Sodium in PDB 1jg3: Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate

All present enzymatic activity of Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate:
2.1.1.77;

The structure of Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate, PDB code: 1jg3 was solved by S.C.Griffith, M.R.Sawaya, D.Boutz, N.Thapar, J.Katz, S.Clarke, T.O.Yeates, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	500.00 / 2.10
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	91.573, 91.573, 124.547, 90.00, 90.00, 120.00
R / Rfree (%)	20.4 / 23.3

The structure of Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate (pdb code 1jg3). 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 L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate, PDB code: 1jg3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate


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 L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:43.4 occ:1.00 OXT C:IAS4 2.4 21.7 1.0 O A:THR73 2.6 22.5 1.0 O A:HOH1307 2.6 27.2 1.0 O A:HOH1185 2.6 34.3 1.0 OG1 A:THR73 2.8 25.5 1.0 C C:IAS4 3.0 22.1 1.0 O C:IAS4 3.1 20.2 1.0 O5' A:ADN500 3.1 34.1 1.0 C A:THR73 3.4 22.4 1.0 C5' A:ADN500 3.8 28.9 1.0 N A:THR73 3.9 25.0 1.0 CA A:THR73 4.0 24.2 1.0 CB A:THR73 4.0 22.1 1.0 CG2 A:VAL219 4.1 23.2 1.0 O A:THR165 4.2 22.1 1.0 OG A:SER75 4.2 21.4 1.0 N A:VAL74 4.3 22.6 1.0 N A:SER75 4.4 23.3 1.0 CA C:IAS4 4.5 22.1 1.0 CB A:VAL219 4.6 25.6 1.0 CA A:VAL74 4.6 22.8 1.0 C A:VAL74 4.6 24.1 1.0 O C:PRO3 4.9 24.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate


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 L-Isoaspartyl (D-Aspartyl) O-Methyltransferase with Adenosine & Vyp(Isp)Ha Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:37.8 occ:1.00 OXT D:IAS4 2.4 18.3 1.0 O B:THR73 2.4 23.0 1.0 O B:HOH1309 2.5 27.9 1.0 O B:HOH1336 2.6 29.8 1.0 OG1 B:THR73 2.8 23.1 1.0 O5' B:ADN550 3.0 34.4 1.0 C D:IAS4 3.1 18.9 1.0 O D:IAS4 3.2 19.2 1.0 C B:THR73 3.3 21.9 1.0 N B:THR73 3.8 22.8 1.0 CA B:THR73 3.9 22.3 1.0 CB B:THR73 3.9 21.6 1.0 C5' B:ADN550 4.0 30.8 1.0 CG2 B:VAL219 4.1 27.4 1.0 OG B:SER75 4.2 22.5 1.0 N B:VAL74 4.2 21.7 1.0 O B:THR165 4.3 18.9 1.0 CG1 B:VAL219 4.3 22.7 1.0 N B:SER75 4.4 21.2 1.0 CA D:IAS4 4.5 20.3 1.0 CA B:VAL74 4.5 21.8 1.0 C B:VAL74 4.5 22.2 1.0 O B:HOH1275 4.6 42.6 1.0 O D:PRO3 4.9 21.5 1.0 CB B:VAL219 4.9 23.8 1.0 CA B:SER75 5.0 22.3 1.0 CG2 B:THR73 5.0 23.0 1.0

S.C.Griffith, M.R.Sawaya, D.R.Boutz, N.Thapar, J.E.Katz, S.Clarke, T.O.Yeates. Crystal Structure of A Protein Repair Methyltransferase From Pyrococcus Furiosus with Its L-Isoaspartyl Peptide Substrate. J.Mol.Biol. V. 313 1103 2001.
ISSN: ISSN 0022-2836
PubMed: 11700066
DOI: 10.1006/JMBI.2001.5095