Sodium in PDB 3s9j: Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution

The structure of Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution, PDB code: 3s9j 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)	28.39 / 1.75
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	113.551, 113.551, 77.697, 90.00, 90.00, 120.00
R / Rfree (%)	14.2 / 16.9

The binding sites of Sodium atom in the Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution (pdb code 3s9j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution, PDB code: 3s9j:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 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 A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na400 b:41.0 occ:1.00 O A:HOH879 2.3 49.6 1.0 O A:HOH878 2.3 32.6 1.0 O A:HOH476 2.4 37.6 1.0 O A:HOH557 2.4 37.2 1.0 O A:HOH477 2.5 34.3 1.0 O A:HOH599 3.6 45.9 1.0 O A:HOH813 3.6 58.9 1.0 OD2 A:ASP46 3.9 30.3 1.0 OE2 A:GLU47 4.3 39.7 1.0 OE1 A:GLU47 4.3 34.4 1.0 CD A:GLU47 4.7 38.3 1.0 CG A:ASP46 4.8 26.1 1.0 CB A:ASP46 4.8 26.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 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 A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.1 occ:1.00 O A:THR49 2.3 20.6 1.0 O A:ASP46 2.4 23.7 1.0 O A:HOH453 2.4 21.8 1.0 OD1 A:ASN378 2.6 38.2 1.0 O A:HOH524 2.7 37.5 1.0 C A:THR49 3.3 21.6 1.0 C A:ASP46 3.3 23.4 1.0 CG A:ASN378 3.8 37.4 1.0 CA A:TYR50 3.9 21.2 1.0 O A:HOH494 4.0 33.0 1.0 N A:TYR50 4.0 20.6 1.0 CB A:LEU45 4.1 20.9 1.0 N A:GLU47 4.1 25.0 1.0 CA A:GLU47 4.1 27.0 1.0 N A:THR49 4.2 20.3 1.0 N A:ASP46 4.2 23.1 1.0 O A:GLU377 4.2 26.0 1.0 CA A:ASP46 4.2 24.6 1.0 CA A:THR49 4.3 19.5 1.0 C A:GLU47 4.4 26.1 1.0 CD1 A:LEU45 4.5 26.9 1.0 ND2 A:ASN378 4.6 37.0 1.0 O A:HOH812 4.6 49.0 1.0 O A:HOH838 4.6 34.4 0.5 C A:TYR50 4.6 22.6 1.0 N A:TYR51 4.6 19.5 1.0 O A:GLU47 4.7 25.5 1.0 C A:LEU45 4.7 22.0 1.0 CA A:ASN378 4.8 26.5 1.0 CB A:ASN378 4.9 30.3 1.0 CG A:LEU45 5.0 23.7 1.0 CD1 A:TYR50 5.0 25.4 1.0 N A:GLN48 5.0 22.7 1.0 CB A:THR49 5.0 22.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 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 A Member of DUF4221 Family (BVU_1028) From Bacteroides Vulgatus Atcc 8482 at 1.75 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:24.6 occ:1.00 O A:LEU95 2.3 24.8 1.0 O A:HOH433 2.3 24.9 1.0 O A:TYR77 2.4 23.6 1.0 O A:HOH484 2.4 27.2 1.0 O A:HOH464 2.5 28.3 1.0 O A:HOH586 2.5 39.1 1.0 C A:LEU95 3.4 26.2 1.0 C A:TYR77 3.5 20.2 1.0 O A:HOH679 3.7 41.1 1.0 CB A:TYR77 3.7 21.3 1.0 O A:HOH680 3.8 45.6 1.0 N A:LEU95 3.9 23.7 1.0 CD2 A:TYR77 4.0 18.1 1.0 O A:HOH678 4.0 50.6 1.0 CA A:TYR77 4.1 22.7 1.0 CA A:LEU95 4.1 24.9 1.0 O A:HOH488 4.3 34.1 1.0 CG A:TYR77 4.3 18.9 1.0 O A:HOH600 4.4 34.6 1.0 CB A:LEU95 4.4 23.9 1.0 N A:HIS96 4.5 26.2 1.0 O A:HOH478 4.5 30.2 1.0 O A:HOH452 4.5 25.4 1.0 N A:ASP78 4.5 20.3 1.0 N A:TYR77 4.7 20.6 1.0 O A:HOH612 4.7 44.4 1.0 CB A:ASP78 4.7 21.1 1.0 CA A:HIS96 4.7 28.3 1.0 O A:HOH594 4.8 53.9 1.0 CA A:ASP78 4.9 20.6 1.0

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