Calcium in PDB 4m6y: Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid

The structure of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4m6y was solved by Y.C.Liu, X.W.Zou, H.C.Chan, C.J.Huang, T.L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.34 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.160, 89.626, 136.622, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 25.5

The structure of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Calcium atom in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid (pdb code 4m6y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4m6y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:47.7 occ:1.00 N A:ASP217 3.7 38.6 1.0 OG1 A:THR220 3.9 46.0 1.0 CG2 A:VAL224 4.1 49.6 1.0 CB A:ASP217 4.1 36.8 1.0 CB A:GLN223 4.2 42.3 1.0 O A:THR220 4.3 40.8 1.0 OE1 A:GLN223 4.4 45.4 1.0 CA A:GLY216 4.5 38.5 1.0 CA A:ASP217 4.5 36.7 1.0 O A:ASP217 4.6 36.1 1.0 C A:GLY216 4.6 40.8 1.0 C A:GLN223 4.6 44.2 1.0 O A:GLN223 4.7 44.3 1.0 N A:VAL224 4.8 46.0 1.0

Calcium binding site 2 out of 4 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:90.4 occ:1.00 OD2 A:ASP309 2.7 47.6 1.0 OD1 A:ASP306 2.8 59.6 1.0 CG A:ASP306 3.5 51.2 1.0 CG A:ASP309 3.6 42.9 1.0 CB A:ASP309 3.8 38.8 1.0 CA A:ASP306 4.0 40.8 1.0 CB A:ASP306 4.0 44.8 1.0 OD2 A:ASP306 4.3 56.1 1.0 OD1 A:ASP309 4.7 46.2 1.0 O A:ASP306 4.8 34.9 1.0 O A:HOH698 4.8 53.9 1.0 N A:ASP306 4.8 37.1 1.0 C A:ASP306 4.9 38.7 1.0 NZ A:LYS322 4.9 50.0 1.0

Calcium binding site 3 out of 4 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:85.1 occ:1.00 O A:HOH703 2.6 44.5 1.0 O A:SER225 2.9 85.4 1.0 N A:GLY228 3.4 77.7 1.0 CA A:GLY228 3.5 68.5 1.0 O A:HOH684 3.8 62.7 1.0 CD2 A:PHE230 3.9 48.4 1.0 CB A:ALA226 3.9 73.9 1.0 C A:GLY228 4.0 65.3 1.0 CB A:PHE230 4.0 44.7 1.0 CG A:PHE230 4.0 47.3 1.0 O A:HOH527 4.0 44.4 1.0 C A:SER225 4.1 75.0 1.0 N A:PHE230 4.2 48.1 1.0 N A:GLU229 4.3 63.2 1.0 O A:VAL224 4.3 50.5 1.0 C A:ALA226 4.5 80.2 1.0 N A:ARG227 4.5 88.4 1.0 CA A:ALA226 4.6 73.9 1.0 O A:GLY228 4.6 60.0 1.0 CE2 A:PHE230 4.6 49.6 1.0 C A:ARG227 4.7 86.6 1.0 CA A:PHE230 4.7 46.2 1.0 N A:ALA226 4.8 73.9 1.0 CD1 A:PHE230 4.8 51.1 1.0 O A:ALA226 4.9 81.4 1.0

Calcium binding site 4 out of 4 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:95.8 occ:1.00 OD2 B:ASP309 2.1 56.3 1.0 CG B:ASP309 3.0 53.3 1.0 OD1 B:ASP306 3.4 75.3 1.0 O B:HF2404 3.5 58.0 1.0 O B:HOH536 3.6 55.2 1.0 CB B:ASP309 3.6 51.8 1.0 NZ B:LYS322 3.7 39.8 1.0 OD1 B:ASP309 3.9 52.8 1.0 C B:HF2404 4.3 57.7 1.0 O3 B:HF2404 4.5 59.2 1.0 CG B:ASP306 4.6 64.0 1.0 CA B:ASP306 4.9 55.9 1.0

X.W.Zou, Y.C.Liu, N.S.Hsu, C.J.Huang, S.Y.Lyu, H.C.Chan, C.Y.Chang, H.W.Yeh, K.H.Lin, C.J.Wu, M.D.Tsai, T.L.Li. Structure and Mechanism of A Nonhaem-Iron Sam-Dependent C-Methyltransferase and Its Engineering to A Hydratase and An O-Methyltransferase Acta Crystallogr.,Sect.D V. 70 1549 2014.
ISSN: ISSN 0907-4449
PubMed: 24914966
DOI: 10.1107/S1399004714005239