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

Protein crystallography data

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

Other elements in 4kic:

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

Iron Binding Sites:

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 4kic

Go back to Iron Binding Sites List in 4kic
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 4kic

Go back to Iron Binding Sites List in 4kic
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

Reference:

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
Page generated: Tue Aug 5 11:58:57 2025

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