Sodium in PDB 8q2o: Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization

The structure of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization, PDB code: 8q2o was solved by C.-Y.Huang, C.Boland, S.S.Kaki, M.Wang, V.Olieric, M.Caffrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.63 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	57.09, 74.49, 115.78, 90, 102.5, 90
R / Rfree (%)	16.3 / 19.9

The binding sites of Sodium atom in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization (pdb code 8q2o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization, PDB code: 8q2o:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:19.2 occ:0.93 O A:ALA136 2.3 21.1 1.0 O A:TYR141 2.4 17.8 1.0 OE1 A:GLU144 2.4 19.7 1.0 O A:GLU144 2.4 17.6 1.0 O A:THR139 2.5 19.6 1.0 O A:HOH843 2.5 28.4 1.0 C A:ALA136 3.4 16.6 1.0 C A:GLU144 3.5 17.0 1.0 CD A:GLU144 3.5 19.8 1.0 C A:TYR141 3.5 19.6 1.0 C A:THR139 3.5 21.7 1.0 OG1 A:THR139 3.6 18.8 1.0 CB A:GLU144 3.8 15.3 1.0 N A:TYR141 4.0 18.8 1.0 CA A:GLU144 4.0 15.3 1.0 CA A:ALA136 4.0 16.2 1.0 N A:THR139 4.0 15.6 1.0 CB A:ALA136 4.0 22.8 1.0 N A:GLU144 4.2 14.3 1.0 CG A:GLU144 4.2 15.8 1.0 CA A:THR139 4.3 17.4 1.0 O A:HOH870 4.3 34.6 1.0 CA A:TYR141 4.3 17.9 1.0 OE2 A:GLU144 4.3 18.9 1.0 C A:ALA140 4.3 23.1 1.0 N A:PRO142 4.3 18.6 1.0 CA A:PRO142 4.4 19.1 1.0 O A:HOH652 4.5 19.2 1.0 N A:GLY137 4.5 17.9 1.0 N A:ALA140 4.5 18.4 1.0 N A:HIS145 4.6 11.7 1.0 CB A:THR139 4.6 18.0 1.0 CA A:ALA140 4.7 20.8 1.0 N A:LEU138 4.8 19.2 1.0 C A:PRO142 4.8 18.7 1.0 CB A:TYR141 4.8 15.2 1.0 CA A:GLY137 4.8 22.9 1.0 CA A:HIS145 4.9 13.3 1.0 O A:ALA140 4.9 24.9 1.0 C A:GLY137 5.0 24.6 1.0

Sodium binding site 2 out of 5 in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:37.7 occ:0.87 NZ A:LYS325 2.6 36.0 1.0 NE A:ARG317 2.9 17.0 1.0 OD1 A:ASN319 3.0 27.4 1.0 OD1 A:ASN273 3.0 19.6 1.0 CE A:LYS325 3.1 25.1 1.0 CD A:LYS325 3.3 23.6 1.0 NH2 A:ARG317 3.3 23.7 1.0 O A:ASN265 3.3 26.1 1.0 CZ A:ARG317 3.5 17.4 1.0 CG A:ASN319 3.6 19.2 1.0 ND2 A:ASN319 3.7 23.3 1.0 CA A:GLY358 3.9 13.8 1.0 CD A:ARG317 4.0 16.6 1.0 O A:GLY358 4.1 16.1 1.0 CB A:SER268 4.1 19.4 1.0 CG A:ASN273 4.2 19.3 1.0 C A:ASN265 4.4 25.3 1.0 CA A:TYR266 4.4 24.9 1.0 C A:GLY358 4.5 18.5 1.0 O A:TYR266 4.5 27.8 1.0 C A:TYR266 4.6 30.3 1.0 CG A:LYS325 4.6 21.2 1.0 N A:SER268 4.7 26.7 1.0 NH1 A:ARG317 4.8 22.1 1.0 CG A:ARG317 4.8 14.6 1.0 N A:TYR266 4.9 25.2 1.0

Sodium binding site 3 out of 5 in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na525 b:29.1 occ:0.86 O A:HOH627 2.8 31.4 1.0 NH2 A:ARG489 2.9 18.6 1.0 O1 A:SO4524 3.0 22.4 0.9 O A:HOH830 3.3 30.8 1.0 CE1 A:HIS16 3.5 19.1 1.0 NE2 A:HIS16 3.7 19.1 1.0 CE1 A:HIS17 3.7 19.0 1.0 CZ2 A:TRP76 3.7 14.9 1.0 CD A:PRO27 3.7 22.3 1.0 CG A:PRO27 3.8 29.0 1.0 CZ A:ARG489 3.8 19.9 1.0 NH1 A:ARG489 3.9 23.6 1.0 CH2 A:TRP76 4.0 13.8 1.0 O4 A:SO4524 4.0 24.9 0.9 S A:SO4524 4.1 21.0 0.9 NE2 A:HIS17 4.3 18.8 1.0 CD A:LYS40 4.5 28.4 1.0 ND1 A:HIS17 4.7 18.1 1.0 NA A:NA526 4.7 25.3 0.8 CE2 A:TRP76 4.7 17.8 1.0 O3 A:SO4524 4.8 19.7 0.9 ND1 A:HIS16 4.8 18.6 1.0 CB A:SER30 4.8 21.9 1.0 ND1 A:HIS18 4.9 19.8 1.0 CE A:LYS40 4.9 24.3 1.0

Sodium binding site 4 out of 5 in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na526 b:25.3 occ:0.85 O1 A:SO4524 2.6 22.4 0.9 O A:LYS40 2.7 18.8 1.0 O A:HOH818 2.7 24.3 1.0 NE2 A:HIS17 2.8 18.8 1.0 CD2 A:HIS17 3.6 18.5 1.0 CD2 A:PHE78 3.6 18.4 1.0 N A:LYS40 3.7 20.1 1.0 O2 A:SO4524 3.7 22.7 0.9 S A:SO4524 3.7 21.0 0.9 C A:LYS40 3.7 20.2 1.0 CH2 A:TRP76 3.8 13.8 1.0 CZ3 A:TRP76 3.8 20.5 1.0 CE1 A:HIS17 3.8 19.0 1.0 CA A:LYS40 4.0 18.3 1.0 CG A:PHE78 4.0 17.8 1.0 CB A:LYS40 4.0 18.2 1.0 O3 A:SO4524 4.1 19.7 0.9 CB A:PHE78 4.1 14.8 1.0 NE2 A:HIS16 4.2 19.1 1.0 CE2 A:PHE78 4.3 22.2 1.0 C A:PRO39 4.3 25.4 1.0 CB A:PRO39 4.5 23.8 1.0 O A:HOH876 4.5 32.3 1.0 CA A:PRO39 4.7 27.1 1.0 NA A:NA525 4.7 29.1 0.9 CG A:HIS17 4.8 20.8 1.0 ND1 A:HIS17 4.9 18.1 1.0 CD2 A:HIS16 4.9 21.0 1.0 N A:ASN41 4.9 14.7 1.0 CD1 A:PHE78 5.0 19.0 1.0 CE1 A:HIS16 5.0 19.1 1.0 CZ2 A:TRP76 5.0 14.9 1.0 O4 A:SO4524 5.0 24.9 0.9

Sodium binding site 5 out of 5 in the Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Alginate Transporter Alge From P. Aeruginosa PAO1 By Using Se-Mag For the the Lipid Cubic Phase Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Na527 b:33.9 occ:0.90 OD2 A:ASP55 2.2 39.2 1.0 O A:GLY63 2.2 50.3 1.0 OD2 A:ASP57 2.4 39.9 1.0 O A:ALA61 2.4 57.4 1.0 OD1 A:ASP57 2.4 43.8 1.0 CG A:ASP57 2.7 35.0 1.0 OD1 A:ASP55 2.7 37.3 1.0 CG A:ASP55 2.8 33.7 1.0 C A:GLY63 3.5 51.0 1.0 C A:ALA61 3.5 54.7 1.0 N A:ALA61 4.1 44.5 1.0 C A:PRO62 4.1 50.9 1.0 CA A:GLY59 4.2 40.4 1.0 N A:GLY63 4.2 57.2 1.0 CB A:ASP57 4.2 30.2 1.0 N A:GLY59 4.2 33.0 1.0 CB A:ASP55 4.3 25.1 1.0 O A:PRO62 4.3 55.0 1.0 CA A:GLY64 4.3 38.2 1.0 CA A:ALA61 4.3 52.5 1.0 N A:GLY64 4.3 46.8 1.0 CA A:GLY63 4.4 61.4 1.0 N A:PRO62 4.5 65.5 1.0 CA A:PRO62 4.5 54.7 1.0 C A:GLY59 4.5 47.0 1.0 N A:THR60 4.6 35.6 1.0 N A:ASP57 4.7 27.2 1.0 CB A:ALA61 4.8 37.5 1.0 CA A:ASP57 4.9 29.5 1.0 CG2 A:THR65 4.9 28.7 1.0 C A:GLY64 4.9 52.0 1.0 O A:HOH832 5.0 41.9 1.0

C.Boland, C.Y.Huang, S.Shanker Kaki, M.Wang, V.Olieric, M.Caffrey. Se-Mag Is A Convenient Additive For Experimental Phasing and Structure Determination of Membrane Proteins Crystallised By the Lipid Cubic Phase (in Meso) Method Crystals 2023.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST13091402