Sodium in PDB 4odi: 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii

All present enzymatic activity of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii:
5.4.2.4;

The structure of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii, PDB code: 4odi was solved by G.Minasov, J.Ruan, H.Ngo, L.Shuvalova, I.Dubrovska, K.Flores, D.Shanmugam, D.Roos, W.F.Anderson, Center For Structural Genomics Of Infectiousdiseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.72 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	97.182, 149.474, 72.120, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23.9

The binding sites of Sodium atom in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii (pdb code 4odi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii, PDB code: 4odi:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:48.1 occ:1.00 O A:HOH410 2.4 33.7 1.0 OD1 A:ASN160 2.4 43.0 1.0 O A:TYR155 2.5 32.1 1.0 O A:VAL158 2.5 43.9 1.0 C A:TYR155 3.5 33.7 1.0 CG A:ASN160 3.6 45.4 1.0 O A:LYS156 3.7 41.0 1.0 C A:VAL158 3.7 41.8 1.0 CD1 A:LEU163 3.8 35.3 1.0 CA A:LYS156 3.9 39.8 1.0 C A:LYS156 3.9 40.4 1.0 N A:LYS156 4.1 37.2 1.0 N A:VAL158 4.2 38.1 1.0 N A:ASN160 4.3 40.5 1.0 ND2 A:ASN160 4.3 48.0 1.0 CA A:VAL158 4.4 39.3 1.0 CE C:MET189 4.4 48.4 1.0 O A:GLY150 4.5 39.1 1.0 CB A:TYR155 4.5 30.2 1.0 C A:PRO159 4.5 40.4 1.0 CA A:ASN160 4.6 41.3 1.0 CA A:TYR155 4.7 33.5 1.0 N A:PRO159 4.7 41.7 1.0 CB A:ASN160 4.8 43.0 1.0 N A:MET157 4.8 39.4 1.0 CB A:VAL158 4.8 36.1 1.0 CA A:GLY150 4.8 33.4 1.0 CA A:PRO159 4.8 39.6 1.0

Sodium binding site 2 out of 4 in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:52.6 occ:1.00 OD1 B:ASN160 2.4 48.8 1.0 O B:TYR155 2.4 37.7 1.0 O B:VAL158 2.6 44.2 1.0 O B:HOH438 2.6 31.3 1.0 O B:HOH451 2.8 43.9 1.0 C B:TYR155 3.4 38.4 1.0 CD1 B:LEU163 3.6 33.6 1.0 CG B:ASN160 3.6 47.9 1.0 C B:VAL158 3.8 45.2 1.0 O B:LYS156 4.0 51.3 1.0 N B:LYS156 4.0 43.8 1.0 CA B:LYS156 4.1 53.4 1.0 C B:LYS156 4.2 52.6 1.0 CB B:TYR155 4.2 32.7 1.0 O B:HOH452 4.2 44.1 1.0 N B:ASN160 4.3 45.9 1.0 N B:VAL158 4.3 43.5 1.0 ND2 B:ASN160 4.4 50.8 1.0 CA B:TYR155 4.4 36.6 1.0 O B:GLY150 4.4 34.3 1.0 CA B:VAL158 4.5 41.4 1.0 CA B:ASN160 4.5 44.1 1.0 C B:PRO159 4.6 43.4 1.0 CA B:GLY150 4.6 35.1 1.0 CB B:ASN160 4.7 47.7 1.0 CB B:VAL158 4.7 39.5 1.0 N B:PRO159 4.8 43.3 1.0 CG B:LEU163 4.9 31.6 1.0 C B:GLY150 4.9 33.7 1.0 CA B:PRO159 4.9 42.4 1.0 O B:PRO149 5.0 32.1 1.0 N B:MET157 5.0 51.1 1.0

Sodium binding site 3 out of 4 in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:52.1 occ:1.00 OD1 C:ASN160 2.3 55.4 1.0 O C:TYR155 2.5 38.4 1.0 O C:HOH417 2.7 39.3 1.0 O C:VAL158 2.7 40.8 1.0 C C:TYR155 3.5 45.7 1.0 CG C:ASN160 3.6 55.6 1.0 CD1 C:LEU163 3.6 46.4 1.0 C C:VAL158 3.9 38.8 1.0 CA C:LYS156 3.9 51.9 1.0 O C:LYS156 3.9 53.1 1.0 C C:LYS156 4.1 50.4 1.0 N C:LYS156 4.1 53.4 1.0 O C:GLY150 4.3 44.7 1.0 ND2 C:ASN160 4.3 60.1 1.0 CB C:TYR155 4.3 41.7 1.0 N C:ASN160 4.3 39.8 1.0 N C:VAL158 4.4 39.0 1.0 CA C:GLY150 4.5 40.0 1.0 CA C:TYR155 4.5 43.4 1.0 CA C:ASN160 4.6 45.3 1.0 C C:PRO159 4.6 35.6 1.0 CA C:VAL158 4.6 39.4 1.0 CB C:ASN160 4.7 50.0 1.0 C C:GLY150 4.7 44.8 1.0 CB C:VAL158 4.9 41.0 1.0 O C:PRO149 4.9 43.9 1.0 CG C:LEU163 4.9 45.0 1.0 CE A:MET189 4.9 40.4 1.0 N C:PRO159 4.9 34.8 1.0 N C:MET157 4.9 50.1 1.0 CA C:PRO159 5.0 34.0 1.0

Sodium binding site 4 out of 4 in the 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:64.7 occ:1.00 O D:TYR155 2.4 51.3 1.0 OD1 D:ASN160 2.6 67.4 1.0 O D:VAL158 2.7 51.6 1.0 C D:TYR155 3.3 51.1 1.0 O D:LYS156 3.7 56.1 1.0 CA D:LYS156 3.8 61.8 1.0 CG D:ASN160 3.8 70.4 1.0 C D:VAL158 3.8 47.1 1.0 CD1 D:LEU163 3.9 51.4 1.0 C D:LYS156 3.9 62.0 1.0 N D:LYS156 3.9 57.0 1.0 N D:VAL158 4.2 46.6 1.0 CB D:TYR155 4.3 46.9 1.0 CA D:TYR155 4.4 46.6 1.0 N D:ASN160 4.5 56.9 1.0 ND2 D:ASN160 4.5 75.2 1.0 CA D:VAL158 4.5 45.5 1.0 O D:GLY150 4.5 56.8 1.0 O D:HOH410 4.6 57.1 1.0 N D:MET157 4.7 58.6 1.0 CE B:MET189 4.8 54.6 1.0 C D:PRO159 4.8 49.0 1.0 CB D:VAL158 4.8 43.8 1.0 CA D:ASN160 4.8 61.8 1.0 CA D:GLY150 4.8 59.2 1.0 N D:PRO159 4.9 44.7 1.0 CB D:ASN160 4.9 65.4 1.0

G.Minasov, J.Ruan, H.Ngo, L.Shuvalova, I.Dubrovska, K.Flores, D.Shanmugam, D.Roos, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 From Toxoplasma Gondii. To Be Published.