Sodium in PDB 4on3: Crystal Structure of Human Sorting Nexin 10 (SNX10)

The structure of Crystal Structure of Human Sorting Nexin 10 (SNX10), PDB code: 4on3 was solved by T.Xu, J.Xu, Q.Wang, J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	67.14 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	205.130, 205.130, 42.220, 90.00, 90.00, 120.00
R / Rfree (%)	18.9 / 22.9

The binding sites of Sodium atom in the Crystal Structure of Human Sorting Nexin 10 (SNX10) (pdb code 4on3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Sorting Nexin 10 (SNX10), PDB code: 4on3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


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 Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:17.7 occ:0.50 NH2 A:ARG61 3.4 12.4 1.0 NH1 A:ARG61 4.2 13.2 1.0 CZ A:ARG61 4.3 13.0 1.0

Sodium binding site 2 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


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 Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na315 b:23.8 occ:1.00 O A:LEU121 2.7 11.2 1.0 O A:ILE34 2.8 16.3 1.0 OG A:SER48 2.9 14.9 1.0 O A:SER48 3.3 17.6 1.0 C A:SER48 3.4 17.0 1.0 CB A:SER48 3.4 15.3 1.0 CG1 A:ILE36 3.5 21.0 1.0 N A:ILE36 3.6 19.0 1.0 C A:ILE34 3.7 18.3 1.0 C A:LEU121 3.8 12.1 1.0 CB A:ILE36 3.8 20.0 1.0 N A:CYS49 3.9 18.7 1.0 CA A:SER48 3.9 15.8 1.0 CA A:CYS49 4.1 20.6 1.0 CA A:CYS35 4.1 20.3 1.0 C A:CYS35 4.2 18.8 1.0 N A:CYS35 4.2 19.6 1.0 N A:VAL50 4.2 17.2 1.0 CB A:VAL50 4.2 15.2 1.0 CG2 A:ILE34 4.3 20.4 1.0 CA A:LEU121 4.3 11.4 1.0 CG1 A:VAL50 4.3 15.5 1.0 C A:CYS49 4.3 19.0 1.0 CA A:ILE36 4.3 19.2 1.0 CB A:LEU121 4.3 11.9 1.0 CD2 A:LEU121 4.5 12.4 1.0 CB A:ILE34 4.5 20.1 1.0 N A:SER48 4.7 15.6 1.0 CD1 A:ILE36 4.7 22.2 1.0 CA A:ILE34 4.8 18.4 1.0 N A:GLN122 4.8 12.6 1.0 CG A:GLN122 4.8 14.2 1.0 CA A:VAL50 4.9 15.1 1.0

Sodium binding site 3 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


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 Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na316 b:21.1 occ:1.00 O A:VAL11 3.4 25.5 1.0 CD A:ARG103 3.5 33.0 1.0 CA A:SER12 3.5 21.9 1.0 N A:VAL13 3.6 19.9 1.0 CG A:ARG103 3.8 27.9 1.0 C A:SER12 4.0 20.4 1.0 CG1 A:VAL13 4.2 23.5 1.0 O A:VAL13 4.2 20.8 1.0 CB A:SER12 4.2 22.4 1.0 C A:VAL11 4.3 23.5 1.0 N A:SER12 4.4 22.3 1.0 CA A:VAL13 4.6 21.3 1.0 OG A:SER12 4.7 23.6 1.0 CB A:ARG103 4.8 24.1 1.0 CB A:VAL13 4.9 22.8 1.0 NE A:ARG103 4.9 41.3 1.0 C A:VAL13 4.9 21.4 1.0

Sodium binding site 4 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


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 Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na317 b:25.1 occ:1.00 OE1 A:GLN122 2.9 12.3 1.0 N A:THR44 3.0 18.8 1.0 ND1 A:HIS118 3.0 17.3 1.0 OG1 A:THR44 3.2 21.6 1.0 CG A:HIS118 3.5 17.0 1.0 CB A:THR44 3.6 21.2 1.0 CB A:HIS118 3.6 16.0 1.0 CD1 A:ILE146 3.7 19.0 1.0 CA A:PHE43 3.7 20.8 1.0 C A:PHE43 3.8 19.2 1.0 CA A:THR44 3.8 19.9 1.0 CE1 A:HIS118 3.9 16.8 1.0 CD A:GLN122 4.0 13.5 1.0 CD2 A:PHE43 4.1 24.3 1.0 CB A:PHE43 4.3 21.1 1.0 O A:ALA42 4.4 25.0 1.0 CA A:HIS118 4.5 15.6 1.0 CD2 A:HIS118 4.5 17.4 1.0 CG A:PHE43 4.6 24.1 1.0 N A:MET45 4.6 17.3 1.0 CG A:GLN122 4.7 14.2 1.0 NE2 A:HIS118 4.7 16.9 1.0 C A:THR44 4.8 19.9 1.0 CB A:GLN122 4.8 14.2 1.0 N A:PHE43 4.9 22.4 1.0 O A:PHE43 4.9 20.7 1.0 CG1 A:ILE146 4.9 19.9 1.0 CE2 A:PHE43 4.9 23.0 1.0 O A:HIS118 4.9 15.8 1.0 C A:HIS118 5.0 14.9 1.0 CG2 A:ILE146 5.0 21.4 1.0

Sodium binding site 5 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na312 b:15.0 occ:1.00 ND1 B:HIS118 2.7 7.5 1.0 OE1 B:GLN122 2.7 13.2 1.0 N B:THR44 2.9 16.4 1.0 CG B:HIS118 3.5 7.6 1.0 OG1 B:THR44 3.5 17.0 1.0 CB B:THR44 3.5 17.4 1.0 CE1 B:HIS118 3.6 7.5 1.0 CB B:HIS118 3.6 7.5 1.0 CA B:PHE43 3.7 20.2 1.0 CD B:GLN122 3.7 12.8 1.0 CA B:THR44 3.8 16.9 1.0 C B:PHE43 3.8 18.2 1.0 CD2 B:PHE43 3.9 22.8 1.0 CD1 B:ILE146 4.0 10.9 1.0 CB B:PHE43 4.2 21.1 1.0 CG B:GLN122 4.3 11.8 1.0 O B:ALA42 4.4 24.3 1.0 CG B:PHE43 4.4 21.7 1.0 N B:MET45 4.4 18.1 1.0 CA B:HIS118 4.5 7.4 1.0 CD2 B:HIS118 4.6 7.5 1.0 NE2 B:HIS118 4.6 7.7 1.0 NE2 B:GLN122 4.7 13.7 1.0 C B:THR44 4.7 17.7 1.0 CB B:GLN122 4.7 11.2 1.0 CE2 B:PHE43 4.8 23.0 1.0 O B:HIS118 4.8 7.6 1.0 N B:PHE43 4.8 20.9 1.0 CG2 B:THR44 4.9 18.4 1.0 C B:HIS118 5.0 7.5 1.0 O B:PHE43 5.0 19.3 1.0

Sodium binding site 6 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na313 b:19.9 occ:1.00 OG B:SER48 2.6 16.5 1.0 O B:LEU121 2.9 10.2 1.0 O B:ILE34 2.9 15.3 1.0 O B:SER48 3.1 16.1 1.0 CG1 B:ILE36 3.4 19.0 1.0 C B:SER48 3.5 16.5 1.0 CB B:SER48 3.5 16.7 1.0 C B:ILE34 3.6 18.2 1.0 N B:ILE36 3.7 17.7 1.0 C B:LEU121 3.8 9.8 1.0 CB B:ILE36 3.9 18.8 1.0 N B:CYS35 3.9 19.0 1.0 CA B:CYS35 4.0 19.9 1.0 C B:CYS35 4.1 18.4 1.0 CA B:SER48 4.1 16.4 1.0 CB B:LEU121 4.1 9.2 1.0 CG2 B:VAL50 4.1 13.1 1.0 N B:CYS49 4.1 17.2 1.0 N B:VAL50 4.2 14.2 1.0 CA B:LEU121 4.2 9.4 1.0 CG2 B:ILE34 4.2 21.0 1.0 CA B:CYS49 4.3 18.7 1.0 CB B:ILE34 4.3 21.3 1.0 CA B:ILE36 4.4 18.3 1.0 C B:CYS49 4.6 16.1 1.0 CA B:ILE34 4.6 19.4 1.0 CD1 B:ILE36 4.8 19.7 1.0 N B:SER48 4.8 16.0 1.0 N B:GLN122 4.9 10.1 1.0 CG B:GLN122 4.9 11.8 1.0 O B:CYS35 5.0 16.9 1.0 CD2 B:LEU121 5.0 9.2 1.0

Sodium binding site 7 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na314 b:25.2 occ:1.00 O B:GLN137 2.7 18.4 1.0 C B:GLN137 3.6 18.5 1.0 CA B:GLN137 3.8 19.2 1.0 CB B:GLN137 3.9 22.3 1.0 CG B:GLN137 4.6 26.8 1.0 N B:THR138 4.8 18.1 1.0

Sodium binding site 8 out of 8 in the Crystal Structure of Human Sorting Nexin 10 (SNX10)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Sorting Nexin 10 (SNX10) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na315 b:25.1 occ:1.00 NE B:ARG103 3.3 52.0 1.0 NH2 B:ARG103 3.5 53.0 1.0 O B:VAL11 3.6 25.2 1.0 N B:VAL13 3.6 21.3 1.0 CA B:SER12 3.8 23.6 1.0 CZ B:ARG103 3.9 52.2 1.0 CB B:ARG103 4.1 31.1 1.0 C B:SER12 4.2 21.0 1.0 CG1 B:VAL13 4.4 21.6 1.0 CD B:ARG103 4.4 48.4 1.0 O B:VAL13 4.4 20.8 1.0 C B:VAL11 4.4 25.3 1.0 CG B:ARG103 4.5 40.6 1.0 CB B:SER12 4.6 25.3 1.0 N B:SER12 4.6 23.8 1.0 CA B:VAL13 4.7 21.8 1.0 OG B:SER12 4.9 28.4 1.0

T.Xu, J.Xu, Q.Wang, J.Liu. Structure of Human SNX10 Reveals Insights Into Its Role in Human Autosomal Recessive Osteopetrosis Proteins 2014.
ISSN: ESSN 1097-0134