Iron in PDB 5k53: Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011

The structure of Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011, PDB code: 5k53 was solved by A.K.Park, H-.W.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.012, 78.265, 108.861, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23.4

The binding sites of Iron atom in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011 (pdb code 5k53). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011, PDB code: 5k53:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe500 b:29.2 occ:1.00 OE1 A:GLU60 2.1 34.2 1.0 ND1 A:HIS63 2.1 25.8 1.0 OE1 A:GLU32 2.1 32.3 1.0 OE2 A:GLU144 2.2 33.1 0.5 OE1 A:GLU144 2.3 30.9 0.5 CD A:GLU144 2.6 31.5 0.5 C1 A:STE502 2.8 33.6 1.0 CD A:GLU32 2.9 29.9 1.0 CE1 A:HIS63 3.0 29.4 1.0 OE2 A:GLU32 3.0 41.4 1.0 C2 A:STE502 3.1 42.6 1.0 CD A:GLU60 3.1 27.5 1.0 CG A:HIS63 3.3 25.7 1.0 FE A:FE501 3.3 29.9 1.0 OE2 A:GLU60 3.5 27.1 1.0 CB A:HIS63 3.7 27.5 1.0 O1 A:STE502 3.9 35.9 1.0 CG A:GLU144 4.1 33.4 0.5 OE2 A:GLU144 4.1 55.5 0.5 NE2 A:HIS63 4.2 26.6 1.0 CG A:GLU32 4.3 28.5 1.0 CD2 A:HIS63 4.3 24.8 1.0 CG A:GLU60 4.3 25.3 1.0 CA A:GLU60 4.4 26.2 1.0 CG1 A:VAL140 4.5 30.0 1.0 CE1 A:HIS147 4.5 27.8 1.0 C3 A:STE502 4.6 37.6 1.0 ND1 A:HIS147 4.6 28.9 1.0 CB A:GLU60 4.6 27.5 1.0 CG A:GLU144 4.7 39.4 0.5 CB A:GLU32 4.8 28.2 1.0 CD A:GLU144 4.9 45.0 0.5 OE1 A:GLU115 4.9 28.4 1.0 CA A:GLU32 5.0 27.6 1.0

Iron binding site 2 out of 4 in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:29.9 occ:1.00 OE2 A:GLU60 2.0 27.1 1.0 OE2 A:GLU115 2.2 29.7 1.0 OE1 A:GLU144 2.2 30.9 0.5 ND1 A:HIS147 2.3 28.9 1.0 OE1 A:GLU115 2.3 28.4 1.0 C1 A:STE502 2.5 33.6 1.0 O1 A:STE502 2.6 35.9 1.0 CD A:GLU115 2.6 30.3 1.0 CD A:GLU60 3.0 27.5 1.0 CE1 A:HIS147 3.2 27.8 1.0 OE1 A:GLU60 3.3 34.2 1.0 CD A:GLU144 3.3 31.5 0.5 FE A:FE500 3.3 29.2 1.0 CG A:HIS147 3.4 26.0 1.0 CB A:HIS147 3.8 26.7 1.0 C2 A:STE502 3.9 42.6 1.0 OE2 A:GLU144 4.0 33.1 0.5 CG A:GLU115 4.1 25.8 1.0 CE2 A:TYR39 4.2 26.8 1.0 CG A:GLU60 4.3 25.3 1.0 NE2 A:GLN110 4.3 32.2 1.0 NE2 A:HIS147 4.3 26.8 1.0 CG A:GLU144 4.4 33.4 0.5 CD2 A:HIS147 4.5 27.3 1.0 OE2 A:GLU144 4.5 55.5 0.5 OH A:TYR39 4.5 29.7 1.0 CB A:GLU144 4.6 29.5 0.5 CB A:ALA35 4.6 31.7 1.0 C3 A:STE502 4.8 37.6 1.0 CG A:GLU144 4.8 39.4 0.5 ND1 A:HIS63 4.8 25.8 1.0 CE1 A:HIS63 4.8 29.4 1.0 CA A:GLU144 4.8 28.9 0.5 CZ A:TYR39 4.9 27.5 1.0 CA A:GLU144 4.9 29.4 0.5 CB A:GLU115 5.0 28.5 1.0

Iron binding site 3 out of 4 in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe500 b:29.9 occ:1.00 OE2 B:GLU60 1.9 31.2 1.0 OE2 B:GLU144 2.1 29.4 0.5 OE2 B:GLU115 2.3 34.7 1.0 ND1 B:HIS147 2.3 30.3 1.0 O1 B:STE502 2.3 35.2 1.0 OE1 B:GLU115 2.3 33.4 1.0 CD B:GLU115 2.6 34.8 1.0 C1 B:STE502 2.7 33.3 1.0 CD B:GLU60 2.9 31.3 1.0 CE1 B:HIS147 3.1 29.7 1.0 CD B:GLU144 3.3 32.9 0.5 OE1 B:GLU60 3.3 33.1 1.0 FE B:FE501 3.3 28.1 1.0 CG B:HIS147 3.4 27.4 1.0 CB B:HIS147 3.8 28.5 1.0 OE1 B:GLU144 3.9 30.8 0.5 CG B:GLU115 4.1 30.1 1.0 C2 B:STE502 4.1 50.5 1.0 CE2 B:TYR39 4.2 30.1 1.0 CG B:GLU60 4.2 29.2 1.0 NE2 B:HIS147 4.3 26.7 1.0 NE2 B:GLN110 4.3 32.7 1.0 CG B:GLU144 4.3 35.8 0.5 CG B:GLU144 4.4 33.7 0.5 CD2 B:HIS147 4.4 26.0 1.0 OH B:TYR39 4.5 29.3 1.0 CB B:GLU144 4.6 30.0 0.5 CB B:ALA35 4.6 29.4 1.0 CA B:GLU144 4.7 29.9 0.5 CE1 B:HIS63 4.8 27.3 1.0 ND1 B:HIS63 4.8 23.6 1.0 CZ B:TYR39 4.8 28.2 1.0 OE1 B:GLU32 4.8 29.6 1.0 OE2 B:GLU144 4.8 45.6 0.5 CA B:GLU144 4.9 29.5 0.5 C3 B:STE502 4.9 44.1 1.0 CB B:GLU115 5.0 29.8 1.0

Iron binding site 4 out of 4 in the Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structures of Aldehyde Deformylating Oxygenase From Oscillatoria Sp. KNUA011 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:28.1 occ:1.00 OE1 B:GLU32 1.9 29.6 1.0 OE1 B:GLU60 2.0 33.1 1.0 OE1 B:GLU144 2.2 30.8 0.5 ND1 B:HIS63 2.2 23.6 1.0 OE2 B:GLU144 2.3 29.4 0.5 CD B:GLU144 2.6 32.9 0.5 C1 B:STE502 2.7 33.3 1.0 CD B:GLU32 2.7 32.1 1.0 OE2 B:GLU32 2.9 41.5 1.0 CE1 B:HIS63 3.0 27.3 1.0 CD B:GLU60 3.0 31.3 1.0 CG B:HIS63 3.3 26.1 1.0 FE B:FE500 3.3 29.9 1.0 C2 B:STE502 3.3 50.5 1.0 OE2 B:GLU60 3.4 31.2 1.0 O1 B:STE502 3.6 35.2 1.0 CB B:HIS63 3.7 27.4 1.0 CG B:GLU144 4.1 33.7 0.5 OE2 B:GLU144 4.1 45.6 0.5 CG B:GLU32 4.2 30.9 1.0 NE2 B:HIS63 4.2 28.5 1.0 CG B:GLU60 4.3 29.2 1.0 CD2 B:HIS63 4.4 27.5 1.0 CA B:GLU60 4.4 28.6 1.0 CG B:GLU144 4.4 35.8 0.5 CE1 B:HIS147 4.4 29.7 1.0 CG1 B:VAL140 4.5 26.4 1.0 CB B:GLU60 4.5 28.2 1.0 ND1 B:HIS147 4.6 30.3 1.0 C3 B:STE502 4.6 44.1 1.0 CB B:GLU32 4.8 28.7 1.0 CD B:GLU144 4.8 41.0 0.5 CA B:GLU32 4.9 24.4 1.0 OE1 B:GLU115 4.9 33.4 1.0

A.K.Park, I.S.Kim, B.W.Jeon, S.J.Roh, M.Y.Ryu, H.R.Baek, S.W.Jo, Y.S.Kim, H.Park, J.H.Lee, H.S.Yoon, H.W.Kim. Crystal Structures of Aldehyde Deformylating Oxygenase From Limnothrix Sp. KNUA012 and Oscillatoria Sp. KNUA011. Biochem.Biophys.Res.Commun. V. 477 395 2016.
ISSN: ESSN 1090-2104
PubMed: 27329814
DOI: 10.1016/J.BBRC.2016.06.090