Sodium in PDB 8ptf: The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.

The structure of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin., PDB code: 8ptf was solved by J.Whittaker, J.M.Felices Martinez, A.Guskov, D.J.Slotboom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.43 / 1.95
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	52.724, 145.391, 116.382, 90, 90, 90
R / Rfree (%)	23.5 / 28.1

The structure of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Sodium atom in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. (pdb code 8ptf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin., PDB code: 8ptf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:40.3 occ:1.00 O A:PHE102 2.4 21.5 1.0 OH A:TYR64 2.5 28.1 1.0 OH A:TYR36 2.9 37.0 1.0 CZ A:TYR64 3.4 28.4 1.0 C A:PHE102 3.5 23.9 1.0 CE2 A:TYR64 3.6 26.0 1.0 CB A:SER361 3.6 32.2 1.0 CD1 A:ILE87 3.7 27.5 1.0 CA A:GLY105 3.8 32.2 1.0 CZ A:TYR36 3.9 38.2 1.0 OG A:SER361 3.9 33.1 1.0 N A:GLY105 3.9 31.4 1.0 CA A:PHE102 3.9 23.7 1.0 NH1 A:ARG52 4.1 48.1 1.0 CD1 A:PHE102 4.2 27.9 1.0 CE2 A:TYR36 4.2 36.6 1.0 O A:ASP101 4.3 23.9 1.0 CG A:PHE102 4.4 27.7 1.0 CE1 A:PHE102 4.4 28.0 1.0 N A:PRO103 4.6 22.9 1.0 C A:THR104 4.7 29.3 1.0 C A:PRO103 4.7 27.4 1.0 CE1 A:TYR64 4.7 27.5 1.0 O A:PRO103 4.7 27.2 1.0 CB A:PHE102 4.8 25.7 1.0 CD A:ARG52 4.8 42.1 1.0 CD2 A:TYR64 4.9 25.2 1.0 CD2 A:PHE102 4.9 27.6 1.0 CZ A:PHE102 4.9 28.8 1.0 N A:THR104 5.0 27.5 1.0 CA A:PRO103 5.0 25.9 1.0 OE1 A:GLU34 5.0 41.1 1.0 N A:PHE102 5.0 24.1 1.0 CA A:SER361 5.0 34.4 1.0

Sodium binding site 2 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:43.6 occ:1.00 O A:VAL327 2.5 37.3 1.0 N A:ASN350 2.8 25.2 1.0 OD1 A:ASN350 2.9 26.1 1.0 N A:GLY329 3.2 28.9 1.0 CA A:ASN350 3.3 26.1 1.0 O A:ALA322 3.4 25.6 1.0 CG A:ASN350 3.5 26.5 1.0 CA A:GLY329 3.6 30.5 1.0 C A:LYS328 3.6 28.8 1.0 C A:VAL327 3.7 32.0 1.0 CD1 A:LEU349 3.8 24.5 1.0 CA A:ALA322 3.8 25.7 1.0 C A:LEU349 3.9 26.9 1.0 CA A:LYS328 3.9 30.7 1.0 CD A:PRO351 3.9 27.3 1.0 CB A:ASN350 4.0 26.0 1.0 C A:ALA322 4.0 25.1 1.0 CA A:LEU349 4.1 27.7 1.0 CB A:ALA322 4.1 24.6 1.0 O A:GLY348 4.1 34.9 1.0 O A:LYS328 4.3 25.3 1.0 N A:LYS328 4.3 32.3 1.0 ND2 A:ASN350 4.4 29.5 1.0 C A:ASN350 4.5 25.4 1.0 O A:GLU321 4.6 28.6 1.0 N A:PRO351 4.7 27.6 1.0 CA A:TYR325 4.7 30.1 1.0 CG A:LEU349 4.7 25.8 1.0 N A:VAL327 4.7 33.9 1.0 C A:TYR325 4.8 32.1 1.0 CA A:VAL327 4.9 33.6 1.0 CB A:LEU349 4.9 26.9 1.0 N A:TYR325 5.0 33.2 1.0

Sodium binding site 3 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na409 b:24.4 occ:1.00 OD1 A:ASP181 2.7 25.3 1.0 ND2 A:ASN161 3.0 24.3 1.0 CG A:ASP181 3.6 26.7 1.0 CB A:LEU180 3.6 22.7 1.0 OD1 A:ASN161 3.8 26.5 1.0 CG A:ASN161 3.8 27.6 1.0 OD2 A:ASP181 3.9 22.3 1.0 C A:LEU180 4.3 28.4 1.0 CD1 A:LEU180 4.4 23.5 1.0 O A:LEU180 4.5 30.8 1.0 CA A:LEU180 4.5 26.4 1.0 CG A:LEU180 4.6 22.9 1.0 N A:ASP181 4.6 32.5 1.0 CB A:ASP181 4.9 29.2 1.0 O A:TYR138 5.0 21.2 1.0

Sodium binding site 4 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na410 b:33.6 occ:1.00 O A:ASP230 2.6 35.9 1.0 O A:ARG227 2.8 20.3 1.0 N A:ASP235 2.8 30.3 1.0 N A:GLY234 3.2 32.1 1.0 C A:ASP230 3.4 38.7 1.0 CA A:ASP235 3.5 29.1 1.0 CB A:ASP235 3.5 32.7 1.0 CA A:GLY228 3.7 25.8 1.0 C A:GLY234 3.8 29.9 1.0 C A:ARG227 3.8 21.8 1.0 C A:ASP235 3.8 30.4 1.0 CA A:GLY234 3.8 30.8 1.0 O A:ASP235 3.9 29.3 1.0 CA A:ILE231 3.9 37.7 1.0 CB A:ALA233 4.0 28.7 1.0 C A:ALA233 4.0 37.6 1.0 CE1 A:TYR236 4.1 25.2 1.0 N A:ILE231 4.1 39.3 1.0 C A:GLY228 4.2 31.0 1.0 C A:ILE231 4.2 45.6 1.0 N A:GLY228 4.2 21.6 1.0 O A:ILE231 4.2 50.8 1.0 CD1 A:TYR236 4.3 25.2 1.0 N A:ASP230 4.3 32.5 1.0 N A:ALA233 4.3 36.2 1.0 CA A:ALA233 4.3 35.4 1.0 CA A:ASP230 4.4 37.0 1.0 O A:HOH570 4.5 23.8 1.0 O A:GLY228 4.6 30.1 1.0 N A:THR229 4.7 33.5 1.0 N A:TYR236 4.7 28.5 1.0 CG A:ASP235 4.8 39.2 1.0 N A:GLU232 4.9 46.6 1.0 O A:GLY234 4.9 27.5 1.0

Sodium binding site 5 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na411 b:43.0 occ:1.00 O A:ILE214 2.7 28.2 1.0 OD2 A:ASP164 3.1 25.7 1.0 OD1 A:ASP164 3.2 25.7 1.0 O A:HOH526 3.3 45.1 1.0 CG A:ASP164 3.5 25.9 1.0 O A:ILE165 3.6 20.2 1.0 C A:ILE214 3.8 28.6 1.0 CD2 A:LEU215 4.0 21.7 1.0 C A:ILE165 4.3 20.8 1.0 N A:ILE214 4.4 25.4 1.0 CB A:CYS166 4.5 23.5 1.0 CG A:LEU215 4.5 25.0 1.0 CG2 A:ILE214 4.5 21.3 1.0 N A:LEU215 4.7 26.3 1.0 CA A:ILE214 4.7 23.6 1.0 N A:ILE165 4.7 21.7 1.0 CA A:LEU215 4.7 24.3 1.0 O A:HOH621 4.8 26.5 1.0 CB A:ASP164 4.8 22.7 1.0 N A:CYS166 4.9 21.3 1.0 CG A:LYS213 4.9 22.3 1.0

Sodium binding site 6 out of 6 in the The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Surface-Exposed Lipo-Protein of BTUG2 in Complex with Cyanocobalamin. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na412 b:14.9 occ:1.00 N A:LEU50 3.2 28.8 1.0 N A:PHE65 3.4 27.0 1.0 CA A:ASN63 3.5 33.3 1.0 C A:ASN63 3.5 32.5 1.0 CB A:PHE65 3.6 24.2 1.0 N A:SER66 3.6 28.9 1.0 CA A:SER49 3.7 26.1 1.0 CB A:SER49 3.8 23.3 1.0 O A:LEU50 3.8 27.4 1.0 OG A:SER66 3.9 30.5 1.0 O A:ASN63 3.9 32.8 1.0 N A:TYR64 3.9 28.4 1.0 C A:SER49 3.9 29.7 1.0 CA A:PHE65 4.0 27.0 1.0 CA A:LEU50 4.1 27.4 1.0 CB A:ASN63 4.1 34.7 1.0 CB A:SER66 4.3 30.9 1.0 C A:PHE65 4.3 29.0 1.0 CB A:LEU50 4.4 28.3 1.0 C A:LEU50 4.4 28.6 1.0 O A:ASN62 4.4 35.6 1.0 C A:TYR64 4.5 31.9 1.0 CA A:SER66 4.5 36.2 1.0 N A:ASN63 4.7 31.4 1.0 CG A:PHE65 4.8 23.8 1.0 CA A:TYR64 4.8 31.8 1.0 O A:SER48 4.8 31.1 1.0 OG A:SER49 5.0 22.0 1.0

J.Whittaker, A.Guskov. The Surface-Exposed Lipo-Protein of BTUG1 in Complex with Cyanocobinamide. To Be Published.