Sodium in PDB 5ybz: High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain

The structure of High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain, PDB code: 5ybz was solved by H.Liu, Z.Li, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.07 / 1.71
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.027, 79.213, 87.495, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 18.7

The structure of High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain (pdb code 5ybz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain, PDB code: 5ybz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:47.4 occ:1.00 OE1 A:GLU141 2.4 26.2 1.0 C2 A:DMS301 3.3 49.8 1.0 S A:DMS301 3.3 49.4 1.0 CD A:GLU141 3.4 32.7 1.0 O A:HOH489 3.5 54.6 1.0 C1 A:DMS301 3.6 35.6 1.0 OE2 A:GLU141 3.6 41.6 1.0 N A:GLU138 3.6 18.0 1.0 CA A:HIS137 4.0 13.5 1.0 CG A:GLU138 4.2 30.4 1.0 C A:HIS137 4.2 17.1 1.0 O A:GLU138 4.2 20.2 1.0 O A:GLN136 4.4 16.9 1.0 CA A:GLU138 4.6 17.2 1.0 CG A:GLU141 4.7 24.9 1.0 CB A:HIS137 4.7 20.1 1.0 O A:DMS301 4.8 36.8 1.0 C A:GLU138 4.8 20.4 1.0 CB A:GLU138 4.8 21.2 1.0 O A:HOH437 4.9 35.4 1.0 N A:HIS137 4.9 16.0 1.0

Sodium binding site 2 out of 2 in the High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:31.5 occ:1.00 OG C:SER214 2.8 16.4 1.0 O1 A:SO4305 2.8 63.1 1.0 ND1 C:HIS176 2.9 23.6 1.0 O A:HOH468 3.0 19.6 1.0 O2 A:SO4305 3.2 44.2 1.0 O D:SER214 3.5 11.4 0.3 S A:SO4305 3.5 59.5 1.0 O D:SER214 3.5 11.2 0.7 O A:HOH407 3.8 17.6 1.0 CB C:SER214 3.8 13.0 1.0 CG C:TYR212 3.8 11.1 1.0 CG C:HIS176 3.8 21.8 1.0 CB C:TYR212 3.8 8.3 1.0 CE1 C:HIS176 3.8 17.3 1.0 CD2 C:TYR212 3.8 12.0 1.0 CB C:HIS176 3.9 9.1 1.0 O A:HOH401 4.0 28.6 1.0 CB D:SER214 4.0 10.5 0.3 CB D:SER214 4.0 10.4 0.7 OG D:SER214 4.2 11.1 0.3 C D:SER214 4.2 11.7 0.3 C D:SER214 4.2 12.5 0.7 O3 A:SO4305 4.4 68.7 1.0 CD1 C:TYR212 4.4 10.0 1.0 CE2 C:TYR212 4.5 10.2 1.0 CA D:SER214 4.6 9.3 0.3 CA D:SER214 4.6 8.5 0.7 CA C:HIS176 4.6 11.0 1.0 O4 A:SO4305 4.6 59.7 1.0 N D:SER214 4.8 9.5 0.3 N D:SER214 4.8 9.3 0.7 OG D:SER214 4.8 12.3 0.7 NE2 C:HIS176 4.9 19.1 1.0 CD2 C:HIS176 5.0 22.4 1.0 CE1 C:TYR212 5.0 10.0 1.0

H.Liu, Z.Li, F.Xu. High Resolution Structure of Complement C1Q-Like Protein 3 C1Q Domain To Be Published.