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

Protein crystallography data

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

Other elements in 5fq7:

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

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

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 5fq7

Go back to Sodium Binding Sites List in 5fq7
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 5fq7

Go back to Sodium Binding Sites List in 5fq7
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 5fq7

Go back to Sodium Binding Sites List in 5fq7
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 5fq7

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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 5fq7

Go back to Sodium Binding Sites List in 5fq7
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 5fq7

Go back to Sodium Binding Sites List in 5fq7
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

Reference:

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
Page generated: Tue Dec 15 10:59:28 2020

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