.0 CA H:SER7 4.0 25.2 1.0 O H:SER7 4.0 23.1 1.0 O H:HOH594 4.1 50.3 1.0 CA H:GLY8 4.3 25.8 1.0 OD2 H:ASP10 4.4 60.7 1.0 CA H:LEU20 4.4 21.4 1.0 CB H:LEU20 4.7 23.0 1.0 CB H:ASP10 4.7 41.0 1.0 O H:HOH480 4.7 35.1 1.0 O H:LYS19 4.7 24.8 1.0 OG1 H:THR113 4.8 24.8 1.0 CG H:LEU20 4.8 23.5 1.0 CB H:THR113 4.8 23.7 1.0 N H:SER7 4.9 26.3 1.0 N H:ASP9 4.9 24.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment


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 Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Na501 b:28.6 occ:1.00 O C:SER286 2.8 22.6 1.0 N C:GLN345 2.8 21.7 1.0 O C:GLY341 2.9 20.0 1.0 O C:TYR342 3.1 20.5 1.0 O C:TYR347 3.2 19.8 1.0 N C:TYR347 3.3 18.6 1.0 N C:TYR346 3.4 20.5 1.0 CA C:GLN345 3.5 25.0 1.0 C C:TYR342 3.5 21.8 1.0 CB C:GLN345 3.6 25.5 1.0 C C:GLN345 3.7 23.4 1.0 CA C:TYR342 3.7 21.1 1.0 N C:ASP344 3.7 21.3 1.0 CB C:SER286 3.8 22.5 1.0 C C:SER286 3.8 23.9 1.0 C C:ASP344 3.8 24.9 1.0 CB C:ASP344 3.9 25.0 1.0 CA C:ASP344 3.9 24.0 1.0 C C:GLY341 3.9 19.4 1.0 CA C:TYR347 4.0 20.3 1.0 C C:TYR347 4.0 19.5 1.0 CB C:TYR347 4.1 20.8 1.0 CA C:SER286 4.1 20.4 1.0 CA C:TYR346 4.2 21.7 1.0 N C:TYR342 4.2 19.8 1.0 C C:TYR346 4.2 20.3 1.0 CG C:GLN345 4.3 29.3 1.0 N C:TRP343 4.5 20.5 1.0 OG C:SER286 4.5 25.1 1.0 C C:TRP343 4.6 25.1 1.0 O C:GLN345 4.7 22.6 1.0 O C:HOH642 4.7 30.3 1.0 CG C:ASP344 4.9 31.3 1.0 O C:ASP344 5.0 23.6 1.0 N C:GLU287 5.0 23.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Na502 b:33.7 occ:1.00 O C:LEU74 2.6 25.5 1.0 OG C:SER314 2.6 22.8 1.0 O C:PRO76 2.7 22.0 1.0 CB C:SER314 3.3 22.3 1.0 N C:PRO76 3.5 23.3 1.0 CD C:PRO76 3.5 25.2 1.0 C C:GLY75 3.6 23.8 1.0 C C:LEU74 3.6 26.5 1.0 CA C:SER314 3.7 22.6 1.0 CA C:GLY75 3.7 26.7 1.0 CB C:ALA78 3.7 20.3 1.0 C C:PRO76 3.8 22.1 1.0 CG C:PRO76 3.9 24.9 1.0 CG1 C:ILE316 4.0 27.2 1.0 CB C:ILE316 4.1 24.1 1.0 N C:GLY75 4.1 24.8 1.0 O C:GLY75 4.1 24.0 1.0 CD C:PRO315 4.2 23.0 1.0 CA C:PRO76 4.2 23.6 1.0 N C:PRO315 4.2 22.2 1.0 C C:SER314 4.2 23.8 1.0 N C:ILE316 4.3 20.4 1.0 N C:ALA78 4.7 19.5 1.0 CB C:PRO76 4.7 24.8 1.0 CA C:ILE316 4.8 22.9 1.0 CA C:ALA78 4.9 20.2 1.0 CA C:LEU74 4.9 25.2 1.0 N C:PRO77 4.9 21.9 1.0 C C:PRO77 4.9 22.2 1.0 N C:SER314 4.9 21.8 1.0 O C:HIS313 5.0 26.0 1.0 N C:LEU74 5.0 24.6 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Glycosylated Lysosomal Membrane Protein (Glmp) Luminal Domain Bound to A Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ C:Na503 b:32.8 occ:1.00 OE1 C:GLU128 2.6 28.6 1.0 OH C:TYR148 2.7 31.1 1.0 O C:SER224 2.9 25.9 1.0 CZ C:TYR148 3.5 28.3 1.0 CE2 C:TYR148 3.5 25.9 1.0 CD C:GLU128 3.6 23.5 1.0 NE C:ARG226 3.7 30.6 1.0 CA C:PRO225 3.8 25.6 1.0 C C:SER224 3.8 27.0 1.0 N C:ARG226 3.9 26.9 1.0 CG C:ARG226 3.9 29.1 1.0 OE2 C:GLU128 3.9 25.8 1.0 CZ C:PHE232 4.0 23.6 1.0 CE2 C:PHE232 4.0 24.2 1.0 C C:PRO225 4.0 28.2 1.0 CD C:ARG226 4.3 32.5 1.0 N C:PRO225 4.3 22.9 1.0 CZ C:ARG226 4.4 30.1 1.0 NH2 C:ARG226 4.5 28.8 1.0 CB C:ALA182 4.6 29.9 1.0 O C:HOH787 4.6 41.2 1.0 O C:HOH645 4.7 38.1 1.0 CB C:ARG226 4.7 28.1 1.0 CA C:ARG226 4.8 29.4 1.0 O C:PRO225 4.8 24.2 1.0 CE1 C:TYR148 4.8 27.9 1.0 CG C:GLU128 4.8 22.2 1.0 CD2 C:TYR148 4.9 22.5 1.0

P.Manzanillo, C.S.Huang, G.Boenig, P.Calses, A.Scherl, M.Reichelt, A.K.Katakam, F.Martin, S.G.Hymowitz, W.Ouyang. Glmp Is Essential For Bone-Marrow Hematopoiesis and Lysosomal Glycolipid Metabolism To Be Published.