Iron in PDB 4kib: Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4kib 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)	26.39 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.332, 78.062, 138.257, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 25.6

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

Calcium

(Ca)

5 atoms

The binding sites of Iron atom in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with S-Adenosyl-L-Homocysteine and Methylphenylpyruvic Acid (pdb code 4kib). 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-Homocysteine and Methylphenylpyruvic Acid, PDB code: 4kib:
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-Homocysteine and Methylphenylpyruvic 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-Homocysteine and Methylphenylpyruvic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe403 b:18.2 occ:1.00 O A:HOH647 1.9 22.0 1.0 O A:HOH646 2.0 15.4 1.0 OAL A:56D402 2.1 20.2 1.0 NE2 A:HIS295 2.1 17.1 1.0 OAK A:56D402 2.1 22.4 1.0 NE2 A:HIS243 2.3 21.9 1.0 CAI A:56D402 2.7 21.3 1.0 CAH A:56D402 2.7 22.1 1.0 CE1 A:HIS295 3.1 16.7 1.0 CE1 A:HIS243 3.1 21.4 1.0 CD2 A:HIS295 3.2 17.5 1.0 CD2 A:HIS243 3.3 21.1 1.0 O A:HOH669 4.0 29.2 1.0 OAM A:56D402 4.0 19.9 1.0 OD2 A:ASP244 4.0 20.3 1.0 OD1 A:ASP244 4.1 21.0 1.0 ND1 A:HIS295 4.2 17.3 1.0 CAG A:56D402 4.3 22.6 1.0 CG A:HIS295 4.3 17.7 1.0 ND1 A:HIS243 4.3 20.6 1.0 O A:HOH668 4.4 26.2 1.0 CG A:HIS243 4.4 20.7 1.0 O A:MSE240 4.4 21.1 1.0 CG A:ASP244 4.5 21.1 1.0 NH2 A:ARG127 4.8 21.2 1.0 CE1 A:PHE291 4.8 21.5 1.0 CAJ A:56D402 4.9 23.1 1.0 CAE A:56D402 4.9 21.0 1.0 CAD A:56D402 5.0 21.9 1.0

Iron binding site 2 out of 2 in the Crystal 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 Iron with other atoms in the Fe binding site number 2 of Crystal 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:Fe403 b:17.8 occ:1.00 O B:HOH643 1.9 15.0 1.0 NE2 B:HIS295 2.0 22.8 1.0 O B:HOH644 2.0 23.7 1.0 NE2 B:HIS243 2.1 24.2 1.0 OAK B:56D402 2.1 23.9 1.0 OAM B:56D402 2.2 23.3 1.0 CAH B:56D402 2.8 24.2 1.0 CAI B:56D402 2.8 23.7 1.0 CE1 B:HIS295 2.8 23.1 1.0 CE1 B:HIS243 3.0 24.0 1.0 CD2 B:HIS243 3.1 23.6 1.0 CD2 B:HIS295 3.1 23.8 1.0 O B:HOH697 3.9 33.9 1.0 ND1 B:HIS295 4.0 23.9 1.0 OAL B:56D402 4.0 22.8 1.0 OD2 B:ASP244 4.1 24.8 1.0 ND1 B:HIS243 4.1 23.4 1.0 CG B:HIS295 4.1 23.9 1.0 CG B:HIS243 4.2 23.4 1.0 OD1 B:ASP244 4.2 26.2 1.0 O B:HOH686 4.2 28.2 1.0 CAG B:56D402 4.3 26.2 1.0 O B:MSE240 4.5 21.8 1.0 CG B:ASP244 4.6 24.7 1.0 CE1 B:PHE291 4.6 21.1 1.0 NH2 B:ARG127 4.7 23.3 1.0 CAE B:56D402 4.9 26.7 1.0 CAJ B:56D402 5.0 25.9 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