Calcium in PDB 4m71: 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: 4m71 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)	28.95 / 2.21
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.833, 93.693, 137.375, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 22.9

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:

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

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

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 4m71). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 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: 4m71:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 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:27.3 occ:1.00 O B:HOH533 3.4 28.6 1.0 NH1 A:ARG12 3.5 34.3 1.0 O A:ARG11 4.1 22.8 1.0 CA B:PRO285 4.2 21.4 1.0 C A:ARG11 4.2 23.4 1.0 CB B:PRO285 4.2 22.4 1.0 N A:ARG12 4.3 22.8 1.0 CB A:ALA15 4.3 20.5 1.0 CB A:ARG11 4.3 31.8 1.0 CZ A:ARG12 4.4 33.1 1.0 CA A:ARG12 4.4 23.2 1.0 CD A:ARG11 4.7 42.3 1.0 N B:PRO285 4.9 23.3 1.0 CA A:ARG11 4.9 26.0 1.0 CG A:ARG11 5.0 38.4 1.0 NE A:ARG12 5.0 33.5 1.0

Calcium binding site 2 out of 14 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:43.0 occ:1.00 CE A:LYS44 3.1 60.3 1.0 CD A:LYS44 3.6 56.9 1.0 C A:LEU45 3.8 35.3 1.0 N A:ASP46 3.9 34.0 1.0 CG A:LYS44 3.9 49.7 1.0 O A:LEU45 4.0 36.3 1.0 CA A:LEU45 4.1 36.1 1.0 CB A:ASP46 4.2 45.7 1.0 NZ A:LYS44 4.2 61.8 1.0 N A:LEU45 4.2 36.6 1.0 CA A:ASP46 4.4 38.7 1.0 OG1 A:THR80 4.5 45.8 1.0 CG2 A:THR80 4.5 43.8 1.0 CB A:LYS44 4.8 42.0 1.0 C A:LYS44 4.8 34.3 1.0

Calcium binding site 3 out of 14 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:37.7 occ:1.00 O A:HOH782 2.3 46.0 1.0 O A:HOH758 2.7 34.9 1.0 CG A:ARG75 3.5 53.0 1.0 O A:HOH752 3.9 44.9 1.0 CD A:PRO85 3.9 28.9 1.0 NE B:ARG282 4.1 44.9 1.0 CA A:GLY72 4.1 28.3 1.0 CD A:ARG75 4.2 58.2 1.0 CG B:ARG282 4.3 33.5 1.0 CD B:ARG282 4.4 39.4 1.0 CG A:PRO85 4.4 32.6 1.0 O A:VAL74 4.5 28.6 1.0 C A:GLY72 4.8 29.7 1.0 O A:GLY72 4.8 30.1 1.0 CB A:ARG75 4.9 44.3 1.0 N A:GLY72 4.9 27.7 1.0

Calcium binding site 4 out of 14 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 A:Ca408 b:52.7 occ:1.00 NH2 A:ARG110 3.4 69.8 1.0 N A:TYR125 3.7 36.5 1.0 C A:TYR125 3.8 36.2 1.0 C A:PHE124 3.8 38.6 1.0 CA A:TYR125 3.9 34.9 1.0 O A:TYR125 4.0 40.1 1.0 CG A:LYS123 4.1 79.1 1.0 O A:PHE124 4.2 43.6 1.0 N A:GLN126 4.2 37.5 1.0 CB A:GLN126 4.2 45.3 1.0 CZ A:ARG110 4.2 69.7 1.0 CA A:PHE124 4.3 40.8 1.0 O A:LYS123 4.3 58.1 1.0 C A:LYS123 4.5 56.8 1.0 N A:PHE124 4.6 46.3 1.0 CA A:GLN126 4.7 40.4 1.0 NE A:ARG110 4.8 61.6 1.0 CE A:LYS123 4.8 89.4 1.0 OE1 A:GLN126 4.9 59.9 1.0 NH1 A:ARG110 5.0 71.1 1.0

Calcium binding site 5 out of 14 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 A:Ca409 b:39.1 occ:1.00 O A:HOH754 3.1 50.6 1.0 O A:HOH607 3.5 23.6 1.0 N A:GLY182 3.6 30.5 1.0 C A:PHE180 3.8 25.9 1.0 O A:HOH730 3.8 35.1 1.0 CA A:PHE180 3.8 23.9 1.0 N A:PRO181 3.9 31.8 1.0 CB A:PHE180 3.9 22.5 1.0 CD A:PRO181 4.0 34.3 1.0 O A:PHE180 4.2 22.5 1.0 CG2 A:THR158 4.3 20.4 1.0 CA A:GLY182 4.3 35.9 1.0 CD1 A:PHE180 4.4 23.2 1.0 C A:PRO181 4.6 32.1 1.0 CG A:PHE180 4.7 21.5 1.0 CA A:PRO181 4.7 32.9 1.0 O A:HOH613 4.9 34.5 1.0

Calcium binding site 6 out of 14 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 6 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:Ca410 b:51.0 occ:1.00 O A:HOH809 2.2 17.0 1.0 O A:HOH522 3.1 18.7 1.0 N A:GLY228 3.4 27.2 1.0 CA A:GLY228 3.5 27.3 1.0 CG A:PHE230 3.7 23.4 1.0 N A:PHE230 3.7 25.0 1.0 CB A:PHE230 3.7 22.8 1.0 C A:GLY228 3.8 24.9 1.0 N A:ALA226 3.8 26.8 1.0 CD2 A:PHE230 3.8 25.4 1.0 N A:GLU229 3.9 25.8 1.0 C A:ALA226 4.1 27.0 1.0 CB A:ALA226 4.2 24.4 1.0 O A:ALA226 4.2 21.6 1.0 CD1 A:PHE230 4.2 22.9 1.0 CA A:ALA226 4.2 26.6 1.0 CA A:PHE230 4.3 23.3 1.0 O A:VAL224 4.3 19.2 1.0 O A:HOH591 4.4 24.0 1.0 N A:ARG227 4.5 30.7 1.0 O A:GLY228 4.5 24.4 1.0 CE2 A:PHE230 4.5 25.4 1.0 C A:ARG227 4.6 30.1 1.0 O A:HOH576 4.6 20.0 1.0 O A:HOH605 4.7 21.7 1.0 C A:GLU229 4.7 26.5 1.0 CA A:GLU229 4.8 30.2 1.0 CE1 A:PHE230 4.8 23.1 1.0 C A:SER225 4.9 26.7 1.0 CZ A:PHE230 5.0 24.8 1.0

Calcium binding site 7 out of 14 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 7 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:Ca411 b:70.8 occ:1.00 O A:VAL265 3.6 19.2 1.0 O A:PRO263 3.8 19.9 1.0 C A:VAL265 4.3 17.0 1.0 O A:HOH511 4.3 12.7 1.0 C A:ASN264 4.5 21.3 1.0 CA A:ASN264 4.5 19.9 1.0 O A:ASN264 4.6 24.4 1.0 CG A:ARG266 4.6 19.8 1.0 O A:HOH583 4.7 27.1 1.0 CA A:ARG266 4.7 17.1 1.0 NH2 A:ARG259 4.8 23.6 1.0 N A:VAL265 4.8 19.4 1.0 NH1 A:ARG259 4.8 21.5 1.0 C A:PRO263 4.8 18.3 1.0 O A:HOH712 4.9 38.8 1.0 N A:ARG266 4.9 17.0 1.0 O A:HOH588 4.9 38.5 1.0

Calcium binding site 8 out of 14 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 8 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:Ca412 b:75.5 occ:1.00 OD2 A:ASP309 2.7 37.4 1.0 O A:HOH676 2.9 43.6 1.0 OD1 A:ASP306 3.1 44.8 1.0 CG A:ASP309 3.7 29.3 1.0 O A:HOH711 3.8 39.0 1.0 CB A:ASP309 4.2 27.8 1.0 CG A:ASP306 4.2 34.7 1.0 NZ A:LYS322 4.5 27.4 1.0 O3 A:HF2404 4.6 29.9 1.0 O A:HOH762 4.6 45.4 1.0 OD1 A:ASP309 4.7 27.3 1.0 CA A:ASP306 4.9 26.9 1.0

Calcium binding site 9 out of 14 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 9 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:Ca413 b:53.4 occ:1.00 OE1 A:GLN113 2.2 58.8 1.0 CD A:GLN113 3.1 50.8 1.0 NE2 A:GLN113 3.3 50.1 1.0 CG B:GLN102 3.9 18.5 1.0 CG A:PRO112 3.9 27.2 1.0 CG A:ARG110 4.0 41.3 1.0 O A:ARG109 4.0 26.6 1.0 CD A:PRO112 4.1 25.5 1.0 NH1 A:ARG109 4.1 41.4 1.0 CA A:ARG110 4.3 28.2 1.0 OD2 B:ASP128 4.3 37.5 1.0 CB B:GLN102 4.3 19.1 1.0 CG A:GLN113 4.5 41.0 1.0 CB A:PRO112 4.7 27.1 1.0 OE1 B:GLU32 4.7 30.7 1.0 CB A:ARG110 4.7 34.9 1.0 C A:ARG109 4.8 25.3 1.0 CA B:GLN102 4.8 19.3 1.0 C A:ARG110 4.9 26.5 1.0

Calcium binding site 10 out of 14 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 10 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:28.4 occ:1.00 CD B:ARG75 4.0 52.1 1.0 NH1 A:ARG282 4.0 44.1 1.0 CD B:PRO85 4.0 25.7 1.0 CG B:PRO85 4.1 27.3 1.0 CG A:ARG282 4.2 32.0 1.0 CD A:ARG282 4.2 33.8 1.0 CA B:GLY72 4.3 21.6 1.0 CG B:ARG75 4.3 45.9 1.0 NE B:ARG75 4.4 57.3 1.0 O B:VAL74 4.7 23.4 1.0 CB B:ARG75 4.7 37.3 1.0 O B:GLY72 5.0 22.6 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