Sodium in PDB 5fub: Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah

All present enzymatic activity of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah:
2.1.1.125;

The structure of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah, PDB code: 5fub was solved by V.Cura, N.Troffer-Charlier, N.Marechal, L.Bonnefond, J.Cavarelli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.41 / 2.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	147.070, 147.070, 127.390, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.8

The structure of Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah (pdb code 5fub). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah, PDB code: 5fub:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah


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 Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1410 b:78.5 occ:1.00 OE1 A:GLU155 2.5 82.1 1.0 CD A:GLU155 3.7 79.6 1.0 OE1 A:GLN171 3.8 56.1 1.0 O A:ALA151 4.0 35.0 1.0 CB A:GLN171 4.3 39.9 1.0 CA A:GLU152 4.3 41.0 1.0 C A:ALA151 4.3 33.7 1.0 CB A:GLU155 4.4 56.0 1.0 N A:GLU152 4.4 33.7 1.0 CG1 A:VAL169 4.5 37.3 1.0 OE2 A:GLU155 4.5 83.5 1.0 CB A:ALA151 4.6 37.6 1.0 CG A:GLU155 4.6 68.2 1.0 CD A:GLN171 4.8 48.7 1.0 N A:GLN171 4.9 41.1 1.0 O A:VAL169 4.9 41.4 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah


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 Zebrafish Protein Arginine Methyltransferase 2 Catalytic Domain with Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1415 b:85.3 occ:1.00 OD2 A:ASP283 2.5 58.1 1.0 CG A:ASP283 3.3 54.7 1.0 OD1 A:ASP283 3.3 56.4 1.0 SG A:CYS224 3.7 66.3 1.0 O A:HOH2084 4.1 67.4 1.0 OG A:SER322 4.4 59.5 1.0 NE2 A:HIS324 4.6 78.3 1.0 CE1 A:HIS324 4.7 77.7 1.0 OE2 A:GLU336 4.7 87.9 1.0 O2 A:EDO1414 4.7 71.9 1.0 CB A:ASP283 4.7 47.4 1.0 OG1 A:THR226 4.8 42.2 1.0 CB A:SER322 4.8 45.1 1.0

V.Cura, N.Marechal, N.Troffer-Charlier, J.M.Strub, M.J.Van Haren, N.I.Martin, S.Cianferani, L.Bonnefond, J.Cavarelli. Structural Studies of Protein Arginine Methyltransferase 2 Reveal Its Interactions with Potential Substrates and Inhibitors. Febs J. V. 284 77 2017.
ISSN: ISSN 1742-4658
PubMed: 27879050
DOI: 10.1111/FEBS.13953