Calcium in PDB 4kic: Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid, PDB code: 4kic 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)	19.00 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.547, 93.498, 142.245, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 23.8

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid also contains other interesting chemical elements:

Iodine	(I)	1 atom
Iron	(Fe)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid (pdb code 4kic). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid, PDB code: 4kic:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and 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 S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:42.0 occ:1.00 O B:HOH602 3.3 36.5 1.0 NH1 A:ARG12 3.4 58.9 1.0 CG A:ARG11 3.7 56.9 1.0 CA B:PRO285 4.0 37.1 1.0 CD A:ARG11 4.0 60.2 1.0 CB B:PRO285 4.1 38.1 1.0 CZ A:ARG12 4.2 59.5 1.0 O A:ARG11 4.3 38.9 1.0 CB A:ALA15 4.4 33.1 1.0 C A:ARG11 4.4 41.3 1.0 N A:ARG12 4.5 40.5 1.0 CA A:ARG12 4.6 42.0 1.0 CB A:ARG11 4.7 47.9 1.0 N B:PRO285 4.8 38.3 1.0 NH2 A:ARG12 4.8 62.8 1.0 O B:HOH603 4.9 35.0 1.0 NE A:ARG12 4.9 54.4 1.0 O B:GLU283 4.9 38.7 1.0 O B:LEU284 4.9 37.4 1.0

Calcium binding site 2 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and 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 S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:40.0 occ:1.00 CG A:ARG75 3.5 57.3 1.0 CD A:ARG75 3.8 64.2 1.0 NH1 B:ARG282 3.9 48.6 1.0 CD A:PRO85 4.1 37.8 1.0 CD B:ARG282 4.2 45.9 1.0 CG B:ARG282 4.4 43.8 1.0 CA A:GLY72 4.4 35.4 1.0 CG A:PRO85 4.4 36.8 1.0 O A:VAL74 4.6 39.6 1.0 CB A:ARG75 4.9 48.2 1.0 CZ B:ARG282 4.9 50.1 1.0

Calcium binding site 3 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and 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 S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:37.3 occ:1.00 O A:HOH651 2.5 38.8 1.0 O A:HOH523 3.4 29.1 1.0 CG A:GLU106 3.6 59.1 1.0 NH2 B:ARG109 3.6 53.1 1.0 C A:ARG127 3.6 32.1 1.0 N A:ASP128 3.8 31.9 1.0 O A:ARG127 3.8 34.7 1.0 CZ B:ARG109 3.9 54.7 1.0 CG A:GLN126 3.9 46.0 1.0 CA A:ARG127 4.0 32.2 1.0 CB A:GLU106 4.0 46.6 1.0 CB A:ASP128 4.1 36.7 1.0 CA A:ASP128 4.2 35.4 1.0 NE B:ARG109 4.2 46.2 1.0 O A:GLN126 4.3 30.9 1.0 N A:ARG127 4.3 32.2 1.0 C A:GLN126 4.3 35.8 1.0 NH1 B:ARG109 4.4 56.0 1.0 CB A:GLN126 4.7 42.7 1.0 CD A:GLU106 4.8 66.2 1.0 CG A:ASP128 5.0 41.6 1.0

Calcium binding site 4 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and 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 S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:32.6 occ:1.00 NH2 A:ARG109 3.2 53.7 1.0 C B:ARG127 3.6 32.1 1.0 O A:HOH631 3.7 42.5 1.0 CZ A:ARG109 3.7 49.4 1.0 N B:ASP128 3.8 31.0 1.0 O B:ARG127 3.8 29.6 1.0 CG B:GLN126 3.9 51.0 1.0 O B:HOH518 3.9 26.6 1.0 CA B:ARG127 3.9 34.6 1.0 CB B:GLU106 4.0 36.6 1.0 CB B:ASP128 4.1 36.1 1.0 CA B:ASP128 4.2 32.7 1.0 NH1 A:ARG109 4.3 56.5 1.0 O B:GLN126 4.3 34.0 1.0 N B:ARG127 4.3 36.8 1.0 NE A:ARG109 4.3 40.9 1.0 C B:GLN126 4.4 34.5 1.0 CG B:GLU106 4.4 43.4 1.0 CB B:GLN126 4.7 40.6 1.0 OE1 B:GLN126 4.8 51.4 1.0 OE2 A:GLU106 4.9 59.3 1.0 CD B:GLN126 4.9 55.9 1.0

Calcium binding site 5 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic 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-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:46.7 occ:1.00 O A:HOH644 3.0 49.6 1.0 N A:ASP217 3.6 38.4 1.0 OG1 A:THR220 3.8 35.1 1.0 CG2 A:VAL224 3.9 61.8 1.0 CB A:ASP217 4.1 37.6 1.0 O A:GLN223 4.2 56.5 1.0 CA A:GLY216 4.2 35.6 1.0 NH2 A:ARG215 4.4 58.4 1.0 CA A:ASP217 4.4 40.3 1.0 CA A:VAL224 4.5 62.5 1.0 C A:GLY216 4.5 36.3 1.0 C A:GLN223 4.5 54.1 1.0 O A:THR220 4.5 35.5 1.0 O A:ASP217 4.6 46.5 1.0 N A:VAL224 4.7 59.1 1.0 CB A:VAL224 4.7 62.2 1.0 C A:ASP217 4.9 40.6 1.0 CB A:GLN223 5.0 50.8 1.0

Calcium binding site 6 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca410 b:45.0 occ:1.00 OE1 A:GLN113 2.2 51.4 1.0 CD A:GLN113 3.1 51.0 1.0 NE2 A:GLN113 3.3 48.6 1.0 O A:ARG109 4.0 35.4 1.0 CG B:GLN102 4.1 34.2 1.0 CD A:PRO112 4.1 37.9 1.0 CA A:ARG110 4.1 32.5 1.0 CB B:GLN102 4.2 33.4 1.0 CG A:ARG110 4.3 43.3 1.0 CG A:PRO112 4.3 36.4 1.0 NH1 A:ARG109 4.5 56.5 1.0 CG A:GLN113 4.5 44.7 1.0 CB A:ARG110 4.6 39.8 1.0 OD2 B:ASP128 4.6 43.5 1.0 CB A:PRO112 4.7 35.9 1.0 C A:ARG110 4.7 31.8 1.0 C A:ARG109 4.8 34.1 1.0 CA B:GLN102 4.8 32.9 1.0 N A:ARG110 4.9 31.5 1.0 NE A:ARG110 4.9 59.8 1.0 OE1 B:GLU32 4.9 35.4 1.0 O B:GLN102 4.9 32.1 1.0 O A:ARG110 5.0 32.0 1.0

Calcium binding site 7 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca411 b:61.3 occ:1.00 O A:LYS123 3.2 56.0 1.0 N A:TYR125 3.8 37.0 1.0 C A:PHE124 3.9 37.8 1.0 C A:TYR125 3.9 35.3 1.0 CA A:TYR125 4.0 37.1 1.0 NH1 A:ARG110 4.0 56.8 1.0 O A:TYR125 4.1 33.4 1.0 C A:LYS123 4.1 51.2 1.0 O A:PHE124 4.3 38.5 1.0 CA A:PHE124 4.3 40.2 1.0 N A:GLN126 4.4 35.8 1.0 CB A:GLN126 4.4 42.7 1.0 N A:PHE124 4.5 43.2 1.0 CZ A:ARG110 4.8 65.0 1.0 CA A:GLN126 5.0 38.9 1.0

Calcium binding site 8 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:52.2 occ:1.00 NH1 B:ARG75 3.6 78.2 1.0 NH1 A:ARG282 4.1 46.8 1.0 CD A:ARG282 4.1 44.9 1.0 CA B:GLY72 4.1 36.4 1.0 CD B:PRO85 4.1 50.7 1.0 CG A:ARG282 4.2 42.1 1.0 O B:VAL74 4.3 45.5 1.0 CG B:PRO85 4.5 50.2 1.0 CG B:ARG75 4.6 60.3 1.0 CB B:ARG75 4.8 49.9 1.0 CZ B:ARG75 4.8 81.6 1.0 O B:GLY72 4.9 34.2 1.0 O B:ALA69 4.9 41.6 1.0 C B:GLY72 4.9 35.5 1.0 N B:GLY72 5.0 35.9 1.0

Calcium binding site 9 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca406 b:46.0 occ:1.00 NH1 B:ARG12 3.2 61.3 1.0 O A:HOH516 3.3 33.1 1.0 O B:ARG11 4.2 45.5 1.0 CB A:PRO285 4.2 41.9 1.0 CA A:PRO285 4.3 39.8 1.0 C B:ARG11 4.3 42.8 1.0 CB B:ARG11 4.3 44.4 1.0 CB B:ALA15 4.4 28.2 1.0 N B:ARG12 4.5 40.0 1.0 CZ B:ARG12 4.5 62.9 1.0 CA B:ARG12 4.5 42.8 1.0 NE B:ARG11 4.7 49.3 1.0 CD B:ARG11 4.8 51.4 1.0 O B:HOH642 4.9 49.8 1.0

Calcium binding site 10 out of 13 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Methionine and Phenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca407 b:50.0 occ:1.00 C B:LEU45 3.8 50.6 1.0 N B:ASP46 3.8 53.9 1.0 CE B:LYS44 4.0 70.3 1.0 CA B:LEU45 4.0 54.8 1.0 CG B:LYS44 4.0 58.0 1.0 O B:LEU45 4.2 46.5 1.0 CB B:ASP46 4.2 60.1 1.0 NZ B:LYS44 4.3 69.3 1.0 N B:LEU45 4.4 54.2 1.0 CA B:ASP46 4.4 55.3 1.0 CG2 B:THR80 4.4 55.8 1.0 CD B:LYS44 4.6 65.8 1.0 C B:LYS44 4.8 52.7 1.0 O B:HOH542 4.8 40.7 1.0 CB B:LYS44 4.9 53.1 1.0 OG1 B:THR80 5.0 58.7 1.0 OD2 B:ASP46 5.0 66.3 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