Calcium in PDB 4m6x: 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: 4m6x 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)	27.94 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.009, 90.219, 136.505, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / 22.7

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 4m6x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 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: 4m6x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 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:59.4 occ:1.00 OD2 A:ASP309 2.7 38.2 1.0 OD1 A:ASP306 2.8 59.3 1.0 O A:HOH571 3.4 38.7 1.0 O A:HOH553 3.5 35.4 1.0 CG A:ASP309 3.6 34.2 1.0 CB A:ASP309 3.8 32.5 1.0 CG A:ASP306 3.9 53.5 1.0 O A:HOH643 3.9 49.8 1.0 CA A:ASP306 4.5 38.4 1.0 OD2 A:ASP306 4.6 62.6 1.0 CB A:ASP306 4.7 43.4 1.0 OD1 A:ASP309 4.7 34.0 1.0 O A:HF2404 4.9 40.1 1.0 O3 A:HF2404 5.0 36.1 1.0

Calcium binding site 2 out of 5 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:69.4 occ:1.00 O A:SER-1 2.2 46.9 1.0 C A:HIS0 2.7 45.9 1.0 O A:HIS0 2.8 55.1 1.0 CA A:HIS0 3.0 42.0 1.0 OG A:SER2 3.2 38.4 1.0 C A:SER-1 3.2 36.4 1.0 N A:MET1 3.3 47.3 1.0 N A:HIS0 3.5 25.7 1.0 N A:SER2 3.6 39.5 1.0 CB A:SER2 4.1 39.7 1.0 CA A:MET1 4.3 42.6 1.0 CB A:HIS0 4.4 41.2 1.0 C A:MET1 4.4 41.3 1.0 CA A:SER2 4.5 40.3 1.0 CA A:SER-1 4.5 45.1 1.0 O A:HOH575 4.6 43.1 1.0 CB A:SER-1 4.8 45.9 1.0 O A:HOH686 4.9 44.0 1.0

Calcium binding site 3 out of 5 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 B:Ca405 b:71.5 occ:1.00 O B:HOH714 3.0 40.8 1.0 N B:GLY228 3.6 49.2 1.0 CD2 B:PHE230 3.6 30.3 1.0 CA B:GLY228 3.6 45.8 1.0 CG B:PHE230 3.7 30.1 1.0 CB B:PHE230 3.7 30.2 1.0 N B:ALA226 3.7 44.1 1.0 N B:PHE230 3.8 30.3 1.0 CB B:ALA226 3.9 44.2 1.0 C B:GLY228 4.0 40.4 1.0 N B:GLU229 4.1 37.0 1.0 CA B:ALA226 4.1 45.1 1.0 C B:ALA226 4.1 46.8 1.0 CE2 B:PHE230 4.3 31.8 1.0 CD1 B:PHE230 4.4 30.6 1.0 O B:HOH520 4.4 30.9 1.0 CA B:PHE230 4.4 31.3 1.0 O B:ALA226 4.4 45.0 1.0 O B:VAL224 4.4 34.3 1.0 N B:ARG227 4.5 53.1 1.0 C B:SER225 4.7 46.6 1.0 O B:HOH644 4.7 36.3 1.0 O B:GLY228 4.8 38.2 1.0 C B:ARG227 4.8 52.3 1.0 C B:GLU229 4.9 32.2 1.0 CZ B:PHE230 4.9 31.2 1.0 O B:HOH713 5.0 46.2 1.0 CE1 B:PHE230 5.0 31.3 1.0 CA B:SER225 5.0 42.6 1.0

Calcium binding site 4 out of 5 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:Ca406 b:73.1 occ:1.00 O B:GLY84 3.1 24.7 1.0 N B:ASP88 3.3 25.6 1.0 O B:PRO85 3.4 26.5 1.0 CG B:ASP88 3.5 29.0 1.0 N B:PHE87 3.6 26.3 1.0 OD2 B:ASP88 3.7 33.4 1.0 OD1 B:ASP88 3.7 29.9 1.0 O B:HOH511 3.8 25.2 1.0 CB B:PHE87 3.8 26.1 1.0 C B:PRO85 3.8 27.3 1.0 CB B:ASP88 3.9 27.4 1.0 CA B:PHE87 4.0 26.3 1.0 C B:PHE87 4.1 26.5 1.0 CA B:ASP88 4.2 27.2 1.0 C B:GLY84 4.2 25.3 1.0 CA B:PRO85 4.3 26.7 1.0 N B:TYR86 4.4 28.0 1.0 C B:TYR86 4.5 26.5 1.0 N B:PRO85 4.7 25.6 1.0 CA B:TYR86 4.8 26.6 1.0 CG B:PHE87 4.9 26.3 1.0

Calcium binding site 5 out of 5 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 5 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:Ca407 b:77.9 occ:1.00 O B:TYR134 3.3 35.6 1.0 CB B:ARG137 3.9 43.0 1.0 NH1 B:ARG137 3.9 77.1 1.0 CZ2 B:TRP31 4.1 25.8 1.0 CH2 B:TRP31 4.2 25.9 1.0 CE1 B:TYR134 4.3 34.7 1.0 CD B:ARG137 4.3 61.8 1.0 CZ B:TYR134 4.3 35.2 1.0 C B:TYR134 4.3 33.0 1.0 CD1 B:TYR134 4.3 34.4 1.0 CE2 B:TYR134 4.4 34.3 1.0 CG B:TYR134 4.5 33.4 1.0 CD2 B:TYR134 4.5 33.9 1.0 CG B:ARG137 4.5 52.5 1.0 N B:GLU138 4.6 32.1 1.0 CA B:TYR134 4.7 34.1 1.0 OH B:TYR134 4.9 35.0 1.0 CB B:GLU138 4.9 31.1 1.0 CZ B:ARG137 5.0 76.3 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