Iron in PDB 4rc6: Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant

All present enzymatic activity of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant:
4.1.99.5;

The structure of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant, PDB code: 4rc6 was solved by C.J.Jia, M.Li, J.J.Li, J.J.Zhang, H.M.Zhang, P.Cao, X.W.Pan, X.F.Lu, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.22 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.633, 61.838, 125.315, 90.00, 90.00, 90.00
R / Rfree (%)	27 / 29.7

The binding sites of Iron atom in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant (pdb code 4rc6). 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 Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant, PDB code: 4rc6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant


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 Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe301 b:30.1 occ:1.00 OE1 A:GLU144 1.9 38.4 1.0 OE2 A:GLU60 2.1 39.4 1.0 ND1 A:HIS147 2.1 31.0 1.0 OE1 A:GLU115 2.3 22.5 1.0 OE2 A:GLU115 2.4 23.8 1.0 CD A:GLU144 2.6 40.2 1.0 CD A:GLU115 2.7 22.4 1.0 CE1 A:HIS147 2.8 31.7 1.0 OE2 A:GLU144 2.8 40.3 1.0 CD A:GLU60 2.9 38.9 1.0 OE1 A:GLU60 2.9 38.3 1.0 FE A:FE2302 3.1 29.4 1.0 O A:HOH401 3.1 4.9 1.0 CG A:HIS147 3.3 30.9 1.0 CB A:HIS147 3.9 29.7 1.0 CG A:GLU144 4.0 39.7 1.0 NE2 A:HIS147 4.1 31.2 1.0 CG A:GLU115 4.2 20.1 1.0 OH A:TYR39 4.3 29.2 1.0 CG A:GLU60 4.3 40.3 1.0 CE2 A:TYR39 4.3 29.1 1.0 CD2 A:HIS147 4.3 31.3 1.0 CB A:GLU144 4.5 33.2 1.0 CA A:GLU144 4.6 33.4 1.0 OE1 A:GLU32 4.7 27.1 1.0 CE1 A:HIS63 4.7 26.5 1.0 CZ A:TYR39 4.8 28.9 1.0 CB A:ALA35 4.8 28.0 1.0 ND1 A:HIS63 4.9 26.6 1.0 NE2 A:GLN110 4.9 18.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant


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 Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe302 b:29.4 occ:1.00 OE1 A:GLU60 1.9 38.3 1.0 OE1 A:GLU32 2.1 27.1 1.0 OE2 A:GLU144 2.1 40.3 1.0 OE2 A:GLU32 2.3 26.2 1.0 ND1 A:HIS63 2.4 26.6 1.0 CD A:GLU32 2.5 27.1 1.0 CD A:GLU144 3.0 40.2 1.0 CD A:GLU60 3.0 38.9 1.0 CE1 A:HIS63 3.0 26.5 1.0 FE A:FE2301 3.1 30.1 1.0 OE1 A:GLU144 3.2 38.4 1.0 O A:HOH401 3.3 4.9 1.0 OE2 A:GLU60 3.4 39.4 1.0 CG A:HIS63 3.5 27.6 1.0 CB A:HIS63 4.0 29.5 1.0 CG A:GLU32 4.0 22.1 1.0 NE2 A:HIS63 4.2 26.8 1.0 CG A:GLU60 4.3 40.3 1.0 CE1 A:HIS147 4.3 31.7 1.0 CG A:GLU144 4.3 39.7 1.0 CA A:GLU60 4.3 41.9 1.0 CD2 A:HIS63 4.4 27.1 1.0 CB A:GLU60 4.5 41.0 1.0 ND1 A:HIS147 4.5 31.0 1.0 O A:GLU60 4.7 42.3 1.0 CG1 A:VAL140 4.8 19.5 1.0 CB A:GLU32 4.8 22.9 1.0 OE1 A:GLU115 4.9 22.5 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:48.7 occ:1.00 OE2 B:GLU60 2.2 53.0 1.0 OE1 B:GLU115 2.3 50.0 1.0 OE2 B:GLU115 2.4 52.8 1.0 OE1 B:GLU144 2.4 63.7 1.0 ND1 B:HIS147 2.5 57.9 1.0 CD B:GLU115 2.7 52.2 1.0 CD B:GLU60 2.7 54.8 1.0 FE B:FE2302 2.7 57.1 1.0 OE1 B:GLU60 2.9 55.4 1.0 CE1 B:HIS147 3.1 59.2 1.0 O B:HOH401 3.1 19.0 1.0 CD B:GLU144 3.5 65.3 1.0 CG B:HIS147 3.6 57.1 1.0 OE2 B:GLU144 3.8 66.5 1.0 CG B:GLU60 3.9 57.2 1.0 CB B:HIS147 4.2 54.2 1.0 CE2 B:TYR39 4.2 44.2 1.0 CG B:GLU115 4.2 48.6 1.0 NE2 B:HIS147 4.3 59.3 1.0 OE1 B:GLU32 4.3 50.0 1.0 CB B:ALA35 4.4 70.3 1.0 CD2 B:HIS147 4.5 58.3 1.0 OH B:TYR39 4.6 42.0 1.0 CG B:GLU144 4.8 61.9 1.0 NE2 B:GLN110 4.9 45.4 1.0 CZ B:TYR39 4.9 43.8 1.0 CA B:GLU144 4.9 58.6 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase 122F Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:57.1 occ:1.00 OE1 B:GLU32 2.0 50.0 1.0 OE2 B:GLU144 2.4 66.5 1.0 OE1 B:GLU60 2.4 55.4 1.0 FE B:FE2301 2.7 48.7 1.0 CD B:GLU32 2.8 50.8 1.0 OE2 B:GLU32 2.9 50.2 1.0 OE1 B:GLU144 3.0 63.7 1.0 CD B:GLU60 3.0 54.8 1.0 CD B:GLU144 3.1 65.3 1.0 ND1 B:HIS63 3.3 72.3 1.0 O B:HOH401 3.5 19.0 1.0 OE2 B:GLU60 3.6 53.0 1.0 CG B:GLU60 3.7 57.2 1.0 CE1 B:HIS63 4.0 73.0 1.0 CG B:HIS63 4.0 73.7 1.0 CE1 B:HIS147 4.2 59.2 1.0 CB B:GLU60 4.2 59.2 1.0 CB B:HIS63 4.3 75.4 1.0 CG B:GLU32 4.3 50.5 1.0 ND1 B:HIS147 4.3 57.9 1.0 OE1 B:GLU115 4.4 50.0 1.0 CA B:GLU60 4.5 61.8 1.0 CG B:GLU144 4.6 61.9 1.0 CB B:GLU32 4.8 53.0 1.0 NE2 B:HIS63 4.8 73.3 1.0 CG1 B:VAL140 4.9 58.6 1.0 CD2 B:HIS63 4.9 72.2 1.0 CA B:GLU32 5.0 53.1 1.0

C.Jia, M.Li, J.Li, J.Zhang, H.Zhang, P.Cao, X.Pan, X.Lu, W.Chang. Structural Insights Into the Catalytic Mechanism of Aldehyde-Deformylating Oxygenases Protein Cell 2014.
ISSN: ESSN 1674-8018
PubMed: 25482408
DOI: 10.1007/S13238-014-0108-2