Iron 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
Calcium	(Ca)	13 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 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 Iron with other atoms in the Fe 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:Fe403 b:28.2 occ:1.00 O3 A:PPY402 1.9 31.4 1.0 O A:HOH502 2.0 18.3 1.0 O2 A:PPY402 2.1 30.9 1.0 O A:HOH501 2.1 23.9 1.0 NE2 A:HIS295 2.1 26.5 1.0 NE2 A:HIS243 2.2 35.1 1.0 C2 A:PPY402 2.6 32.0 1.0 C1 A:PPY402 2.7 32.4 1.0 CE1 A:HIS243 3.1 32.6 1.0 CD2 A:HIS295 3.1 27.6 1.0 CE1 A:HIS295 3.2 25.5 1.0 CD2 A:HIS243 3.2 34.0 1.0 OD2 A:ASP244 3.9 37.8 1.0 O1 A:PPY402 3.9 33.4 1.0 OD1 A:ASP244 4.0 36.2 1.0 C3 A:PPY402 4.1 34.0 1.0 O A:MET240 4.1 31.9 1.0 ND1 A:HIS243 4.2 32.5 1.0 ND1 A:HIS295 4.2 28.2 1.0 CG A:HIS295 4.2 28.2 1.0 CG A:ASP244 4.3 38.9 1.0 CG A:HIS243 4.3 30.3 1.0 O A:HOH606 4.5 25.3 1.0 C6' A:PPY402 4.7 37.0 1.0 CE1 A:PHE291 4.8 37.4 1.0 C1' A:PPY402 4.9 35.8 1.0 O A:HOH518 4.9 35.7 1.0

Iron binding site 2 out of 2 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 Iron with other atoms in the Fe 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 B:Fe403 b:29.1 occ:1.00 O B:HOH501 2.0 22.6 1.0 O3 B:PPY402 2.0 37.1 1.0 O B:HOH502 2.0 23.8 1.0 O1 B:PPY402 2.1 33.1 1.0 NE2 B:HIS295 2.1 29.2 1.0 NE2 B:HIS243 2.2 33.0 1.0 C2 B:PPY402 2.7 33.6 1.0 C1 B:PPY402 2.8 34.0 1.0 CE1 B:HIS295 3.1 30.5 1.0 CD2 B:HIS295 3.1 29.1 1.0 CE1 B:HIS243 3.1 33.0 1.0 CD2 B:HIS243 3.2 32.7 1.0 O B:HOH599 3.8 28.1 1.0 OD2 B:ASP244 4.0 35.8 1.0 O2 B:PPY402 4.0 34.1 1.0 OD1 B:ASP244 4.0 31.4 1.0 O B:MET240 4.1 33.7 1.0 C3 B:PPY402 4.2 36.4 1.0 ND1 B:HIS295 4.2 32.8 1.0 CG B:HIS295 4.2 27.5 1.0 ND1 B:HIS243 4.3 33.2 1.0 CG B:HIS243 4.3 32.4 1.0 CG B:ASP244 4.4 35.7 1.0 O B:HOH633 4.6 31.0 1.0 NH2 B:ARG127 4.8 34.1 1.0 C6' B:PPY402 4.8 32.9 1.0 CE1 B:PHE291 4.9 30.3 1.0 C1' B:PPY402 5.0 33.3 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