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Sodium in PDB 5fq6: 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: 5fq6 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) 48.80 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 222.027, 91.941, 261.219, 90.00, 98.23, 90.00
R / Rfree (%) 19.8 / 25.5

Other elements in 5fq6:

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

Calcium (Ca) 4 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 5fq6). 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 the Suscd Complex BT2261-2264 From Bacteroides Thetaiotaomicron, PDB code: 5fq6:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5fq6

Go back to Sodium Binding Sites List in 5fq6
Sodium binding site 1 out of 4 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:30.7
occ:1.00
O B:ALA631 2.2 64.9 1.0
OD1 B:ASN633 2.2 53.9 1.0
O A:ALA82 2.3 76.8 1.0
C B:ALA631 3.3 58.5 1.0
CG B:ASN633 3.4 59.6 1.0
C A:ALA82 3.5 62.2 1.0
OG B:SER630 3.9 80.1 1.0
CA A:GLY83 4.0 64.5 1.0
C B:GLY632 4.1 73.2 1.0
N B:ASN633 4.1 61.3 1.0
CA B:ASN633 4.1 64.0 1.0
CA B:ALA631 4.1 59.6 1.0
CB B:ALA631 4.1 64.5 1.0
N A:GLY83 4.2 64.0 1.0
O B:GLY632 4.2 86.7 1.0
N B:ALA631 4.3 59.5 1.0
OD1 A:ASP87 4.3 82.9 1.0
ND2 B:ASN633 4.3 59.7 1.0
N B:GLY632 4.4 64.1 1.0
CB B:ASN633 4.4 58.9 1.0
O B:GLY686 4.5 74.8 1.0
CG A:GLU86 4.6 57.9 1.0
CA B:GLY632 4.6 67.3 1.0
O A:GLY83 4.6 74.5 1.0
CA A:ALA82 4.6 55.3 1.0
CB A:GLU86 4.7 54.7 1.0
C A:GLY83 4.8 67.0 1.0
CB A:ALA82 4.9 45.4 1.0
C B:SER630 5.0 56.4 1.0
CB B:SER630 5.0 69.3 1.0

Sodium binding site 2 out of 4 in 5fq6

Go back to Sodium Binding Sites List in 5fq6
Sodium binding site 2 out of 4 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
D:Na1986

b:34.5
occ:1.00
OD1 D:ASN633 2.0 54.1 1.0
O C:ALA82 2.3 72.2 1.0
O D:ALA631 2.4 54.7 1.0
CG D:ASN633 3.2 58.8 1.0
OG D:SER630 3.3 72.4 1.0
C C:ALA82 3.4 64.7 1.0
C D:ALA631 3.6 49.8 1.0
CA C:GLY83 3.7 68.8 1.0
ND2 D:ASN633 3.8 57.6 1.0
N C:GLY83 4.0 68.2 1.0
N D:ALA631 4.3 48.9 1.0
CA D:ALA631 4.3 45.9 1.0
N D:ASN633 4.3 45.8 1.0
C D:GLY632 4.4 49.2 1.0
CB D:ASN633 4.4 55.1 1.0
CA D:ASN633 4.4 53.1 1.0
CB D:SER630 4.5 61.7 1.0
O C:GLY83 4.5 78.9 1.0
CB D:ALA631 4.5 53.3 1.0
OD1 C:ASP87 4.6 58.2 1.0
N D:GLY632 4.6 54.7 1.0
C C:GLY83 4.6 72.2 1.0
CA C:ALA82 4.7 62.2 1.0
O D:GLY632 4.7 47.2 1.0
C D:SER630 4.7 50.7 1.0
CA D:GLY632 4.7 47.7 1.0
OD2 C:ASP87 4.8 71.3 1.0
O D:GLY686 4.9 72.7 1.0
CB C:ALA82 4.9 67.3 1.0
CB C:GLU86 5.0 48.1 1.0
CG C:GLU86 5.0 56.1 1.0

Sodium binding site 3 out of 4 in 5fq6

Go back to Sodium Binding Sites List in 5fq6
Sodium binding site 3 out of 4 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
I:Na1986

b:33.0
occ:1.00
OD1 I:ASN633 2.2 51.0 1.0
O I:ALA631 2.4 68.7 1.0
O H:ALA82 2.5 68.5 1.0
CG I:ASN633 3.3 48.0 1.0
C I:ALA631 3.6 50.3 1.0
OG I:SER630 3.6 46.4 1.0
C H:ALA82 3.6 50.4 1.0
CA H:GLY83 3.8 45.2 1.0
ND2 I:ASN633 3.8 44.8 1.0
N H:GLY83 4.1 45.2 1.0
N I:ALA631 4.3 44.5 1.0
CA I:ALA631 4.4 48.0 1.0
C I:GLY632 4.4 46.6 1.0
N I:ASN633 4.4 40.1 1.0
CB I:SER630 4.5 47.8 1.0
N I:GLY632 4.6 43.9 1.0
CB I:ASN633 4.6 38.4 1.0
O H:GLY83 4.6 62.0 1.0
CB I:ALA631 4.6 52.7 1.0
CA I:GLY632 4.7 37.5 1.0
C H:GLY83 4.7 55.2 1.0
O I:GLY632 4.7 60.9 1.0
CA I:ASN633 4.7 42.8 1.0
OD2 H:ASP87 4.7 80.8 1.0
OD1 H:ASP87 4.8 75.4 1.0
C I:SER630 4.8 54.5 1.0
CA H:ALA82 4.9 44.2 1.0

Sodium binding site 4 out of 4 in 5fq6

Go back to Sodium Binding Sites List in 5fq6
Sodium binding site 4 out of 4 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
M:Na1986

b:42.6
occ:1.00
O M:ALA631 2.2 70.5 1.0
OD1 M:ASN633 2.2 60.5 1.0
O L:ALA82 2.4 74.6 1.0
C M:ALA631 3.4 55.5 1.0
CG M:ASN633 3.4 50.2 1.0
C L:ALA82 3.6 62.6 1.0
C M:GLY632 4.0 56.1 1.0
CA L:GLY83 4.1 62.1 1.0
O M:GLY632 4.1 62.7 1.0
ND2 M:ASN633 4.2 40.1 1.0
CA M:ALA631 4.2 58.4 1.0
N M:ASN633 4.2 55.1 1.0
CB M:ALA631 4.2 60.5 1.0
N L:GLY83 4.3 61.0 1.0
N M:GLY632 4.3 52.0 1.0
CA M:ASN633 4.3 56.0 1.0
N M:ALA631 4.4 55.0 1.0
OG M:SER630 4.4 63.2 1.0
CA M:GLY632 4.4 52.2 1.0
CB M:ASN633 4.5 46.3 1.0
O M:GLY686 4.6 67.6 1.0
O L:GLY83 4.6 69.5 1.0
CA L:ALA82 4.7 61.2 1.0
CG L:GLU86 4.9 48.9 1.0
CB L:ALA82 4.9 46.8 1.0
CB L:GLU86 4.9 51.5 1.0
C L:GLY83 4.9 67.4 1.0
C M:SER630 4.9 52.3 1.0
OD1 L:ASP87 5.0 92.9 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: Mon Oct 7 21:04:56 2024

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