Iron in PDB 4qur: Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation

The structure of Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation, PDB code: 4qur was solved by R.Agarwal, B.Andi, A.Gizzi, J.B.Bonanno, S.C.Almo, A.M.Orville, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.57 / 1.76
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.065, 98.065, 178.654, 90.00, 90.00, 120.00
R / Rfree (%)	20.3 / 22.8

The structure of Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Iron atom in the Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation (pdb code 4qur). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation, PDB code: 4qur:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation


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 Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:20.6 occ:1.00 FE1 A:FES501 0.0 20.6 1.0 S1 A:FES501 2.2 20.0 1.0 S2 A:FES501 2.2 18.4 1.0 ND1 A:HIS88 2.2 19.2 1.0 ND1 A:HIS109 2.2 20.1 1.0 FE2 A:FES501 2.7 19.7 1.0 CG A:HIS88 3.2 19.5 1.0 CE1 A:HIS109 3.2 19.5 1.0 CG A:HIS109 3.2 19.9 1.0 CE1 A:HIS88 3.3 21.1 1.0 CB A:HIS88 3.4 18.7 1.0 CB A:HIS109 3.5 19.1 1.0 N A:HIS109 3.8 22.1 1.0 CB A:TYR108 4.0 18.9 1.0 CA A:HIS109 4.2 22.9 1.0 N A:ARG89 4.3 17.2 1.0 CG A:TYR108 4.3 20.9 1.0 NE2 A:HIS109 4.3 22.7 1.0 CD2 A:HIS88 4.3 18.8 1.0 NE2 A:HIS88 4.3 20.2 1.0 CD2 A:HIS109 4.4 21.1 1.0 SG A:CYS86 4.5 20.5 1.0 SG A:CYS106 4.5 19.9 1.0 CD2 A:TYR108 4.5 18.5 1.0 CB A:ARG89 4.6 17.6 1.0 C A:TYR108 4.7 20.2 1.0 CA A:HIS88 4.7 17.3 1.0 CD1 A:TRP111 4.8 22.1 1.0 NE1 A:TRP111 4.9 20.0 1.0 CA A:TYR108 4.9 19.3 1.0 CD A:ARG89 4.9 16.6 1.0 C A:HIS109 5.0 21.7 1.0 C A:HIS88 5.0 19.7 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation


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 Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:19.7 occ:1.00 FE2 A:FES501 0.0 19.7 1.0 S2 A:FES501 2.2 18.4 1.0 S1 A:FES501 2.2 20.0 1.0 SG A:CYS106 2.4 19.9 1.0 SG A:CYS86 2.4 20.5 1.0 FE1 A:FES501 2.7 20.6 1.0 CB A:CYS86 3.1 16.8 1.0 CB A:CYS106 3.1 18.9 1.0 CB A:HIS88 4.0 18.7 1.0 CB A:TYR108 4.2 18.9 1.0 N A:HIS109 4.4 22.1 1.0 ND1 A:HIS88 4.5 19.2 1.0 CB A:SER91 4.5 16.9 1.0 CA A:CYS86 4.6 18.6 1.0 CA A:CYS106 4.6 19.1 1.0 ND1 A:HIS109 4.6 20.1 1.0 CB A:TRP111 4.7 20.7 1.0 CG A:HIS88 4.7 19.5 1.0 N A:ARG89 4.7 17.2 1.0 CG A:TRP111 4.8 20.7 1.0 N A:HIS88 4.9 16.7 1.0 N A:TYR108 4.9 19.2 1.0 CA A:TYR108 5.0 19.3 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation


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 Stachydrine Demethylase in Complex with Cyanide, Oxygen, and N-Methyl Proline in A New Orientation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:23.8 occ:1.00 O1 A:OXY506 1.8 34.0 0.4 C A:CYN507 1.8 33.3 0.6 OD1 A:ASP360 1.9 26.9 1.0 O2 A:OXY506 2.1 34.6 0.4 NE2 A:HIS204 2.1 24.3 1.0 NE2 A:HIS209 2.1 25.1 1.0 CG A:ASP360 2.8 22.6 1.0 N A:CYN507 2.9 33.6 0.6 CE1 A:HIS204 2.9 23.4 1.0 OD2 A:ASP360 3.0 22.7 1.0 CD2 A:HIS209 3.0 26.9 1.0 CE1 A:HIS209 3.1 26.0 1.0 CD2 A:HIS204 3.2 21.0 1.0 OD1 A:ASN198 3.8 22.1 1.0 ND1 A:HIS204 4.1 23.9 1.0 ND1 A:HIS209 4.2 24.6 1.0 CG A:HIS209 4.2 27.3 1.0 CB A:ASP360 4.2 19.7 1.0 CG A:HIS204 4.2 23.2 1.0 SG A:CYS205 4.5 27.4 1.0 CG A:ASN198 4.6 19.1 1.0 O A:HOH783 4.6 18.7 1.0 CG2 A:THR356 4.6 21.3 1.0 ND2 A:ASN198 4.7 19.2 1.0 CA A:ASP360 4.7 20.3 1.0 O A:ASN198 4.7 21.4 1.0

R.Agarwal, B.Andi, A.Gizzi, J.B.Bonanno, S.C.Almo, A.M.Orville. Tracking Photoelectron Induced in-Crystallo Enzyme Catalysis To Be Published.