Iron in PDB 4qup: Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets

The structure of Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets, PDB code: 4qup 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)	34.48 / 1.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.746, 97.746, 177.984, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 21.7

The structure of Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets also contains other interesting chemical elements:

Cobalt

(Co)

1 atom

The binding sites of Iron atom in the Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets (pdb code 4qup). 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 with N-Methyl Proline From Low X-Ray Dose Composite Datasets, PDB code: 4qup:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets


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 with N-Methyl Proline From Low X-Ray Dose Composite Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:23.6 occ:1.00 FE1 A:FES501 0.0 23.6 1.0 ND1 A:HIS109 2.2 23.8 1.0 S1 A:FES501 2.2 22.2 1.0 ND1 A:HIS88 2.2 22.4 1.0 S2 A:FES501 2.2 21.8 1.0 FE2 A:FES501 2.7 21.7 1.0 CE1 A:HIS109 3.1 21.4 1.0 CE1 A:HIS88 3.2 24.4 1.0 CG A:HIS88 3.2 22.6 1.0 CG A:HIS109 3.2 23.9 1.0 CB A:HIS88 3.4 21.3 1.0 CB A:HIS109 3.5 21.3 1.0 N A:HIS109 3.8 23.6 1.0 CB A:TYR108 4.0 22.3 1.0 CA A:HIS109 4.2 26.3 1.0 NE2 A:HIS109 4.2 26.2 1.0 NE2 A:HIS88 4.3 23.0 1.0 CD2 A:HIS88 4.3 21.7 1.0 CD2 A:HIS109 4.3 24.0 1.0 N A:ARG89 4.4 20.4 1.0 CG A:TYR108 4.4 23.9 1.0 SG A:CYS86 4.4 22.0 1.0 SG A:CYS106 4.5 21.5 1.0 CD2 A:TYR108 4.5 23.3 1.0 C A:TYR108 4.7 23.1 1.0 CB A:ARG89 4.7 21.0 1.0 CA A:HIS88 4.8 21.4 1.0 CD1 A:TRP111 4.8 23.1 1.0 CD A:ARG89 4.9 22.0 1.0 NE1 A:TRP111 4.9 21.6 1.0 C A:HIS109 4.9 24.0 1.0 CA A:TYR108 4.9 23.5 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets


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 with N-Methyl Proline From Low X-Ray Dose Composite Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.7 occ:1.00 FE2 A:FES501 0.0 21.7 1.0 S2 A:FES501 2.2 21.8 1.0 S1 A:FES501 2.2 22.2 1.0 SG A:CYS106 2.3 21.5 1.0 SG A:CYS86 2.4 22.0 1.0 FE1 A:FES501 2.7 23.6 1.0 CB A:CYS106 3.1 22.4 1.0 CB A:CYS86 3.1 19.6 1.0 CB A:HIS88 4.0 21.3 1.0 CB A:TYR108 4.2 22.3 1.0 ND1 A:HIS88 4.4 22.4 1.0 N A:HIS109 4.4 23.6 1.0 CB A:SER91 4.5 20.6 1.0 ND1 A:HIS109 4.5 23.8 1.0 CA A:CYS106 4.6 22.6 1.0 CA A:CYS86 4.6 22.1 1.0 CB A:TRP111 4.7 22.7 1.0 CG A:HIS88 4.7 22.6 1.0 N A:ARG89 4.8 20.4 1.0 CG A:TRP111 4.9 23.0 1.0 N A:TYR108 4.9 22.9 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Stachydrine Demethylase with N-Methyl Proline From Low X-Ray Dose Composite Datasets


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 with N-Methyl Proline From Low X-Ray Dose Composite Datasets within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:33.0 occ:1.00 OD1 A:ASP360 1.8 30.7 1.0 O A:HOH786 2.1 29.9 1.0 NE2 A:HIS204 2.1 30.3 1.0 NE2 A:HIS209 2.1 29.9 1.0 O A:3BY503 2.4 48.5 1.0 C A:3BY503 2.5 43.2 1.0 CG A:ASP360 2.6 24.7 1.0 OXT A:3BY503 2.6 42.3 1.0 OD2 A:ASP360 2.6 25.3 1.0 CE1 A:HIS204 2.9 30.6 1.0 CE1 A:HIS209 3.0 31.2 1.0 CD2 A:HIS209 3.1 32.7 1.0 CD2 A:HIS204 3.3 31.7 1.0 OD1 A:ASN198 3.7 26.6 1.0 CA A:3BY503 3.9 47.0 1.0 CB A:ASP360 4.0 24.5 1.0 ND1 A:HIS204 4.1 33.1 1.0 ND1 A:HIS209 4.2 28.2 1.0 CG A:HIS209 4.2 31.9 1.0 CG A:HIS204 4.3 30.0 1.0 CG A:ASN198 4.4 25.5 1.0 ND2 A:ASN198 4.4 24.4 1.0 O A:HOH785 4.5 21.2 1.0 O A:ASN198 4.5 26.7 1.0 CA A:ASP360 4.6 23.8 1.0 SG A:CYS205 4.6 36.2 1.0 N A:3BY503 4.6 49.4 1.0 CG2 A:THR356 4.8 23.4 1.0 CN A:3BY503 4.9 35.5 1.0 CB A:3BY503 4.9 54.3 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.