Calcium in PDB 4m72: Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus

The structure of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus, PDB code: 4m72 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)	29.06 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.871, 97.136, 135.234, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 19.6

The structure of Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus 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 (pdb code 4m72). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus, PDB code: 4m72:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:42.1 occ:1.00 CE A:LYS44 3.6 54.6 1.0 C A:LEU45 3.9 31.6 1.0 CG A:LYS44 4.0 42.6 1.0 N A:ASP46 4.0 34.8 1.0 CD A:LYS44 4.1 46.6 1.0 O A:LEU45 4.2 33.3 1.0 CG2 A:THR80 4.2 41.2 1.0 CA A:LEU45 4.2 31.9 1.0 CB A:ASP46 4.2 38.6 1.0 NZ A:LYS44 4.4 58.2 1.0 CA A:ASP46 4.5 34.6 1.0 N A:LEU45 4.5 33.2 1.0 CB A:THR80 4.6 37.7 1.0 C A:LYS44 4.8 34.0 1.0 CB A:LYS44 4.8 38.9 1.0

Calcium binding site 2 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:38.5 occ:1.00 O A:HOH749 2.2 55.0 1.0 O A:HOH647 2.9 33.5 1.0 CG A:ARG75 3.5 46.7 1.0 O A:HOH505 3.6 45.8 1.0 CD A:ARG75 3.8 55.9 1.0 CD A:PRO85 3.9 24.6 1.0 NH1 B:ARG282 4.0 39.6 1.0 CD B:ARG282 4.1 33.0 1.0 CA A:GLY72 4.1 23.9 1.0 CG A:PRO85 4.1 25.4 1.0 CG B:ARG282 4.3 29.3 1.0 NE A:ARG75 4.5 58.6 1.0 O A:VAL74 4.6 23.4 1.0 O B:HOH658 4.8 50.0 1.0 C A:GLY72 4.8 24.3 1.0 O A:GLY72 4.9 24.8 1.0 CZ B:ARG282 4.9 41.1 1.0 NE B:ARG282 4.9 37.7 1.0 CB A:ARG75 5.0 41.2 1.0

Calcium binding site 3 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:8.2 occ:1.00 O A:HOH778 1.5 58.5 1.0 O A:HOH767 3.1 58.1 1.0 N A:ASP217 3.7 22.3 1.0 O A:HOH593 3.8 33.4 1.0 OG1 A:THR220 3.8 20.8 1.0 OE1 A:GLN223 3.9 28.3 1.0 CA A:GLY216 4.1 20.4 1.0 CB A:ASP217 4.1 22.1 1.0 CG2 A:VAL224 4.2 17.1 1.0 CB A:GLN223 4.2 20.2 1.0 O A:THR220 4.4 15.8 1.0 C A:GLY216 4.4 22.0 1.0 CA A:ASP217 4.5 22.6 1.0 O A:GLN223 4.6 19.4 1.0 C A:GLN223 4.6 19.7 1.0 NH2 A:ARG215 4.6 49.0 1.0 O A:HOH703 4.7 33.2 1.0 O A:ASP217 4.8 21.1 1.0 N A:VAL224 4.9 18.5 1.0 CD A:GLN223 4.9 23.3 1.0 CA A:VAL224 4.9 18.7 1.0

Calcium binding site 4 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:67.0 occ:1.00 O A:HOH827 2.0 35.8 1.0 O A:HOH529 2.5 46.6 1.0 O A:HOH768 2.6 37.1 1.0 OD2 A:ASP309 3.0 25.1 1.0 CG A:ASP309 3.9 24.2 1.0 OD1 A:ASP306 4.0 39.8 1.0 O A:HOH874 4.0 51.6 1.0 CB A:ASP309 4.3 19.9 1.0 O A:HF2404 4.3 28.1 1.0 O3 A:HF2404 4.4 35.2 1.0 NZ A:LYS322 4.6 36.5 1.0 C A:HF2404 4.7 33.0 1.0 O A:HOH702 4.8 43.5 1.0 OD1 A:ASP309 4.9 22.1 1.0

Calcium binding site 5 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca409 b:45.9 occ:1.00 O B:HOH508 3.1 13.8 1.0 NH1 A:ARG12 3.6 28.2 1.0 CA B:PRO285 4.1 22.2 1.0 CB B:PRO285 4.1 23.7 1.0 O A:ARG11 4.1 19.8 1.0 O A:HOH789 4.2 38.9 1.0 C A:ARG11 4.2 23.0 1.0 CB A:ARG11 4.3 26.3 1.0 CB A:ALA15 4.3 18.6 1.0 O B:HOH655 4.4 31.6 1.0 N A:ARG12 4.5 23.3 1.0 CD A:ARG11 4.5 37.7 1.0 CA A:ARG12 4.6 25.7 1.0 CZ A:ARG12 4.6 27.5 1.0 CG A:ARG11 4.7 34.9 1.0 O B:HOH532 4.8 19.2 1.0 N B:PRO285 4.9 22.3 1.0 CA A:ARG11 4.9 21.9 1.0 O B:LEU284 4.9 25.3 1.0

Calcium binding site 6 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:34.7 occ:1.00 O B:HOH662 3.0 29.4 1.0 O B:HOH835 3.3 50.7 1.0 O B:HOH804 3.7 48.2 1.0 NH1 A:ARG282 3.9 33.9 1.0 CD B:ARG75 3.9 46.6 1.0 CD B:PRO85 4.0 23.3 1.0 CG B:PRO85 4.1 23.0 1.0 CA B:GLY72 4.2 19.4 1.0 CD A:ARG282 4.2 27.3 1.0 CG A:ARG282 4.3 26.5 1.0 CG B:ARG75 4.5 41.6 1.0 NE B:ARG75 4.5 49.5 1.0 O B:VAL74 4.6 22.4 1.0 CB B:ARG75 4.7 33.0 1.0 O B:GLY72 4.9 21.9 1.0 CZ A:ARG282 4.9 32.4 1.0 C B:GLY72 4.9 21.6 1.0

Calcium binding site 7 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca406 b:49.4 occ:1.00 O B:HOH790 2.2 47.2 1.0 CE B:LYS44 3.1 67.3 1.0 O B:HOH808 3.3 65.7 1.0 CD B:LYS44 3.4 61.2 1.0 CG B:LYS44 3.9 48.3 1.0 C B:LEU45 3.9 30.7 1.0 N B:ASP46 3.9 34.4 1.0 O B:LEU45 4.1 32.2 1.0 CA B:LEU45 4.2 29.6 1.0 CB B:ASP46 4.2 30.9 1.0 CG2 B:THR80 4.3 35.2 1.0 CA B:ASP46 4.4 35.0 1.0 O B:HOH752 4.5 58.6 1.0 N B:LEU45 4.5 30.2 1.0 NZ B:LYS44 4.5 73.2 1.0 CB B:THR80 4.7 34.3 1.0 CB B:LYS44 4.7 39.9 1.0 C B:LYS44 4.8 31.9 1.0 O B:LYS44 5.0 30.0 1.0

Calcium binding site 8 out of 8 in the Mutant Structure of Methyltransferase From Streptomyces Hygroscopicus


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca407 b:58.0 occ:1.00 CE B:LYS123 3.2 74.2 1.0 CD B:LYS123 3.5 67.9 1.0 O B:LYS123 3.6 47.7 1.0 O B:HOH827 3.7 49.4 1.0 O B:HOH722 3.7 57.3 1.0 N B:TYR125 3.9 32.8 1.0 C B:TYR125 3.9 30.4 1.0 CA B:TYR125 4.0 30.8 1.0 C B:PHE124 4.0 30.6 1.0 O B:TYR125 4.1 28.1 1.0 N B:GLN126 4.3 31.6 1.0 O B:PHE124 4.3 29.3 1.0 C B:LYS123 4.4 39.1 1.0 CG B:LYS123 4.4 56.0 1.0 CB B:GLN126 4.4 36.9 1.0 CA B:PHE124 4.5 31.9 1.0 NZ B:LYS123 4.6 82.1 1.0 N B:PHE124 4.8 32.3 1.0 CA B:GLN126 4.9 35.5 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