Sodium in PDB 5fq7: Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron

The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq7 was solved by A.J.Glenwright, K.R.Pothula, D.S.Chorev, A.Basle, C.V.Robinson, U.Kleinekathoefer, D.N.Bolam, B.Van Den Berg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.43 / 3.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.591, 180.159, 245.747, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.5

The structure of Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron (pdb code 5fq7). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1986 b:27.6 occ:1.00 OD2 A:ASP231 3.5 66.1 1.0 OE2 B:GLU493 3.6 54.4 1.0 OE1 B:GLU493 3.8 54.3 1.0 CD B:GLU493 4.1 54.4 1.0 CD1 B:ILE513 4.2 60.7 1.0 OD1 A:ASP231 4.3 66.0 1.0 CG A:ASP231 4.3 64.8 1.0

Sodium binding site 2 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1987 b:30.1 occ:1.00 O B:ILE283 2.2 71.6 1.0 OD1 B:ASP280 2.2 65.4 1.0 O B:GLY281 2.3 70.7 1.0 O B:THR285 2.4 69.4 1.0 OD1 B:ASP288 2.6 72.7 1.0 OD2 B:ASP288 2.8 78.3 1.0 CG B:ASP288 3.1 73.0 1.0 CG B:ASP280 3.4 65.7 1.0 C B:ILE283 3.4 64.7 1.0 C B:GLY281 3.5 70.5 1.0 C B:THR285 3.5 70.3 1.0 N B:THR285 3.9 72.7 1.0 C B:PRO284 3.9 71.9 1.0 OD2 B:ASP280 4.0 65.8 1.0 N B:GLY281 4.0 73.5 1.0 O B:ASP280 4.0 80.3 1.0 C B:ASP280 4.0 74.2 1.0 N B:ILE283 4.1 65.0 1.0 CA B:PRO284 4.2 68.1 1.0 O B:PRO284 4.3 75.0 1.0 N B:PRO284 4.3 65.6 1.0 CA B:THR285 4.3 69.3 1.0 CA B:ILE283 4.3 64.5 1.0 CA B:GLY281 4.3 71.9 1.0 C B:MET282 4.4 66.4 1.0 N B:MET282 4.5 69.7 1.0 N B:ASP286 4.5 70.9 1.0 CB B:ASP280 4.6 66.2 1.0 CB B:ASP288 4.6 71.3 1.0 CA B:MET282 4.7 69.6 1.0 CA B:ASP280 4.7 65.8 1.0 CB B:ILE283 4.8 63.5 1.0 N B:ASP288 4.9 68.7 1.0 CA B:ASP286 4.9 71.0 1.0 O B:MET282 4.9 68.5 1.0 N B:ALA287 5.0 67.9 1.0

Sodium binding site 3 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1988 b:43.5 occ:1.00 OD1 B:ASP850 2.4 88.0 1.0 CG B:ASP850 3.0 86.9 1.0 OD2 B:ASP850 3.0 87.6 1.0 OE1 F:GLU13 3.8 0.4 1.0 O B:ALA847 4.0 82.9 1.0 NZ F:LYS14 4.2 88.3 1.0 OE2 F:GLU13 4.2 0.3 1.0 O B:TYR848 4.3 90.7 1.0 CD F:GLU13 4.3 0.7 1.0 CB B:ASP850 4.3 84.9 1.0 CG F:PRO7 4.3 99.3 1.0 O F:GLY8 4.4 91.5 1.0 N B:ASP850 4.5 83.0 1.0 CA B:ASP850 4.5 82.5 1.0 CE F:LYS14 4.6 90.4 1.0 OE2 B:GLU197 4.6 82.9 1.0 OE1 B:GLU197 4.7 78.2 1.0 CD F:PRO7 4.8 99.5 1.0 CB F:PRO7 4.8 96.2 1.0

Sodium binding site 4 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1481 b:44.4 occ:1.00 OD1 C:ASP478 2.1 83.4 1.0 O C:ARG408 2.2 78.3 1.0 OD2 C:ASP411 2.3 76.0 1.0 OD1 C:ASP411 2.4 75.3 1.0 OXT C:LYS480 2.4 82.8 1.0 CG C:ASP411 2.6 75.6 1.0 CG C:ASP478 3.1 77.2 1.0 C C:LYS480 3.2 82.2 1.0 C C:ARG408 3.5 74.4 1.0 OD2 C:ASP478 3.6 73.8 1.0 O C:ARG409 3.6 79.4 1.0 N C:LYS480 3.8 79.9 1.0 O C:LYS480 3.8 83.2 1.0 CB C:ASP411 4.0 75.3 1.0 CA C:LYS480 4.0 81.1 1.0 CA C:ARG408 4.2 72.1 1.0 CB C:ASP478 4.3 73.7 1.0 CG C:LYS480 4.3 84.6 1.0 C C:ARG409 4.3 74.5 1.0 CA C:ASP478 4.4 72.7 1.0 N C:ARG409 4.4 72.2 1.0 N C:ILE479 4.5 76.5 1.0 CA C:ARG409 4.5 72.5 1.0 N C:ASP411 4.6 77.9 1.0 CA C:ASP411 4.6 76.2 1.0 C C:ASP478 4.7 76.7 1.0 CB C:LYS480 4.7 82.8 1.0 CB C:ARG408 4.9 73.0 1.0 O C:ILE407 4.9 72.4 1.0 C C:ILE479 4.9 81.4 1.0

Sodium binding site 5 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1986 b:35.4 occ:1.00 OD1 D:ASP850 2.2 82.4 1.0 CG D:ASP850 3.0 81.5 1.0 OD2 D:ASP850 3.2 80.7 1.0 OE2 E:GLU13 4.0 94.8 1.0 OE1 E:GLU13 4.2 90.8 1.0 CB D:ASP850 4.3 78.3 1.0 O E:GLY8 4.4 88.9 1.0 CD E:GLU13 4.4 91.6 1.0 O D:ALA847 4.5 70.3 1.0 OE1 D:GLU197 4.5 86.8 1.0 OE2 D:GLU197 4.5 85.2 1.0 N D:ASP850 4.5 76.1 1.0 CA D:ASP850 4.6 76.5 1.0 CG E:PRO7 4.8 99.0 1.0 CD D:GLU197 4.8 84.3 1.0 O D:TYR848 5.0 92.3 1.0

Sodium binding site 6 out of 6 in the Crystal Structure of the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron


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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1987 b:34.7 occ:1.00 OD1 D:ASP280 2.2 71.8 1.0 O D:GLY281 2.2 74.8 1.0 O D:ILE283 2.3 66.0 1.0 OD1 D:ASP288 2.4 75.2 1.0 O D:THR285 2.4 68.4 1.0 OD2 D:ASP288 2.6 75.5 1.0 CG D:ASP288 2.8 74.9 1.0 C D:GLY281 3.4 76.2 1.0 CG D:ASP280 3.4 70.6 1.0 C D:ILE283 3.5 65.2 1.0 C D:THR285 3.6 67.9 1.0 C D:ASP280 3.8 72.7 1.0 N D:GLY281 3.8 74.8 1.0 O D:ASP280 3.9 76.7 1.0 OD2 D:ASP280 4.1 71.8 1.0 CA D:GLY281 4.1 78.1 1.0 C D:PRO284 4.1 70.1 1.0 N D:THR285 4.2 69.4 1.0 N D:ILE283 4.2 70.6 1.0 CA D:PRO284 4.3 68.0 1.0 CB D:ASP288 4.4 74.5 1.0 N D:PRO284 4.4 65.3 1.0 CA D:ILE283 4.4 65.3 1.0 O D:PRO284 4.4 72.9 1.0 N D:MET282 4.4 75.3 1.0 C D:MET282 4.5 75.4 1.0 CA D:ASP280 4.5 70.7 1.0 CB D:ASP280 4.5 69.2 1.0 CA D:THR285 4.6 68.3 1.0 N D:ASP286 4.6 71.0 1.0 N D:ASP288 4.6 69.8 1.0 CA D:ASP286 4.7 72.6 1.0 CA D:MET282 4.8 75.9 1.0 CB D:ILE283 4.8 63.1 1.0 N D:ALA287 4.8 62.2 1.0 O D:ASP288 4.9 86.8 1.0 C D:ASP286 5.0 69.9 1.0

A.J.Glenwright, K.R.Pothula, S.P.Bhamidimarri, D.S.Chorev, A.Basle, S.J.Firbank, H.Zheng, C.V.Robinson, M.Winterhalter, U.Kleinekathofer, D.N.Bolam, B.Van Den Berg. Structural Basis For Nutrient Acquisition By Dominant Members of the Human Gut Microbiota. Nature V. 541 407 2017.
ISSN: ESSN 1476-4687
PubMed: 28077872
DOI: 10.1038/NATURE20828