Sodium in PDB 4jhg: Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin

The structure of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin, PDB code: 4jhg was solved by M.Ruszkowski, K.Tusnio, A.Ciesielska, K.Brzezinski, M.Dauter, Z.Dauter, M.Sikorski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.92 / 1.85
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.110, 96.110, 113.244, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin (pdb code 4jhg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin, PDB code: 4jhg:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin


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 Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:32.5 occ:1.00 O A:HOH347 2.2 35.7 1.0 O A:PHE59 2.4 37.9 1.0 O A:HOH345 2.4 37.7 1.0 O A:HOH348 2.4 37.7 1.0 O A:GLY61 2.4 35.3 1.0 O A:HOH346 2.9 50.0 1.0 C A:GLY61 3.5 36.5 1.0 N A:GLY61 3.6 36.1 1.0 C A:PHE59 3.6 37.3 1.0 C A:VAL60 4.0 37.0 1.0 CA A:GLY61 4.0 40.4 1.0 CA A:VAL60 4.2 38.0 1.0 N A:VAL60 4.3 36.0 1.0 CG2 A:THR58 4.3 39.6 1.0 OE1 A:GLU40 4.4 53.7 1.0 O A:GLY64 4.4 34.2 1.0 N A:ASP62 4.6 40.1 1.0 O A:VAL60 4.6 41.6 1.0 CA A:PHE59 4.7 32.6 1.0 N A:PHE59 4.7 32.6 1.0 N A:GLY64 4.7 37.9 1.0 N A:PHE63 4.8 37.6 1.0 O A:HOH391 4.9 48.1 1.0 CA A:ASP62 5.0 38.2 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:55.1 occ:1.00 O A:SER65 2.2 33.5 1.0 O A:HOH395 2.4 52.0 1.0 O A:HOH328 2.4 47.1 1.0 OG1 A:THR66 2.7 29.7 0.5 C A:SER65 3.2 34.6 1.0 CB A:THR66 3.5 40.0 0.5 O A:HOH400 3.5 68.2 1.0 OG1 A:THR66 3.7 40.4 0.5 CA A:THR66 3.7 32.1 0.5 CA A:THR66 3.8 30.4 0.5 CB A:THR66 3.8 25.3 0.5 N A:THR66 3.8 31.6 1.0 N A:SER65 4.0 32.6 1.0 CA A:SER65 4.2 30.8 1.0 OE1 A:GLU86 4.4 43.9 0.4 CD A:GLU86 4.4 39.0 0.4 CG A:GLU86 4.6 49.4 0.4 CG2 A:THR66 4.6 24.6 0.5 O A:GLU86 4.7 31.7 1.0 O A:HOH344 4.7 34.8 1.0 OE2 A:GLU86 4.8 39.5 0.4 CG2 A:THR66 4.8 49.1 0.5 C A:GLY64 5.0 39.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Medicago Truncatula Nodulin 13 (MTN13) in Complex with Trans-Zeatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:61.2 occ:1.00 O A:HOH302 2.3 56.2 1.0 O A:THR0 2.3 33.1 1.0 O A:HOH416 2.6 44.4 1.0 O A:GLY124 2.7 62.4 1.0 C A:THR0 3.5 32.3 1.0 N A:GLY124 3.5 58.7 1.0 C A:GLY124 3.5 71.5 1.0 CA A:GLY124 4.0 59.6 1.0 CE1 A:PHE-1 4.0 58.8 1.0 N A:THR0 4.0 36.7 1.0 CA A:THR0 4.2 33.8 1.0 CZ A:PHE-1 4.3 59.5 1.0 OD2 A:ASP125 4.4 74.2 1.0 CD1 A:PHE-1 4.4 52.9 1.0 N A:MET1 4.5 31.6 1.0 O A:HOH415 4.5 43.7 1.0 C A:LYS123 4.6 61.0 1.0 N A:ASP125 4.6 60.2 1.0 CA A:MET1 4.6 34.6 1.0 CB A:THR0 4.7 35.9 1.0 O A:THR122 4.8 50.7 1.0 CA A:LYS123 4.8 63.0 1.0 CE2 A:PHE-1 4.9 51.0 1.0 CB A:MET1 4.9 34.4 1.0 CA A:ASP125 5.0 61.1 1.0

M.Ruszkowski, K.Szpotkowski, M.Sikorski, M.Jaskolski. The Landscape of Cytokinin Binding By A Plant Nodulin. Acta Crystallogr.,Sect.D V. 69 2365 2013.
ISSN: ISSN 0907-4449
PubMed: 24311578
DOI: 10.1107/S0907444913021975