Sodium in PDB 4ij7: Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg

The structure of Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg, PDB code: 4ij7 was solved by S.E.Zographos, K.E.Tsitsanou, C.E.Drakou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.22 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	80.650, 89.110, 43.400, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 24.5

The binding sites of Sodium atom in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg (pdb code 4ij7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg, PDB code: 4ij7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:33.7 occ:1.00 OD1 A:ASP97 2.5 18.6 1.0 ND2 A:ASN100 3.4 16.5 1.0 CG A:ASP97 3.6 22.1 1.0 CA A:ASP97 3.8 20.5 1.0 NE A:ARG96 3.8 30.3 1.0 CD B:LYS108 4.1 23.8 1.0 CG B:LYS108 4.1 19.1 1.0 CB A:ASP97 4.2 18.3 1.0 N A:ASP97 4.3 22.1 1.0 CD A:ARG96 4.4 26.1 1.0 O A:ARG96 4.4 17.9 1.0 CG A:ARG96 4.4 26.0 1.0 CG A:ASN100 4.4 21.9 1.0 C A:ARG96 4.5 21.9 1.0 CE B:LYS108 4.5 23.0 1.0 CB A:ASN100 4.5 19.4 1.0 CB B:LYS108 4.6 17.1 1.0 OD2 A:ASP97 4.6 21.1 1.0 CZ A:ARG96 4.7 30.7 1.0 NH2 A:ARG96 4.8 26.9 1.0 C A:ASP97 4.9 20.1 1.0 O A:ASP97 4.9 19.4 1.0

Sodium binding site 2 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:38.9 occ:1.00 O A:MET47 2.4 28.4 1.0 O A:HOH318 3.1 25.7 1.0 O A:GLY49 3.4 23.9 1.0 C A:MET47 3.5 31.3 1.0 O A:HOH323 3.6 36.3 1.0 CB B:ALA150 3.7 30.1 1.0 C A:ASP48 3.8 28.8 1.0 O A:ASP48 3.9 26.2 1.0 CA A:PRO51 4.0 27.5 1.0 CA A:ASP48 4.0 32.9 1.0 N A:ASP48 4.2 29.8 1.0 N A:PRO51 4.2 26.8 1.0 N A:GLY49 4.2 24.3 1.0 C A:GLY49 4.2 28.0 1.0 O A:ILE50 4.3 29.0 1.0 C A:ILE50 4.4 31.0 1.0 O A:GLN44 4.4 26.7 1.0 CA A:MET47 4.6 29.5 1.0 CB A:PRO51 4.7 29.0 1.0 N A:MET47 4.8 29.0 1.0 CA A:GLY49 4.8 30.5 1.0 CG A:PRO51 4.8 31.4 1.0 CB A:MET47 4.9 28.1 1.0 CD A:PRO51 4.9 29.1 1.0 N A:ARG52 5.0 23.2 1.0

Sodium binding site 3 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:48.1 occ:1.00 NH1 A:ARG52 2.1 43.9 1.0 O A:GLU120 2.5 37.4 1.0 CZ A:ARG52 3.0 48.0 1.0 NH2 A:ARG52 3.1 50.7 1.0 N A:SER122 3.5 43.5 1.0 OE1 A:GLU126 3.6 44.6 1.0 C A:GLU120 3.6 38.4 1.0 CB A:SER122 3.8 46.6 1.0 CD1 A:ILE128 3.9 29.4 1.0 CB A:LEU119 3.9 29.6 1.0 C A:PRO121 4.0 44.3 1.0 CA A:SER122 4.1 46.7 1.0 CA A:PRO121 4.1 42.1 1.0 CD A:GLU126 4.2 45.1 1.0 NE A:ARG52 4.2 37.7 1.0 N A:GLU120 4.3 36.6 1.0 OE2 A:GLU126 4.3 39.6 1.0 N A:PRO121 4.3 38.5 1.0 CD1 A:LEU119 4.6 27.9 1.0 CA A:GLU120 4.6 40.1 1.0 CG A:LEU119 4.7 25.0 1.0 C A:LEU119 4.7 33.5 1.0 O A:PRO121 4.8 44.3 1.0 CD A:ARG52 4.9 35.8 1.0 CA A:LEU119 4.9 30.7 1.0

Sodium binding site 4 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:37.6 occ:1.00 OE1 A:GLU104 2.4 29.0 1.0 OE1 B:GLU104 2.6 31.6 1.0 O A:HOH347 2.8 23.4 1.0 NZ B:LYS108 3.4 25.1 1.0 CD A:GLU104 3.4 26.5 1.0 CB B:GLU104 3.5 18.0 1.0 CB A:GLU104 3.6 17.3 1.0 CD B:GLU104 3.8 27.7 1.0 CA A:ALA101 4.0 18.7 1.0 CG A:GLU104 4.1 19.9 1.0 CE B:LYS108 4.2 23.0 1.0 CG B:GLU104 4.2 25.5 1.0 O A:ALA101 4.3 18.4 1.0 O B:ALA101 4.3 16.3 1.0 OE2 A:GLU104 4.4 25.0 1.0 NZ A:LYS108 4.4 28.0 1.0 O A:HOH362 4.5 35.1 1.0 CB A:ALA101 4.5 15.5 1.0 C B:GLU104 4.5 21.4 1.0 CA B:ALA101 4.6 20.8 1.0 N B:LEU105 4.6 18.1 1.0 CA B:GLU104 4.6 21.2 1.0 C A:ALA101 4.7 18.2 1.0 O B:HOH318 4.8 22.2 1.0 O A:ASN100 4.8 16.4 1.0 OE2 B:GLU104 4.8 30.1 1.0 N A:ALA101 4.9 19.5 1.0 CA A:GLU104 4.9 19.3 1.0 O B:GLU104 4.9 20.1 1.0 C B:ALA101 4.9 19.2 1.0

Sodium binding site 5 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:37.4 occ:1.00 O B:LEU119 2.5 27.4 1.0 O B:LYS118 3.5 30.3 1.0 C B:LEU119 3.6 29.3 1.0 O B:HOH362 3.8 36.5 1.0 C B:LYS118 3.8 23.8 1.0 CG1 B:ILE128 4.0 25.9 1.0 CB B:ILE128 4.0 23.5 1.0 CG2 B:ILE128 4.0 22.5 1.0 N B:LEU119 4.3 23.0 1.0 O B:ALA117 4.3 21.7 1.0 CA B:LYS118 4.4 22.8 1.0 OE1 B:GLU120 4.4 40.5 1.0 CA B:GLU120 4.4 31.5 1.0 N B:GLU120 4.4 26.4 1.0 CA B:LEU119 4.6 24.7 1.0 CD B:GLU120 4.6 42.1 1.0 OE2 B:GLU120 4.7 43.9 1.0 CD B:PRO121 4.9 32.3 1.0

Sodium binding site 6 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:45.2 occ:1.00 OE2 B:GLU104 2.4 30.1 1.0 CD B:GLU104 3.3 27.7 1.0 O B:HOH316 3.4 28.7 1.0 NZ A:LYS108 3.5 28.0 1.0 O A:HOH306 3.7 20.8 1.0 OE1 B:GLU104 3.7 31.6 1.0 CE A:LYS108 3.8 23.3 1.0 CG B:GLU104 4.5 25.5 1.0 CB B:ASN100 4.6 19.9 1.0

Sodium binding site 7 out of 7 in the Crystal Structure of Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg


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 Odorant Binding Protein 48 From Anopheles Gambiae (AGAMOBP48) with Peg within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:44.3 occ:1.00 O B:GLY70 2.4 34.7 1.0 C B:GLY70 3.6 32.0 1.0 CE1 B:HIS130 3.6 21.8 1.0 OE2 B:GLU114 3.9 27.0 1.0 CA B:MET71 4.0 31.7 1.0 NE2 B:HIS130 4.0 22.9 1.0 CG1 B:ILE132 4.0 23.3 1.0 CB B:ILE132 4.0 22.1 1.0 CG B:MET71 4.2 39.0 1.0 N B:MET71 4.2 35.1 1.0 CG2 B:ILE132 4.4 20.5 1.0 CD1 B:ILE132 4.4 19.3 1.0 ND1 B:HIS130 4.5 19.9 1.0 CB B:MET71 4.6 39.6 1.0 CA B:GLY70 4.7 26.7 1.0 N B:LEU72 4.9 27.4 1.0 CD2 B:HIS130 5.0 23.2 1.0

K.E.Tsitsanou, C.E.Drakou, T.Thireou, A.Vitlin Gruber, G.Kythreoti, A.Azem, D.Fessas, E.Eliopoulos, K.Iatrou, S.E.Zographos. Crystal and Solution Studies of the "Plus-C" Odorant-Binding Protein 48 From Anopheles Gambiae: Control of Binding Specificity Through Three-Dimensional Domain Swapping. J.Biol.Chem. V. 288 33427 2013.
ISSN: ISSN 0021-9258
PubMed: 24097978
DOI: 10.1074/JBC.M113.505289