Sodium in PDB 5icc: Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine

All present enzymatic activity of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine:
2.1.1.128;

The structure of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine, PDB code: 5icc was solved by A.Y.Robin, M.Graindorge, C.Giustini, R.Dumas, M.Matringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.81 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	73.640, 108.990, 40.910, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 20.6

The structure of Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine (pdb code 5icc). 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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine, PDB code: 5icc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine


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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:16.3 occ:1.00 O A:HOH605 2.7 31.7 1.0 OH A:TYR90 2.7 10.9 1.0 O A:HOH574 2.8 17.4 1.0 CE2 A:TYR90 3.4 13.7 1.0 CZ A:TYR90 3.5 13.1 1.0 CD1 A:TYR67 3.5 11.1 1.0 CE1 A:TYR67 3.5 11.1 1.0 CB A:LEU88 4.0 18.9 1.0 CB A:LEU49 4.0 11.9 1.0 CD1 A:LEU88 4.0 24.7 1.0 CD2 A:LEU49 4.3 14.6 1.0 CG A:LEU49 4.6 11.6 1.0 O A:LEU88 4.6 15.3 1.0 CG A:LEU88 4.6 20.6 1.0 CD1 A:LEU49 4.7 11.6 1.0 CD2 A:TYR90 4.8 10.7 1.0 N A:LEU49 4.8 10.8 1.0 CE1 A:TYR90 4.8 11.5 1.0 CG A:TYR67 4.8 9.2 1.0 O1 A:EDO415 4.9 49.6 1.0 CE A:LYS81 4.9 23.7 1.0 CZ A:TYR67 4.9 9.4 1.0 CA A:LEU49 5.0 11.2 1.0 NZ A:LYS81 5.0 22.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine


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 (S)-Norcoclaurine 6-O-Methyltransferase with S- Adenosyl-L-Homocysteine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:5.0 occ:1.00 OG1 A:THR297 3.1 7.9 1.0 N A:ASP289 3.2 10.5 1.0 NH1 A:ARG300 3.3 11.3 1.0 CD A:ARG300 3.6 8.2 1.0 CB A:ASP289 3.7 14.4 1.0 CA A:THR297 3.8 6.8 1.0 CB A:THR297 3.8 6.3 1.0 ND1 A:HIS294 3.8 13.8 1.0 O A:ASP289 3.9 16.2 1.0 CA A:ASP289 4.0 15.1 1.0 CG2 A:THR297 4.0 8.2 1.0 O A:ILE287 4.1 12.3 1.0 C A:LEU288 4.2 11.4 1.0 CA A:LEU288 4.3 12.6 1.0 CZ A:ARG300 4.3 11.8 1.0 N A:THR297 4.4 5.5 1.0 C A:ASP289 4.4 16.1 1.0 NE A:ARG300 4.5 9.1 1.0 CB A:HIS294 4.6 10.3 1.0 CG A:HIS294 4.6 13.0 1.0 CD1 A:LEU288 4.6 27.0 1.0 CE1 A:HIS294 4.7 7.1 1.0 CB A:ARG300 4.8 5.8 1.0 CG A:ARG300 4.8 9.1 1.0 C A:THR297 5.0 7.5 1.0

A.Y.Robin, C.Giustini, M.Graindorge, M.Matringe, R.Dumas. Crystal Structure of Norcoclaurine-6-O-Methyltransferase, A Key Rate-Limiting Step in the Synthesis of Benzylisoquinoline Alkaloids. Plant J. V. 87 641 2016.
ISSN: ESSN 1365-313X
PubMed: 27232113
DOI: 10.1111/TPJ.13225