Calcium in PDB 4kif: Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic Acid

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic Acid, PDB code: 4kif 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)	29.43 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.431, 88.708, 137.005, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 24.8

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

Calcium binding site 1 out of 4 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic 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 Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:44.5 occ:1.00 O A:HOH790 2.6 43.8 1.0 O A:HOH672 3.2 24.9 1.0 CG A:GLU106 3.4 42.6 1.0 CB A:GLU106 3.5 35.9 1.0 NH2 B:ARG109 3.5 41.7 1.0 C A:ARG127 3.7 37.3 1.0 N A:ASP128 3.8 39.7 1.0 O A:ARG127 4.0 37.6 1.0 NE2 A:GLN126 4.0 61.4 1.0 CA A:ARG127 4.0 39.0 1.0 CZ B:ARG109 4.0 40.8 1.0 CB A:ASP128 4.0 40.1 1.0 CA A:ASP128 4.2 40.5 1.0 N A:ARG127 4.3 42.4 1.0 NE B:ARG109 4.3 36.1 1.0 C A:GLN126 4.5 46.9 1.0 CD A:GLN126 4.6 62.5 1.0 O A:GLN126 4.6 42.5 1.0 CB A:GLN126 4.6 54.8 1.0 NH1 B:ARG109 4.7 37.3 1.0 CA A:GLU106 4.9 33.7 1.0 CD A:GLU106 4.9 48.0 1.0 CG A:GLN126 5.0 60.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic 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 Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:57.2 occ:1.00 O A:HOH784 2.5 39.7 1.0 OD2 A:ASP309 2.9 33.0 1.0 OD1 A:ASP306 3.0 45.4 1.0 CG A:ASP309 3.9 28.9 1.0 CB A:ASP309 4.1 27.3 1.0 CG A:ASP306 4.2 36.6 1.0 O A:HF2503 4.9 31.2 1.0 CA A:ASP306 4.9 29.3 1.0 CB A:ASP306 5.0 32.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic 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 Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca507 b:44.6 occ:1.00 C A:LEU45 3.9 39.0 1.0 O A:LEU45 4.1 37.1 1.0 N A:ASP46 4.1 37.9 1.0 CA A:LEU45 4.3 39.4 1.0 N A:LEU45 4.3 36.6 1.0 CB A:LYS44 4.3 45.7 1.0 CB A:ASP46 4.3 43.3 1.0 CG2 A:THR80 4.6 49.3 1.0 CA A:ASP46 4.6 40.3 1.0 CD A:LYS44 4.7 60.9 1.0 OG1 A:THR80 4.8 43.6 1.0 C A:LYS44 4.8 37.2 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with Phenylpyruvic 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 Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca504 b:72.9 occ:1.00 O B:SER-1 1.8 34.2 1.0 O B:HIS0 2.4 39.6 1.0 C B:SER-1 3.0 27.2 1.0 OG B:SER-1 3.1 29.6 1.0 OG B:SER2 3.2 41.2 1.0 C B:HIS0 3.3 41.8 1.0 CA B:HIS0 3.5 37.6 1.0 N B:HIS0 3.7 23.3 1.0 CB B:SER-1 3.9 32.8 1.0 CA B:SER-1 4.0 33.3 1.0 N B:SER2 4.4 39.8 1.0 O B:HOH757 4.6 45.1 1.0 N B:MET1 4.6 41.8 1.0 CB B:SER2 4.6 41.4 1.0 CB B:HIS0 5.0 41.5 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