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

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4kib 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)	26.39 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.332, 78.062, 138.257, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.6

The structure of Crystal 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 Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid (pdb code 4kib). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4kib:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal 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 Crystal 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:38.4 occ:1.00 N A:ASP217 3.3 32.2 1.0 O A:HOH639 3.7 39.6 1.0 O A:HOH682 3.9 38.1 1.0 CA A:GLY216 3.9 34.8 1.0 CB A:ASP217 3.9 30.7 1.0 OG1 A:THR220 4.1 35.1 1.0 C A:GLY216 4.1 33.5 1.0 CG2 A:VAL224 4.2 38.2 1.0 CA A:ASP217 4.2 30.7 1.0 CB A:GLN223 4.2 45.9 1.0 O A:GLN223 4.3 41.3 1.0 CA A:VAL224 4.4 43.0 1.0 C A:GLN223 4.4 42.3 1.0 N A:VAL224 4.5 41.2 1.0 O A:ASP217 4.5 26.2 1.0 O A:THR220 4.8 30.2 1.0 C A:ASP217 4.8 29.9 1.0 CB A:VAL224 4.9 39.8 1.0

Calcium binding site 2 out of 5 in the Crystal 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 Crystal 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:37.6 occ:1.00 N A:GLY182 3.4 33.2 1.0 C A:PHE180 3.6 31.4 1.0 N A:PRO181 3.7 31.9 1.0 CA A:PHE180 3.7 32.0 1.0 CB A:PHE180 3.9 31.7 1.0 CD A:PRO181 3.9 32.6 1.0 CA A:GLY182 4.0 35.4 1.0 CG2 A:THR158 4.0 34.1 1.0 O A:PHE180 4.1 31.6 1.0 C A:PRO181 4.4 33.0 1.0 CA A:PRO181 4.5 32.4 1.0 CG A:PRO181 4.6 32.8 1.0 CD1 A:PHE180 4.6 29.4 1.0 N A:VAL183 4.7 35.0 1.0 C A:GLY182 4.7 36.9 1.0 CG A:PHE180 4.8 30.9 1.0 O A:HOH741 4.9 49.2 1.0

Calcium binding site 3 out of 5 in the Crystal 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 Crystal 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:37.6 occ:1.00 O A:HOH795 2.5 41.2 1.0 O A:HOH513 3.3 24.4 1.0 C A:ARG127 3.7 24.1 1.0 CG A:GLU106 3.7 34.3 1.0 NH2 B:ARG109 3.7 33.5 1.0 N A:ASP128 3.7 24.9 1.0 CG A:GLN126 3.8 38.4 1.0 CB A:GLU106 3.9 29.0 1.0 CZ B:ARG109 3.9 34.2 1.0 CA A:ARG127 4.0 25.6 1.0 O A:ARG127 4.0 23.7 1.0 CB A:ASP128 4.0 26.9 1.0 NH1 B:ARG109 4.2 36.9 1.0 CA A:ASP128 4.2 25.5 1.0 N A:ARG127 4.3 26.2 1.0 NE B:ARG109 4.3 33.4 1.0 C A:GLN126 4.5 29.2 1.0 O A:GLN126 4.5 27.4 1.0 CD A:GLN126 4.6 42.7 1.0 CB A:GLN126 4.8 34.5 1.0 OE1 A:GLN126 4.9 47.9 1.0 CG A:ASP128 5.0 29.7 1.0

Calcium binding site 4 out of 5 in the Crystal 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 Crystal 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:44.2 occ:1.00 OD1 B:ASP306 2.2 44.1 1.0 OD2 B:ASP309 2.5 29.3 1.0 O B:HOH612 2.8 30.9 1.0 CG B:ASP306 3.5 38.9 1.0 CG B:ASP309 3.5 28.0 1.0 CB B:ASP309 3.9 26.9 1.0 CA B:ASP306 4.2 30.6 1.0 CB B:ASP306 4.3 35.1 1.0 OD2 B:ASP306 4.3 43.0 1.0 NZ B:LYS322 4.5 29.4 1.0 OD1 B:ASP309 4.6 27.6 1.0 O3 B:HF2404 4.7 38.1 1.0 N B:ASP306 4.8 30.2 1.0

Calcium binding site 5 out of 5 in the Crystal 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 Crystal 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:43.9 occ:1.00 CG B:LYS44 3.5 50.5 1.0 CD B:LYS44 3.6 53.8 1.0 CE B:LYS44 3.7 54.7 1.0 N B:ASP46 3.9 33.4 1.0 C B:LEU45 4.0 32.0 1.0 CB B:ASP46 4.1 34.1 1.0 CA B:LEU45 4.3 32.1 1.0 O B:LEU45 4.4 29.2 1.0 OG1 B:THR80 4.4 38.2 1.0 CA B:ASP46 4.4 33.6 1.0 NZ B:LYS44 4.5 57.6 1.0 CG2 B:THR80 4.6 35.3 1.0 N B:LEU45 4.6 35.0 1.0 C B:LYS44 4.9 36.6 1.0 CB B:LYS44 4.9 45.5 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