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Sodium in PDB 5eq3: Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound

Protein crystallography data

The structure of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound, PDB code: 5eq3 was solved by L.V.Loukachevitch, K.M.Mcculloch, K.R.Vann, Z.Wawrzak, S.Anderson, T.M.Iverson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.23 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 174.620, 47.005, 64.026, 90.00, 102.15, 90.00
R / Rfree (%) 19.8 / 24.3

Other elements in 5eq3:

The structure of Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound (pdb code 5eq3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound, PDB code: 5eq3:

Sodium binding site 1 out of 1 in 5eq3

Go back to Sodium Binding Sites List in 5eq3
Sodium binding site 1 out of 1 in the Crystal Structure of the Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound


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 Srpa Adhesin From Streptococcus Sanguinis with A Sialyl Galactose Disaccharide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na505

b:59.0
occ:1.00
O B:HOH631 2.4 52.0 1.0
O B:HOH734 2.4 51.6 1.0
O B:HOH750 2.4 55.3 1.0
O B:HOH654 2.9 50.9 1.0
O B:HOH723 2.9 45.8 1.0
O B:HOH735 3.1 48.8 1.0
CB B:ASN320 4.1 51.0 1.0
ND2 B:ASN309 4.4 41.7 1.0
O B:ASN315 4.5 36.0 1.0
O B:GLY314 4.5 38.3 1.0
O B:ASN320 4.5 44.6 1.0
O B:HOH686 4.6 35.9 1.0
CA B:ASN315 4.7 34.6 1.0
O B:HOH767 4.7 52.0 1.0
C B:ASN315 4.9 33.2 1.0
O B:PRO321 4.9 34.2 1.0
CG B:ASN320 5.0 58.0 1.0
C B:ASN320 5.0 50.4 1.0

Reference:

B.A.Bensing, L.V.Loukachevitch, K.M.Mcculloch, H.Yu, K.R.Vann, Z.Wawrzak, S.Anderson, X.Chen, P.M.Sullam, T.M.Iverson. Structural Basis For Sialoglycan Binding By the Streptococcus Sanguinis Srpa Adhesin. J.Biol.Chem. V. 291 7230 2016.
ISSN: ESSN 1083-351X
PubMed: 26833566
DOI: 10.1074/JBC.M115.701425
Page generated: Tue Dec 15 10:56:57 2020

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