Sodium in PDB 6m3d: X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex

The structure of X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex, PDB code: 6m3d was solved by T.Sunami, Y.Hirano, T.Tamada, H.Kono, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.17 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.798, 61.437, 39.976, 90.00, 106.45, 90.00
R / Rfree (%)	18.8 / 23.6

The binding sites of Sodium atom in the X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex (pdb code 6m3d). 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 X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex, PDB code: 6m3d:

Sodium binding site 1 out of 1 in the X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Crystal Structure of Tandemly Connected Engrailed Homeodomains (Ehd) with R53A Mutations and Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na101 b:22.2 occ:1.00 OP2 A:DA8 2.6 16.4 0.5 OP2 A:DA8 2.8 16.5 0.5 ND2 C:ASN138 2.8 16.9 1.0 O A:HOH213 2.9 20.8 1.0 C2' A:DA8 3.2 19.4 0.5 O5' A:DA8 3.2 18.9 0.5 CA C:TRP135 3.4 15.8 1.0 O5' A:DA8 3.4 13.2 0.5 C8 A:DA8 3.5 17.1 0.5 P A:DA8 3.5 16.9 0.5 C8 A:DA8 3.6 16.9 0.5 C2' A:DA8 3.6 16.4 0.5 P A:DA8 3.7 16.6 0.5 O C:ILE134 3.7 16.0 1.0 N C:TRP135 3.7 15.4 1.0 CG C:ASN138 3.8 18.3 1.0 CD1 C:TRP135 3.8 18.7 1.0 CB C:ASN138 3.9 17.4 1.0 O A:HOH223 3.9 19.1 1.0 C C:ILE134 3.9 16.6 1.0 CG2 C:ILE134 3.9 18.3 1.0 CB C:TRP135 4.0 14.4 1.0 C3' A:DA8 4.0 18.7 0.5 CG C:TRP135 4.1 16.5 1.0 N9 A:DA8 4.2 14.6 0.5 C1' A:DA8 4.2 16.4 0.5 C3' A:DA8 4.3 18.7 0.5 N9 A:DA8 4.4 14.2 0.5 N7 A:DA8 4.4 15.9 0.5 N7 A:DA8 4.4 15.9 0.5 C C:TRP135 4.5 14.2 1.0 O3' A:DT7 4.5 19.8 0.5 C5' A:DA8 4.5 18.8 0.5 O3' A:DT7 4.5 18.4 0.5 O C:TRP135 4.5 15.4 1.0 C1' A:DA8 4.5 18.1 0.5 C5' A:DA8 4.6 20.4 0.5 C4' A:DA8 4.7 19.4 0.5 OP2 A:DA9 4.7 20.2 0.5 OP1 A:DA8 4.7 17.5 0.5 CE2 C:PHE95 4.7 27.8 0.5 N7 A:DA9 4.8 11.6 0.5 NE1 C:TRP135 4.8 16.6 1.0 O4' A:DA8 4.8 17.4 0.5 CB C:ILE134 4.8 16.0 1.0 C4' A:DA8 4.9 21.1 0.5 OP1 A:DA8 5.0 21.2 0.5 OD1 C:ASN138 5.0 19.0 1.0 N7 A:DA9 5.0 12.5 0.5 CA C:ILE134 5.0 20.2 1.0

T.Sunami, Y.Hirano, T.Tamada, H.Kono. Structural Basis For Designing An Array of Engrailed Homeodomains. Acta Crystallogr D Struct V. 76 824 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 32876058
DOI: 10.1107/S2059798320009237