Sodium in PDB 5mfu: PA3825-Eal Mn-Pgpg Structure

The structure of PA3825-Eal Mn-Pgpg Structure, PDB code: 5mfu was solved by S.Horrell, D.Bellini, R.Strange, A.Wagner, M.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.66 / 2.15
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.780, 64.780, 135.787, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26.1

The structure of PA3825-Eal Mn-Pgpg Structure also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Sodium atom in the PA3825-Eal Mn-Pgpg Structure (pdb code 5mfu). 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 PA3825-Eal Mn-Pgpg Structure, PDB code: 5mfu:

Sodium binding site 1 out of 1 in the PA3825-Eal Mn-Pgpg Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of PA3825-Eal Mn-Pgpg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:35.3 occ:1.00 O A:HOH666 2.4 41.6 1.0 OP2 A:G503 2.5 57.5 1.0 OD2 A:ASP160 2.7 39.1 1.0 O2' A:G504 2.7 25.0 1.0 O A:HOH609 2.8 38.6 1.0 OD2 A:ASP161 3.2 43.9 1.0 O3' A:G504 3.2 22.4 1.0 P A:G503 3.5 69.7 1.0 OP1 A:G503 3.6 60.1 1.0 CG A:ASP160 3.6 43.2 1.0 OD1 A:ASN98 3.7 18.2 1.0 MN A:MN501 3.7 47.3 1.0 C2' A:G504 3.9 24.4 1.0 CG A:ASP161 4.0 42.9 1.0 OD1 A:ASP161 4.0 49.4 1.0 C3' A:G504 4.1 23.7 1.0 OP3 A:G503 4.2 59.3 1.0 CB A:ASP160 4.2 40.7 1.0 CG A:ASN98 4.4 17.6 1.0 OG1 A:THR132 4.5 38.0 1.0 CB A:THR132 4.5 39.2 1.0 OD1 A:ASP160 4.5 50.7 1.0 C1' A:G504 4.6 22.2 1.0 O A:HOH683 4.7 31.6 1.0 O5' A:G503 4.8 61.8 1.0 O A:HOH620 4.9 45.6 1.0

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Dimerisation Induced Formation of the Active Site and the Identification of Three Metal Sites in Eal-Phosphodiesterases. Sci Rep V. 7 42166 2017.
ISSN: ESSN 2045-2322
PubMed: 28186120
DOI: 10.1038/SREP42166