Iron in PDB 4rc7: Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y Mutant

All present enzymatic activity of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y Mutant:
4.1.99.5;

The structure of Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y Mutant, PDB code: 4rc7 was solved by C.J.Jia, M.Li, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.41 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.014, 62.109, 125.003, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 23.8

The binding sites of Iron atom in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y Mutant (pdb code 4rc7). 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 F86YF87Y Mutant, PDB code: 4rc7:
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 F86YF87Y 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 F86YF87Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1002 b:35.1 occ:1.00 OE1 A:GLU32 2.1 24.6 1.0 OE1 A:GLU60 2.1 20.4 1.0 ND1 A:HIS63 2.4 16.4 1.0 OE2 A:GLU144 2.9 37.4 1.0 CD A:GLU32 2.9 22.7 1.0 OE2 A:GLU32 3.1 24.7 1.0 C1 A:PL31001 3.1 34.2 1.0 CE1 A:HIS63 3.2 16.5 1.0 O1 A:PL31001 3.2 31.7 1.0 CD A:GLU60 3.2 20.0 1.0 FE A:FE21003 3.3 31.6 1.0 CG A:HIS63 3.5 17.3 1.0 OE2 A:GLU60 3.6 20.8 1.0 CD A:GLU144 3.7 34.4 1.0 CB A:HIS63 3.9 17.9 1.0 OE1 A:GLU144 4.1 41.4 1.0 CG A:GLU32 4.4 20.9 1.0 NE2 A:HIS63 4.4 17.2 1.0 CE1 A:HIS147 4.5 19.8 1.0 C2 A:PL31001 4.5 37.5 1.0 CG A:GLU60 4.5 20.0 1.0 CA A:GLU60 4.5 20.6 1.0 CD2 A:HIS63 4.5 17.3 1.0 CG A:GLU144 4.6 27.5 1.0 CG1 A:VAL140 4.6 21.4 1.0 ND1 A:HIS147 4.7 18.8 1.0 CB A:GLU60 4.7 19.7 1.0 CB A:GLU32 4.8 18.8 1.0 C3 A:PL31001 5.0 37.2 1.0 CA A:GLU32 5.0 18.1 1.0 OE1 A:GLU115 5.0 20.6 1.0

Iron binding site 2 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y 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 F86YF87Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1003 b:31.6 occ:1.00 OE2 A:GLU60 2.1 20.8 1.0 OE2 A:GLU115 2.2 21.9 1.0 ND1 A:HIS147 2.3 18.8 1.0 O1 A:PL31001 2.4 31.7 1.0 OE1 A:GLU115 2.6 20.6 1.0 CD A:GLU115 2.7 20.2 1.0 CD A:GLU60 3.0 20.0 1.0 CE1 A:HIS147 3.1 19.8 1.0 OE1 A:GLU60 3.1 20.4 1.0 FE A:FE21002 3.3 35.1 1.0 CG A:HIS147 3.4 18.6 1.0 C1 A:PL31001 3.5 34.2 1.0 OE1 A:GLU144 3.8 41.4 1.0 CB A:HIS147 3.8 17.4 1.0 CD A:GLU144 4.1 34.4 1.0 CE2 A:TYR39 4.2 18.1 1.0 CG A:GLU115 4.2 18.8 1.0 NE2 A:GLN110 4.3 15.7 1.0 NE2 A:HIS147 4.3 18.7 1.0 OE2 A:GLU144 4.3 37.4 1.0 CG A:GLU60 4.4 20.0 1.0 OH A:TYR39 4.4 18.6 1.0 CD2 A:HIS147 4.5 19.1 1.0 CB A:ALA35 4.7 15.2 1.0 CA A:GLU144 4.7 21.2 1.0 C2 A:PL31001 4.8 37.5 1.0 CG A:GLU144 4.8 27.5 1.0 CZ A:TYR39 4.8 19.2 1.0 ND1 A:HIS63 4.9 16.4 1.0 CE1 A:HIS63 4.9 16.5 1.0 OE1 A:GLU32 5.0 24.6 1.0 CB A:GLU144 5.0 22.9 1.0

Iron binding site 3 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y 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 F86YF87Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1002 b:47.3 occ:0.50 OE1 B:GLU60 2.2 46.2 1.0 OE1 B:GLU32 2.2 35.9 1.0 OE2 B:GLU32 2.3 38.8 1.0 O B:HOH1150 2.5 39.0 1.0 CD B:GLU32 2.6 34.9 1.0 CD B:GLU60 2.8 41.2 1.0 OE2 B:GLU60 2.9 48.9 1.0 FE B:FE21003 3.2 61.5 0.5 ND1 B:HIS63 3.3 29.9 1.0 O1 B:PL31001 3.3 44.1 1.0 C1 B:PL31001 3.3 44.7 1.0 OE2 B:GLU144 3.8 42.5 1.0 CG B:GLU32 4.1 29.2 1.0 CG B:GLU60 4.1 33.3 1.0 CG B:HIS63 4.2 29.9 1.0 CA B:GLU60 4.2 29.3 1.0 CB B:HIS63 4.2 28.6 1.0 CE1 B:HIS63 4.2 31.0 1.0 CB B:GLU60 4.3 29.9 1.0 CD B:GLU144 4.7 40.8 1.0 CG1 B:VAL140 4.8 21.3 1.0 OH B:TYR122 4.8 26.1 1.0 C2 B:PL31001 4.8 41.2 1.0 CB B:GLU32 4.9 26.9 1.0 O B:GLU60 4.9 28.1 1.0 OE1 B:GLU115 5.0 41.8 1.0

Iron binding site 4 out of 4 in the Crystal Structure of Cyanobacterial Aldehyde-Deformylating Oxygenase F86YF87Y 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 F86YF87Y Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe1003 b:61.5 occ:0.50 OE2 B:GLU60 1.9 48.9 1.0 OE1 B:GLU115 2.1 41.8 1.0 O1 B:PL31001 2.2 44.1 1.0 O B:HOH1150 2.2 39.0 1.0 CD B:GLU60 2.7 41.2 1.0 CD B:GLU115 2.8 37.7 1.0 OE2 B:GLU115 2.8 38.7 1.0 OE1 B:GLU60 3.0 46.2 1.0 FE B:FE21002 3.2 47.3 0.5 C1 B:PL31001 3.3 44.7 1.0 CG B:GLU60 4.0 33.3 1.0 NE2 B:GLN110 4.1 25.3 1.0 CB B:ALA35 4.3 25.4 1.0 CG B:GLU115 4.3 32.7 1.0 OE1 B:GLU144 4.3 43.0 1.0 OE2 B:GLU144 4.4 42.5 1.0 OE1 B:GLU32 4.4 35.9 1.0 CE2 B:TYR39 4.4 30.3 1.0 C2 B:PL31001 4.5 41.2 1.0 CD B:GLU144 4.7 40.8 1.0 OH B:TYR39 4.7 31.2 1.0 CB B:GLU115 4.9 26.0 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