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Sodium in PDB 5gqc: Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form

Enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form

All present enzymatic activity of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form:
3.2.1.140;

Protein crystallography data

The structure of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form, PDB code: 5gqc was solved by C.Yamada, T.Arakawa, T.Katayama, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 143.39 / 2.36
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.317, 142.716, 157.008, 90.00, 114.04, 90.00
R / Rfree (%) 18.2 / 24

Other elements in 5gqc:

The structure of Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form also contains other interesting chemical elements:

Calcium (Ca) 14 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form (pdb code 5gqc). 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 Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form, PDB code: 5gqc:

Sodium binding site 1 out of 1 in 5gqc

Go back to Sodium Binding Sites List in 5gqc
Sodium binding site 1 out of 1 in the Crystal Structure of Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form


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 Lacto-N-Biosidase Lnbx From Bifidobacterium Longum Subsp. Longum, Ligand-Free Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:38.4
occ:1.00
 O A:VAL182 2.1 38.6 1.0
OD1 A:ASP178 2.3 57.1 1.0
OD2 A:ASP238 2.5 48.1 1.0
C A:VAL182 3.2 43.1 1.0
O A:ASP179 3.2 44.4 1.0
CG A:ASP238 3.3 42.9 1.0
OD1 A:ASP238 3.3 45.5 1.0
CG A:ASP178 3.4 53.2 1.0
OD2 A:ASP178 3.9 55.0 1.0
N A:TYR183 4.0 40.4 1.0
CA A:TYR183 4.1 45.4 1.0
OD1 A:ASP236 4.1 38.5 1.0
C A:ASP179 4.1 41.1 1.0
CB A:VAL182 4.2 46.0 1.0
CA A:VAL182 4.2 45.7 1.0
N A:ASP179 4.2 37.0 1.0
CB A:ASP178 4.5 45.6 1.0
O A:HOH869 4.6 39.1 1.0
N A:VAL182 4.6 48.2 1.0
CB A:TYR183 4.6 47.6 1.0
CB A:ASP238 4.7 40.3 1.0
CB A:ASP236 4.7 39.8 1.0
CD1 A:TYR183 4.7 56.3 1.0
CG1 A:VAL182 4.8 45.9 1.0
CA A:ASP178 4.8 42.9 1.0
CA A:ASP179 4.8 38.7 1.0
CG A:ASP236 4.9 44.2 1.0
N A:ALA180 5.0 41.8 1.0

Reference:

C.Yamada, A.Gotoh, M.Sakanaka, M.Hattie, K.A.Stubbs, A.Katayama-Ikegami, J.Hirose, S.Kurihara, T.Arakawa, M.Kitaoka, S.Okuda, T.Katayama, S.Fushinobu. Molecular Insight Into Evolution of Symbiosis Between Breast-Fed Infants and A Member of the Human Gut Microbiome Bifidobacterium Longum Cell Chem Biol V. 24 515 2017.
ISSN: ESSN 2451-9456
PubMed: 28392148
DOI: 10.1016/J.CHEMBIOL.2017.03.012
Page generated: Sun Aug 17 23:59:53 2025

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