Iron in PDB 4kvr: Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y)

All present enzymatic activity of Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y):
4.1.99.5;

The structure of Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y), PDB code: 4kvr was solved by C.W.Levy, B.Khara, N.Menon, D.Mansell, D.Das, E.N.G.Marsh, D.Leys, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.32 / 1.88
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.240, 78.240, 117.830, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 21.8

The binding sites of Iron atom in the Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y) (pdb code 4kvr). 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 Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y), PDB code: 4kvr:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y)


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 Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:32.7 occ:1.00 OE1 A:GLU73 2.0 34.3 1.0 OE1 A:GLU45 2.0 31.8 1.0 OE2 A:GLU157 2.1 48.0 1.0 ND1 A:HIS76 2.2 29.4 1.0 O A:6NA301 2.3 36.8 1.0 OE1 A:GLU157 2.5 40.1 1.0 CD A:GLU157 2.7 46.3 1.0 CD A:GLU45 2.9 25.1 1.0 CE1 A:HIS76 3.1 37.5 1.0 CD A:GLU73 3.1 31.9 1.0 OE2 A:GLU45 3.1 36.3 1.0 FE A:FE303 3.3 34.0 1.0 CG A:HIS76 3.3 30.3 1.0 C A:6NA301 3.5 39.9 1.0 OE2 A:GLU73 3.6 32.0 1.0 CB A:HIS76 3.8 28.4 1.0 OXT A:6NA301 3.9 37.5 1.0 CG A:GLU157 4.2 35.9 1.0 NE2 A:HIS76 4.2 32.9 1.0 CG A:GLU45 4.3 28.4 1.0 CE1 A:HIS160 4.3 35.7 1.0 CA A:GLU73 4.4 28.8 1.0 CG A:GLU73 4.4 26.6 1.0 CD2 A:HIS76 4.4 28.2 1.0 ND1 A:HIS160 4.6 34.4 1.0 CB A:GLU73 4.6 26.7 1.0 CA A:6NA301 4.7 31.7 1.0 CG1 A:VAL153 4.8 38.0 1.0 CB A:6NA301 4.8 32.6 1.0 CB A:GLU45 4.8 28.9 1.0 OE1 A:GLU128 4.9 32.7 1.0 CA A:GLU45 4.9 27.4 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y)


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 Prochlorococcus Marinus Aldehyde-Deformylating Oxygenase (Mutant V41Y) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe303 b:34.0 occ:1.00 OE2 A:GLU73 2.0 32.0 1.0 OE2 A:GLU128 2.2 30.1 1.0 OE1 A:GLU157 2.2 40.1 1.0 ND1 A:HIS160 2.2 34.4 1.0 OE1 A:GLU128 2.3 32.7 1.0 OXT A:6NA301 2.5 37.5 1.0 CD A:GLU128 2.5 29.7 1.0 CD A:GLU73 2.9 31.9 1.0 CE1 A:HIS160 2.9 35.7 1.0 OE1 A:GLU73 3.0 34.3 1.0 O A:6NA301 3.2 36.8 1.0 C A:6NA301 3.2 39.9 1.0 CD A:GLU157 3.3 46.3 1.0 FE A:FE302 3.3 32.7 1.0 CG A:HIS160 3.4 37.6 1.0 CB A:HIS160 3.9 36.7 1.0 OE2 A:GLU157 3.9 48.0 1.0 CG A:GLU128 4.1 26.4 1.0 NE2 A:HIS160 4.1 42.6 1.0 CG A:GLU73 4.3 26.6 1.0 CE2 A:TYR52 4.3 29.0 1.0 CD2 A:HIS160 4.4 41.0 1.0 CG A:GLU157 4.4 35.9 1.0 CB A:GLU157 4.4 50.2 1.0 OH A:TYR52 4.5 28.8 1.0 NE2 A:GLN123 4.5 27.8 1.0 CB A:ALA48 4.5 26.6 1.0 CA A:6NA301 4.7 31.7 1.0 CA A:GLU157 4.7 41.2 1.0 ND1 A:HIS76 4.9 29.4 1.0 CE1 A:HIS76 4.9 37.5 1.0 OE1 A:GLU45 4.9 31.8 1.0 CZ A:TYR52 4.9 30.8 1.0 CB A:GLU128 5.0 27.4 1.0

B.Khara, N.Menon, C.Levy, D.Mansell, D.Das, E.N.Marsh, D.Leys, N.S.Scrutton. Production of Propane and Other Short-Chain Alkanes By Structure-Based Engineering of Ligand Specificity in Aldehyde-Deformylating Oxygenase. Chembiochem V. 14 1204 2013.
ISSN: ISSN 1439-4227
PubMed: 23757044
DOI: 10.1002/CBIC.201300307