Iron in PDB 4quq: Crystal Structure of Stachydrine Demethylase in Complex with Azide

The structure of Crystal Structure of Stachydrine Demethylase in Complex with Azide, PDB code: 4quq 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)	33.09 / 2.27
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.440, 98.440, 178.752, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 25.5

The structure of Crystal Structure of Stachydrine Demethylase in Complex with Azide 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 Azide (pdb code 4quq). 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 Azide, PDB code: 4quq:
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 Azide


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:34.9 occ:1.00 FE1 A:FES501 0.0 34.9 1.0 ND1 A:HIS109 2.0 35.2 1.0 ND1 A:HIS88 2.1 38.4 1.0 S1 A:FES501 2.2 40.5 1.0 S2 A:FES501 2.2 36.8 1.0 FE2 A:FES501 2.7 33.3 1.0 CE1 A:HIS88 2.9 34.9 1.0 CE1 A:HIS109 3.0 36.3 1.0 CG A:HIS109 3.0 41.0 1.0 CG A:HIS88 3.1 31.3 1.0 CB A:HIS109 3.4 37.5 1.0 CB A:HIS88 3.5 33.2 1.0 N A:HIS109 3.9 40.0 1.0 CB A:TYR108 4.0 37.1 1.0 NE2 A:HIS88 4.1 35.6 1.0 NE2 A:HIS109 4.1 38.2 1.0 CD2 A:HIS109 4.2 40.6 1.0 CD2 A:HIS88 4.2 35.8 1.0 CA A:HIS109 4.2 41.3 1.0 N A:ARG89 4.3 30.6 1.0 SG A:CYS86 4.4 36.2 1.0 CG A:TYR108 4.4 36.6 1.0 SG A:CYS106 4.4 35.4 1.0 CD2 A:TYR108 4.5 42.3 1.0 CD1 A:TRP111 4.7 31.6 1.0 C A:TYR108 4.7 39.5 1.0 CA A:HIS88 4.8 35.4 1.0 CB A:ARG89 4.8 34.5 1.0 NE1 A:TRP111 4.8 28.8 1.0 C A:HIS109 4.9 40.3 1.0 CA A:TYR108 4.9 36.1 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Stachydrine Demethylase in Complex with Azide


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:33.3 occ:1.00 FE2 A:FES501 0.0 33.3 1.0 S2 A:FES501 2.2 36.8 1.0 SG A:CYS86 2.2 36.2 1.0 SG A:CYS106 2.2 35.4 1.0 S1 A:FES501 2.2 40.5 1.0 FE1 A:FES501 2.7 34.9 1.0 CB A:CYS86 3.0 35.4 1.0 CB A:CYS106 3.2 38.5 1.0 CB A:HIS88 4.0 33.2 1.0 ND1 A:HIS88 4.2 38.4 1.0 CB A:TYR108 4.3 37.1 1.0 OG A:SER91 4.3 45.0 0.5 CB A:SER91 4.4 26.3 0.5 CA A:CYS86 4.5 33.4 1.0 ND1 A:HIS109 4.5 35.2 1.0 CB A:SER91 4.6 36.0 0.5 N A:HIS109 4.6 40.0 1.0 CA A:CYS106 4.6 37.8 1.0 CG A:HIS88 4.6 31.3 1.0 CB A:TRP111 4.8 32.9 1.0 N A:ARG89 4.8 30.6 1.0 N A:HIS88 4.9 34.0 1.0 CG A:TRP111 4.9 33.6 1.0 N A:TYR108 4.9 34.4 1.0 N A:SER91 4.9 32.5 1.0 C A:CYS86 5.0 35.2 1.0 CA A:HIS88 5.0 35.4 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Stachydrine Demethylase in Complex with Azide


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 Azide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe502 b:55.4 occ:1.00 OD1 A:ASP360 2.0 41.6 1.0 N1 A:AZI505 2.1 50.4 1.0 NE2 A:HIS209 2.2 61.2 1.0 NE2 A:HIS204 2.2 40.0 1.0 N2 A:AZI505 2.8 55.1 1.0 CG A:ASP360 2.8 39.6 1.0 CE1 A:HIS204 2.9 41.8 1.0 OD2 A:ASP360 3.0 36.5 1.0 CE1 A:HIS209 3.1 56.1 1.0 CD2 A:HIS209 3.2 64.4 1.0 CD2 A:HIS204 3.4 43.7 1.0 ND2 A:ASN198 3.7 31.3 1.0 N3 A:AZI505 3.8 58.4 1.0 ND1 A:HIS204 4.1 41.6 1.0 CB A:ASP360 4.3 37.2 1.0 ND1 A:HIS209 4.3 57.2 1.0 SG A:CYS205 4.3 64.6 1.0 O A:ASN198 4.3 34.1 1.0 CG A:HIS209 4.3 68.2 1.0 CG A:ASN198 4.4 32.2 1.0 OD1 A:ASN198 4.4 33.3 1.0 CG A:HIS204 4.4 43.8 1.0 O A:HOH641 4.4 27.0 1.0 CA A:ASP360 4.8 35.9 1.0 CG2 A:THR356 5.0 35.8 1.0 O A:GLU201 5.0 47.7 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.