Sodium in PDB 4flj: Human METAP1 with Bengamide Analog Y08, in Mn Form

All present enzymatic activity of Human METAP1 with Bengamide Analog Y08, in Mn Form:
3.4.11.18;

The structure of Human METAP1 with Bengamide Analog Y08, in Mn Form, PDB code: 4flj was solved by Q.Z.Ye, W.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.58 / 1.74
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.992, 77.355, 48.479, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.2

The structure of Human METAP1 with Bengamide Analog Y08, in Mn Form also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Human METAP1 with Bengamide Analog Y08, in Mn Form (pdb code 4flj). 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 Human METAP1 with Bengamide Analog Y08, in Mn Form, PDB code: 4flj:

Sodium binding site 1 out of 1 in the Human METAP1 with Bengamide Analog Y08, in Mn Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human METAP1 with Bengamide Analog Y08, in Mn Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:23.0 occ:1.00 O A:VAL209 2.2 22.1 1.0 O A:HOH734 2.2 23.0 1.0 O A:ASN207 2.4 21.9 1.0 O A:SER363 2.4 21.3 1.0 C A:ASN207 3.3 20.1 1.0 O A:HOH608 3.3 19.4 1.0 C A:VAL209 3.4 20.0 1.0 C A:SER363 3.5 19.4 1.0 N A:ASN207 3.6 20.3 1.0 C A:VAL206 3.8 19.7 1.0 N A:VAL209 3.8 18.6 1.0 CA A:ASN207 3.8 21.0 1.0 N A:SER363 3.9 19.8 1.0 O A:SER205 4.0 19.3 1.0 O A:VAL206 4.0 21.3 1.0 CA A:SER363 4.1 18.4 1.0 CA A:VAL209 4.2 17.6 1.0 CB A:SER363 4.2 20.8 1.0 C A:SER205 4.3 19.8 1.0 N A:GLU208 4.3 20.9 1.0 O A:HOH614 4.3 21.3 1.0 C A:GLU208 4.4 20.1 1.0 N A:ILE210 4.4 19.5 1.0 N A:VAL206 4.5 19.2 1.0 N A:ALA364 4.5 19.2 1.0 CA A:VAL206 4.5 20.2 1.0 CB A:SER205 4.6 19.0 1.0 CD1 A:ILE225 4.6 25.6 1.0 CB A:VAL209 4.6 17.4 1.0 CG1 A:ILE225 4.7 20.7 1.0 CA A:ALA364 4.7 19.0 1.0 CA A:GLU208 4.7 19.5 1.0 CA A:ILE210 4.7 19.3 1.0 OG A:SER363 5.0 20.9 1.0

W.Xu, J.P.Lu, Q.Z.Ye. Structural Analysis of Bengamide Derivatives As Inhibitors of Methionine Aminopeptidases. J.Med.Chem. V. 55 8021 2012.
ISSN: ISSN 0022-2623
PubMed: 22913487
DOI: 10.1021/JM3008695