Sodium in PDB 3ned: Mrouge

The structure of Mrouge, PDB code: 3ned was solved by S.L.Mayo, R.A.Chica, M.M.Moore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	56.60 / 0.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.807, 42.760, 61.203, 90.00, 112.35, 90.00
R / Rfree (%)	13.3 / 15.7

The binding sites of Sodium atom in the Mrouge (pdb code 3ned). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Mrouge, PDB code: 3ned:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Mrouge


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mrouge within 5.0Å range: probe atom residue distance (Å) B Occ A:Na232 b:8.9 occ:1.00 O A:HOH600 2.6 55.5 1.0 O A:HOH244 3.2 18.7 1.0 N A:ASN128 3.2 6.2 0.4 N A:ASN128 3.2 5.3 0.6 CB A:THR127 3.7 5.6 1.0 CA A:THR127 3.7 5.2 1.0 OD1 A:ASN23 3.9 6.7 1.0 CG2 A:THR127 4.0 6.7 1.0 CA A:ASN23 4.0 6.7 1.0 C A:THR127 4.0 5.1 1.0 CA A:ASN128 4.1 5.8 0.4 CA A:ASN128 4.2 5.5 0.6 CG A:ASN23 4.3 6.4 1.0 C A:ASN23 4.6 7.6 1.0 CB A:ASN23 4.6 7.9 1.0 N A:ASN23 4.7 5.9 1.0 CB A:ASN128 4.8 4.9 0.4 O A:GLY126 4.9 5.3 1.0 OG1 A:THR127 5.0 5.8 1.0 N A:GLY24 5.0 7.3 1.0

Sodium binding site 2 out of 3 in the Mrouge


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mrouge within 5.0Å range: probe atom residue distance (Å) B Occ A:Na234 b:9.9 occ:1.00 O A:HOH489 2.8 8.4 1.0 O A:GLU10 2.8 5.3 1.0 N A:TYR38 2.9 5.2 1.0 C A:ARG36 3.1 5.1 1.0 N A:PRO37 3.2 5.2 1.0 CA A:ARG36 3.4 4.9 1.0 CB A:ARG36 3.4 5.6 1.0 CA A:GLU10 3.5 5.4 1.0 CB A:TYR38 3.5 6.4 1.0 C A:GLU10 3.5 5.0 1.0 N A:GLU39 3.5 6.3 1.0 CA A:TYR38 3.5 6.0 1.0 CD1 A:TYR38 3.6 6.6 1.0 O A:ARG36 3.6 5.3 1.0 CD A:PRO37 3.7 5.5 1.0 CB A:GLU10 3.7 6.6 1.0 C A:PRO37 3.9 5.2 1.0 C A:TYR38 3.9 5.9 1.0 CG A:GLU39 4.0 8.1 1.0 CG A:TYR38 4.0 6.1 1.0 CA A:PRO37 4.1 5.4 1.0 OE2 A:GLU39 4.2 10.6 1.0 CG A:GLU10 4.2 8.0 1.0 CD A:GLU39 4.3 7.9 1.0 CG A:ARG36 4.3 6.8 1.0 CB A:GLU39 4.4 7.0 1.0 CA A:GLU39 4.6 6.1 1.0 CE1 A:TYR38 4.7 7.1 1.0 OE1 A:GLU10 4.7 11.7 1.0 CB A:PRO37 4.7 6.0 1.0 O A:LYS9 4.8 6.1 1.0 N A:PHE11 4.8 5.2 1.0 N A:GLU10 4.8 6.0 1.0 O A:HOH616 4.8 17.6 1.0 CG A:PRO37 4.8 6.0 1.0 N A:ARG36 4.9 5.0 1.0 CD A:GLU10 5.0 9.8 1.0 O A:TYR38 5.0 9.1 1.0

Sodium binding site 3 out of 3 in the Mrouge


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mrouge within 5.0Å range: probe atom residue distance (Å) B Occ A:Na235 b:8.3 occ:1.00 O A:HOH631 3.0 30.6 1.0 OG1 A:THR41 3.1 6.9 1.0 NH1 A:ARG36 3.2 8.7 1.0 O A:HOH532 3.3 11.8 0.6 O A:THR41 3.6 5.5 1.0 C A:THR41 3.6 4.9 1.0 CB A:THR41 3.7 6.2 1.0 N A:GLN42 3.7 4.9 1.0 CA A:GLY35 3.7 5.8 1.0 CD A:ARG36 3.7 10.8 1.0 CA A:GLN42 3.8 5.2 1.0 CZ A:ARG36 4.1 6.8 1.0 N A:ARG36 4.2 5.0 1.0 CA A:THR41 4.2 5.8 1.0 C A:GLN42 4.3 5.4 1.0 NE A:ARG36 4.3 8.7 1.0 O A:GLU34 4.3 5.8 1.0 C A:GLY35 4.4 4.7 1.0 O A:HOH532 4.5 15.4 0.4 N A:THR43 4.5 5.5 1.0 CG A:ARG36 4.6 6.8 1.0 N A:GLY35 4.7 5.1 1.0 O A:HOH620 4.8 27.1 1.0 O A:HOH448 4.8 9.9 1.0 CE1 A:TYR214 4.9 11.8 1.0 C A:GLU34 4.9 4.8 1.0 CG2 A:THR43 4.9 7.6 1.0 CB A:ARG36 4.9 5.6 1.0 O A:GLN42 4.9 5.4 1.0 O A:HOH514 5.0 10.5 1.0 CG2 A:THR41 5.0 7.8 1.0

R.A.Chica, M.M.Moore, B.D.Allen, S.L.Mayo. Generation of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries. Proc. Natl. Acad. Sci. V. 107 20257 2010U.S.A..
ISSN: ESSN 1091-6490
PubMed: 21059931
DOI: 10.1073/PNAS.1013910107