Sodium in PDB 6yro: Streptococcus Suis Sadp Mutant - N285D

The structure of Streptococcus Suis Sadp Mutant - N285D, PDB code: 6yro was solved by A.C.Papageorgiou, S.Haataja, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.68 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	126.132, 80.799, 130.740, 90.00, 113.13, 90.00
R / Rfree (%)	17.4 / 22.2

The binding sites of Sodium atom in the Streptococcus Suis Sadp Mutant - N285D (pdb code 6yro). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Streptococcus Suis Sadp Mutant - N285D, PDB code: 6yro:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Streptococcus Suis Sadp Mutant - N285D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Streptococcus Suis Sadp Mutant - N285D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:44.1 occ:0.94 O A:HOH934 2.0 37.5 1.0 O A:HOH804 2.1 44.0 1.0 NE2 A:HIS194 2.3 33.7 1.0 OD1 A:ASP285 2.4 32.0 1.0 OD2 A:ASP285 2.7 38.1 1.0 CG A:ASP285 2.9 35.0 1.0 NE2 A:GLN286 3.1 48.4 1.0 CE1 A:HIS194 3.2 36.2 1.0 CD2 A:HIS194 3.3 34.3 1.0 CD2 A:PHE318 4.1 29.1 1.0 CE2 A:PHE318 4.2 32.5 1.0 CD A:GLN286 4.2 45.9 1.0 ND1 A:HIS194 4.3 35.0 1.0 CB A:ASP285 4.3 24.9 1.0 CG A:HIS194 4.4 32.5 1.0 N A:GLN286 4.5 25.4 1.0 CG A:PHE318 4.6 29.0 1.0 CG A:GLN286 4.7 34.8 1.0 CZ A:PHE318 4.8 30.1 1.0

Sodium binding site 2 out of 3 in the Streptococcus Suis Sadp Mutant - N285D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Streptococcus Suis Sadp Mutant - N285D within 5.0Å range: probe atom residue distance (Å) B Occ C:Na802 b:52.4 occ:1.00 O C:HOH1039 2.3 47.2 1.0 O C:THR163 2.5 27.1 1.0 O C:HOH980 2.6 32.9 1.0 O C:HOH987 3.3 47.3 1.0 O C:HOH1043 3.4 48.5 1.0 O C:HOH971 3.5 52.7 1.0 C C:THR163 3.7 25.3 1.0 NE2 C:GLN146 3.8 22.8 1.0 C C:SER164 4.0 26.9 1.0 O C:SER164 4.0 24.0 1.0 CA C:SER164 4.2 27.6 1.0 CB C:SER166 4.3 32.3 1.0 OG C:SER166 4.4 39.7 1.0 N C:SER164 4.4 27.2 1.0 N C:VAL165 4.4 26.2 1.0 O C:HOH930 4.5 34.1 1.0 C C:VAL165 4.7 26.4 1.0 CB C:THR163 4.8 29.9 1.0 CA C:THR163 4.8 24.1 1.0 CB C:ASP184 4.8 28.4 1.0 N C:SER166 4.8 26.3 1.0 O C:VAL165 4.9 29.3 1.0 CD C:GLN146 5.0 30.0 1.0

Sodium binding site 3 out of 3 in the Streptococcus Suis Sadp Mutant - N285D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Streptococcus Suis Sadp Mutant - N285D within 5.0Å range: probe atom residue distance (Å) B Occ E:Na401 b:57.1 occ:1.00 ND1 E:HIS216 2.8 58.6 1.0 OD2 E:ASP212 3.0 44.1 1.0 CE1 E:HIS216 3.8 56.7 1.0 OD1 E:ASN214 3.8 59.8 1.0 CG E:HIS216 3.8 55.9 1.0 CB E:HIS216 4.0 41.3 1.0 CG E:ASP212 4.1 43.3 1.0 O E:HOH515 4.2 36.7 1.0 OD1 E:ASP212 4.4 43.9 1.0 CG E:ASN214 4.6 52.2 1.0 CB E:ASN214 4.6 51.4 1.0 NE2 E:HIS216 4.9 58.0 1.0 CD2 E:HIS216 5.0 55.4 1.0

M.M.Johansson, E.Belurier, A.C.Papageorgiou, A.P.Sundin, J.Rahkila, U.J.Nilsson, S.Maatsola, T.Nyholm, J.Kapyla, L.Reino, J.Finne, S.Teneberg, S.Haataja. Streptococcus Suis Sadp Adhesin Binding Mechanism to the Host Globo Series Glycolipid Receptors To Be Published.