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Sodium in PDB 4ak2: Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus

Protein crystallography data

The structure of Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus, PDB code: 4ak2 was solved by E.C.Lowe, A.Basle, M.Czjzek, S.Thomas, H.Murray, S.J.Firbank, D.N.Bolam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.20 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 52.600, 68.150, 85.140, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus (pdb code 4ak2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus, PDB code: 4ak2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4ak2

Go back to Sodium Binding Sites List in 4ak2
Sodium binding site 1 out of 2 in the Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1715

b:29.7
occ:1.00
O A:HOH2096 2.6 34.4 1.0
O A:ASP583 2.9 12.6 1.0
OG A:SER690 2.9 10.9 0.5
N A:GLN670 3.3 11.9 1.0
O A:HOH2214 3.5 24.4 1.0
C A:GLY669 3.6 11.8 1.0
CB A:ASP583 3.7 14.2 1.0
CB A:SER690 3.8 12.5 0.5
CB A:SER690 3.8 14.1 0.5
CA A:GLY669 3.9 12.2 1.0
CA A:GLN670 3.9 12.1 1.0
C A:ASP583 4.0 11.7 1.0
CE1 A:PHE585 4.1 15.8 1.0
CB A:GLN670 4.1 13.8 1.0
OE1 A:GLN508 4.1 28.3 1.0
O A:GLY669 4.1 12.8 1.0
CG1 A:ILE668 4.2 14.1 1.0
CD1 A:PHE585 4.2 14.4 1.0
OG A:SER690 4.3 17.2 0.5
N A:GLY669 4.3 10.9 1.0
CA A:ASP583 4.5 13.5 1.0
C A:ILE668 4.6 10.2 1.0
O A:ILE668 4.6 13.0 1.0
O A:ARG582 4.6 13.8 1.0
CD1 A:ILE668 4.7 17.5 1.0
NE2 A:HIS483 4.7 15.2 1.0
CG2 A:ILE668 4.8 13.2 1.0
CG A:ASP583 4.9 16.5 1.0
CD A:GLN508 5.0 27.1 1.0

Sodium binding site 2 out of 2 in 4ak2

Go back to Sodium Binding Sites List in 4ak2
Sodium binding site 2 out of 2 in the Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of BT4661, A Suse-Like Surface Located Polysaccharide Binding Protein From the Bacteroides Thetaiotaomicron Heparin Utilisation Locus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1716

b:35.7
occ:1.00
O A:HOH2376 2.3 39.9 1.0
OG A:SER614 2.6 18.1 1.0
O A:LEU655 2.7 13.9 1.0
O A:HOH2272 3.3 24.9 1.0
CB A:SER614 3.4 19.6 1.0
O A:HOH2329 3.4 27.7 1.0
C A:LEU655 3.6 11.8 1.0
CA A:LEU655 3.7 13.5 1.0
CB A:LEU655 4.0 13.1 1.0
CD2 A:LEU655 4.3 18.9 1.0
SD A:MET611 4.3 16.3 1.0
O A:ARG657 4.5 16.5 1.0
CD2 A:LEU639 4.5 15.5 1.0
CE A:MET611 4.5 20.4 1.0
O A:HOH2324 4.5 29.0 1.0
CA A:SER614 4.7 17.6 1.0
CG A:LEU655 4.8 13.9 1.0
N A:TRP656 4.8 12.5 1.0
C A:SER614 4.8 17.5 1.0
O A:MET611 5.0 15.0 1.0

Reference:

A.Cartmell, E.C.Lowe, A.Basle, S.J.Firbank, D.A.Ndeh, H.Murray, N.Terrapon, V.Lombard, B.Henrissat, J.E.Turnbull, M.Czjzek, H.J.Gilbert, D.N.Bolam. How Members of the Human Gut Microbiota Overcome the Sulfation Problem Posed By Glycosaminoglycans. Proc. Natl. Acad. Sci. V. 114 7037 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28630303
DOI: 10.1073/PNAS.1704367114
Page generated: Tue Dec 15 06:33:00 2020

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