Sodium in PDB 3ihv: Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution

The structure of Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution, PDB code: 3ihv was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.908, 72.318, 131.629, 90.00, 97.31, 90.00
R / Rfree (%)	16.2 / 19.3

The structure of Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution (pdb code 3ihv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution, PDB code: 3ihv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution


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 Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na5 b:25.8 occ:1.00 O A:HOH572 2.1 24.2 1.0 O A:TRP516 2.3 9.5 1.0 O A:GLY513 2.4 5.2 1.0 O A:HOH901 2.5 10.4 1.0 O A:TYR514 2.9 6.7 1.0 C A:TYR514 3.4 6.9 1.0 C A:TRP516 3.5 10.3 1.0 C A:GLY513 3.6 5.7 1.0 CA A:TYR514 3.7 6.8 1.0 N A:TRP516 4.0 6.9 1.0 N A:TYR514 4.1 5.6 1.0 CA A:TRP516 4.2 8.4 1.0 C A:TRP515 4.3 6.2 1.0 N A:TRP515 4.4 6.5 1.0 N A:GLU517 4.5 11.5 1.0 CB A:TRP516 4.6 9.1 1.0 CA A:GLU517 4.7 13.7 1.0 O A:TRP515 4.7 4.8 1.0 CA A:GLY513 4.8 5.9 1.0 CA A:TRP515 4.9 6.4 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution


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 Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na7 b:16.9 occ:1.00 O A:PHE287 2.2 11.4 1.0 O A:ASN411 2.3 7.9 1.0 O A:HOH811 2.3 7.8 1.0 O A:HOH726 2.4 7.7 1.0 OD1 A:ASN413 2.5 9.3 1.0 O A:HOH685 2.8 14.5 1.0 CG A:ASN413 3.3 8.1 1.0 C A:PHE287 3.4 10.7 1.0 C A:ASN411 3.4 7.4 1.0 ND2 A:ASN413 3.5 7.4 1.0 N A:PHE287 3.9 8.7 1.0 CA A:GLY274 4.0 12.2 1.0 CB A:ASN411 4.0 7.9 1.0 CA A:ASN411 4.1 7.2 1.0 CB A:TYR288 4.2 13.3 1.0 CA A:PHE287 4.2 8.5 1.0 N A:GLY274 4.3 12.0 1.0 OG A:SER286 4.3 9.4 1.0 N A:TYR288 4.4 12.0 1.0 N A:ASN413 4.4 6.4 1.0 O A:HOH1057 4.4 36.6 1.0 N A:VAL412 4.5 7.1 1.0 CA A:TYR288 4.5 12.1 1.0 C A:VAL412 4.5 6.9 1.0 CB A:ASN413 4.6 7.2 1.0 O A:HOH904 4.6 13.9 1.0 CB A:PHE287 4.7 7.8 1.0 CA A:VAL412 4.7 6.7 1.0 O A:HOH1121 4.7 19.9 1.0 CA A:ASN413 4.8 7.1 1.0 C A:SER286 4.8 8.8 1.0 O A:THR271 4.9 7.8 1.0 CD1 A:TYR288 5.0 15.5 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution


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 Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na6 b:17.2 occ:1.00 O B:PHE287 2.2 12.0 1.0 O B:ASN411 2.3 8.7 1.0 OD1 B:ASN413 2.4 5.0 1.0 O B:HOH662 2.5 7.9 1.0 O B:HOH905 2.5 11.7 1.0 O B:HOH714 2.8 17.9 1.0 CG B:ASN413 3.2 7.1 1.0 C B:PHE287 3.4 11.1 1.0 C B:ASN411 3.4 7.5 1.0 ND2 B:ASN413 3.5 8.0 1.0 N B:PHE287 3.9 8.0 1.0 CA B:GLY274 4.0 12.3 1.0 CB B:ASN411 4.1 7.6 1.0 CA B:ASN411 4.1 7.0 1.0 CA B:PHE287 4.2 9.2 1.0 N B:ASN413 4.3 7.2 1.0 CB B:TYR288 4.3 13.6 1.0 N B:GLY274 4.4 12.6 1.0 OG B:SER286 4.4 9.1 1.0 N B:TYR288 4.4 11.8 1.0 N B:VAL412 4.4 6.4 1.0 C B:VAL412 4.5 7.2 1.0 CB B:ASN413 4.5 6.5 1.0 CA B:TYR288 4.6 12.9 1.0 CB B:PHE287 4.6 8.6 1.0 CA B:VAL412 4.6 7.3 1.0 CA B:ASN413 4.8 6.6 1.0 C B:SER286 4.8 8.8 1.0 O B:HOH880 4.8 15.3 1.0 O B:HOH605 4.8 20.8 1.0 O B:THR271 4.9 10.2 1.0 CA B:SER286 5.0 8.4 1.0 O B:VAL412 5.0 6.8 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution


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 Susd Homolog (NP_813570.1) From Bacteroides Thetaiotaomicron Vpi-5482 at 1.70 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Na8 b:30.2 occ:1.00 O B:HOH892 2.2 23.7 1.0 O B:TRP516 2.4 8.2 1.0 O B:GLY513 2.4 6.7 1.0 O B:HOH916 2.4 12.9 1.0 O B:TYR514 2.9 8.8 1.0 C B:TYR514 3.4 8.3 1.0 C B:TRP516 3.6 9.6 1.0 C B:GLY513 3.6 7.2 1.0 CA B:TYR514 3.7 8.2 1.0 N B:TRP516 4.0 7.9 1.0 N B:TYR514 4.1 7.4 1.0 CA B:TRP516 4.3 8.2 1.0 N B:TRP515 4.4 7.6 1.0 C B:TRP515 4.4 7.7 1.0 O B:HOH636 4.6 32.0 1.0 N B:GLU517 4.6 10.6 1.0 CB B:TRP516 4.7 8.6 1.0 O B:TRP515 4.7 7.2 1.0 CA B:GLU517 4.8 12.2 1.0 CA B:GLY513 4.8 7.0 1.0 CA B:TRP515 4.9 7.1 1.0

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.