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Sodium in PDB 5nns: Crystal Structure of HILPMO9B

Protein crystallography data

The structure of Crystal Structure of HILPMO9B, PDB code: 5nns was solved by M.Dimarogona, M.Sandgren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.695, 46.375, 86.492, 90.00, 103.23, 90.00
R / Rfree (%) 20 / 25.1

Other elements in 5nns:

The structure of Crystal Structure of HILPMO9B also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of HILPMO9B (pdb code 5nns). 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 HILPMO9B, PDB code: 5nns:

Sodium binding site 1 out of 1 in 5nns

Go back to Sodium Binding Sites List in 5nns
Sodium binding site 1 out of 1 in the Crystal Structure of HILPMO9B


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 HILPMO9B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:35.8
occ:1.00
O A:HOH472 2.3 27.5 1.0
O A:HOH527 2.3 26.3 1.0
OD1 A:ASP95 2.5 33.7 1.0
O A:HOH449 2.6 23.8 1.0
OG1 A:THR97 3.1 23.0 1.0
OG A:SER62 3.5 25.0 1.0
CG A:ASP95 3.7 32.5 1.0
O A:HOH467 3.8 19.0 1.0
NE2 A:GLN172 3.9 19.1 1.0
OD2 A:ASP95 4.2 33.8 1.0
N A:THR97 4.3 24.9 1.0
CB A:THR97 4.3 24.0 1.0
N A:CYS96 4.4 27.6 1.0
CB A:SER62 4.5 24.8 1.0
CB A:ASP95 4.9 31.2 1.0
CA A:ASP95 4.9 30.2 1.0
CB A:CYS96 4.9 26.3 1.0
CA A:THR97 5.0 24.1 1.0

Reference:

B.Liu, A.A.Kognole, M.Wu, B.Westereng, M.F.Crowley, S.Kim, M.Dimarogona, C.M.Payne, M.Sandgren. Structural and Molecular Dynamics Studies of A C1-Oxidizing Lytic Polysaccharide Monooxygenase From Heterobasidion Irregulare Reveal Amino Acids Important For Substrate Recognition. Febs J. V. 285 2225 2018.
ISSN: ISSN 1742-4658
PubMed: 29660793
DOI: 10.1111/FEBS.14472
Page generated: Tue Dec 15 11:21:32 2020

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