Iron in PDB 6qkj: Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine

The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj was solved by A.R.Stampfli, B.N.Badri, T.Schirmer, F.P.Seebeck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.68 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	108.143, 201.288, 108.332, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.8

The structure of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Iron atom in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine (pdb code 6qkj). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine, PDB code: 6qkj:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:21.8 occ:1.00 NE2 A:HIS153 2.1 23.1 1.0 NE2 A:HIS157 2.1 22.8 1.0 NE2 A:HIS62 2.1 20.5 1.0 NAT A:AVJ502 2.1 24.4 1.0 CL A:CL503 2.5 57.4 1.0 CL A:CL504 2.5 44.4 1.0 CE1 A:HIS153 3.0 23.2 1.0 CE1 A:HIS157 3.0 23.4 1.0 CD2 A:HIS157 3.1 22.0 1.0 CE1 A:HIS62 3.1 21.7 1.0 CD2 A:HIS62 3.1 20.7 1.0 CD2 A:HIS153 3.1 23.5 1.0 CAM A:AVJ502 3.1 24.2 1.0 CAZ A:AVJ502 3.2 24.9 1.0 ND1 A:HIS157 4.2 24.1 1.0 ND1 A:HIS62 4.2 20.6 1.0 CG A:HIS157 4.2 23.0 1.0 ND1 A:HIS153 4.2 21.5 1.0 CG A:HIS62 4.2 21.6 1.0 CG A:HIS153 4.2 22.8 1.0 CAY A:AVJ502 4.3 24.4 1.0 NAR A:AVJ502 4.3 25.4 1.0 OG A:SER92 4.5 27.9 0.5 CB A:SER92 4.6 30.8 0.5 CB A:SER92 4.6 33.8 0.5 OG A:SER92 4.8 34.5 0.5

Iron binding site 2 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:23.1 occ:1.00 OE2 A:GLU9 1.9 30.0 1.0 NE2 A:HIS25 2.1 28.8 1.0 OE2 A:GLU148 2.1 21.1 1.0 N3 A:IMD506 2.2 26.6 1.0 OE1 A:GLU148 2.6 23.7 1.0 C4 A:IMD506 2.6 26.9 1.0 CD A:GLU148 2.6 23.4 1.0 CD A:GLU9 2.7 33.9 1.0 OE1 A:GLU9 2.8 32.6 1.0 CD2 A:HIS25 3.0 27.6 1.0 CE1 A:HIS25 3.1 29.9 1.0 C2 A:IMD506 3.4 26.6 1.0 C5 A:IMD506 3.9 26.7 1.0 CG A:GLU9 4.1 36.0 1.0 ND1 A:HIS25 4.1 27.3 1.0 CG A:HIS25 4.1 28.5 1.0 CZ3 A:TRP22 4.2 27.3 1.0 CG A:GLU148 4.2 24.0 1.0 CH2 A:TRP22 4.2 28.5 1.0 N1 A:IMD506 4.2 26.8 1.0 O A:HOH690 4.2 30.8 1.0 CE1 A:HIS152 4.5 24.1 1.0 CD1 A:LEU151 4.7 26.8 1.0 O A:HOH611 4.7 41.4 1.0 CB A:GLU148 4.9 23.9 1.0 ND1 A:HIS152 5.0 28.3 1.0

Iron binding site 3 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:24.8 occ:1.00 NE2 B:HIS157 2.1 24.0 1.0 NE2 B:HIS153 2.1 30.6 1.0 NE2 B:HIS62 2.1 26.1 1.0 NAT B:AVJ502 2.1 29.0 1.0 CL B:CL504 2.5 56.5 1.0 CL B:CL503 2.7 63.0 1.0 CE1 B:HIS157 3.0 24.9 1.0 CD2 B:HIS157 3.1 24.8 1.0 CE1 B:HIS62 3.1 25.6 1.0 CE1 B:HIS153 3.1 31.8 1.0 CD2 B:HIS62 3.1 25.4 1.0 CD2 B:HIS153 3.1 30.6 1.0 CAZ B:AVJ502 3.1 28.8 1.0 CAM B:AVJ502 3.1 28.2 1.0 ND1 B:HIS157 4.1 26.0 1.0 ND1 B:HIS62 4.2 25.9 1.0 CG B:HIS157 4.2 25.6 1.0 ND1 B:HIS153 4.2 31.6 1.0 CG B:HIS62 4.2 26.0 1.0 CG B:HIS153 4.2 29.6 1.0 NAR B:AVJ502 4.2 29.9 1.0 CAY B:AVJ502 4.3 28.6 1.0 OG B:SER92 4.4 42.7 0.5 CB B:SER92 4.6 44.3 0.5 CB B:SER92 4.6 44.4 0.5 OG B:SER92 4.7 42.4 0.5

Iron binding site 4 out of 4 in the Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Egtb From Chloracidobacterium Thermophilum, A Type II Sulfoxide Synthase in Complex with N,N,N-Trimethyl-Histidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe505 b:47.6 occ:1.00 OE2 B:GLU148 2.1 59.5 1.0 NE2 B:HIS25 2.2 44.1 1.0 N3 B:IMD506 2.6 55.1 1.0 C4 B:IMD506 2.7 54.0 1.0 CD B:GLU148 2.8 50.5 1.0 OE1 B:GLU148 2.9 50.0 1.0 CD2 B:HIS25 2.9 42.5 1.0 CE1 B:HIS25 3.4 41.1 1.0 C2 B:IMD506 3.8 55.0 1.0 CZ3 B:TRP22 3.9 48.9 1.0 C5 B:IMD506 3.9 50.3 1.0 CH2 B:TRP22 4.0 46.3 1.0 CG B:HIS25 4.1 40.4 1.0 ND1 B:HIS25 4.3 40.0 1.0 CG B:GLU148 4.3 43.9 1.0 CE1 B:HIS152 4.4 29.3 1.0 N1 B:IMD506 4.4 52.7 1.0 CD1 B:LEU151 4.7 35.8 1.0 CE3 B:TRP22 4.9 47.3 1.0 CB B:GLU148 5.0 37.9 1.0 ND1 B:HIS152 5.0 29.5 1.0

A.R.Stampfli, K.V.Goncharenko, M.Meury, B.N.Dubey, T.Schirmer, F.P.Seebeck. An Alternative Active Site Architecture For O2ACTIVATION in the Ergothioneine Biosynthetic Egtb From Chloracidobacterium Thermophilum. J.Am.Chem.Soc. V. 141 5275 2019.
ISSN: ESSN 1520-5126
PubMed: 30883103
DOI: 10.1021/JACS.8B13023