Sodium in PDB 7w5o: Crystal Structure of ERK2 with An Allosteric Inhibitor

All present enzymatic activity of Crystal Structure of ERK2 with An Allosteric Inhibitor:
2.7.11.24;

The structure of Crystal Structure of ERK2 with An Allosteric Inhibitor, PDB code: 7w5o was solved by M.Yoshida, T.Kinoshita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.32 / 2.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	82.812, 82.812, 274.44, 90, 90, 90
R / Rfree (%)	22.5 / 27.9

The structure of Crystal Structure of ERK2 with An Allosteric Inhibitor also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Sodium atom in the Crystal Structure of ERK2 with An Allosteric Inhibitor (pdb code 7w5o). 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 ERK2 with An Allosteric Inhibitor, PDB code: 7w5o:

Sodium binding site 1 out of 1 in the Crystal Structure of ERK2 with An Allosteric Inhibitor


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 ERK2 with An Allosteric Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:79.0 occ:1.00 H5' A:5ID401 3.3 102.9 1.0 NZ A:LYS54 3.3 90.2 1.0 CB A:ASP167 3.4 55.1 1.0 SG A:CYS166 3.6 53.2 1.0 O5' A:5ID401 3.8 85.7 1.0 O A:HOH514 3.8 53.1 1.0 O1 A:SIN403 3.9 90.6 1.0 CA A:ASP167 3.9 50.9 1.0 N A:ASP167 4.0 51.6 1.0 CG A:ASP167 4.1 68.9 1.0 H8 A:5ID401 4.1 106.2 1.0 H5'2 A:5ID401 4.2 94.9 1.0 OD1 A:ASP167 4.2 69.1 1.0 OD1 A:ASN154 4.2 53.2 1.0 C5' A:5ID401 4.6 79.1 1.0 H32 A:SIN403 4.6 101.8 1.0 CB A:CYS166 4.6 48.2 1.0 IAE A:5ID401 4.6 128.8 1.0 CE A:LYS54 4.7 87.4 1.0 C8 A:5ID401 4.8 88.5 1.0 C A:CYS166 4.8 50.8 1.0 OD2 A:ASP167 4.9 67.7 1.0

M.Yoshida, H.Nagao, H.Sugiyama, M.Sawa, T.Kinoshita. Identification of A Novel Target Site For Atp-Independent ERK2 Inhibitors. Biochem.Biophys.Res.Commun. V. 593 73 2022.
ISSN: ESSN 1090-2104
PubMed: 35063772
DOI: 10.1016/J.BBRC.2022.01.035