Iron in PDB 6rpd: Structure of Ferrous Kpdyp in Complex with Cyanide

The structure of Structure of Ferrous Kpdyp in Complex with Cyanide, PDB code: 6rpd was solved by V.Pfanzagl, J.Beale, S.Hofbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.62 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.570, 75.740, 75.710, 90.00, 107.85, 90.00
R / Rfree (%)	17.1 / 18.9

The structure of Structure of Ferrous Kpdyp in Complex with Cyanide also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Structure of Ferrous Kpdyp in Complex with Cyanide (pdb code 6rpd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Structure of Ferrous Kpdyp in Complex with Cyanide, PDB code: 6rpd:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Structure of Ferrous Kpdyp in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Ferrous Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:15.2 occ:1.00 FE A:HEM401 0.0 15.2 1.0 NA A:HEM401 2.0 15.3 1.0 NB A:HEM401 2.0 14.6 1.0 ND A:HEM401 2.0 15.2 1.0 NC A:HEM401 2.0 14.8 1.0 NE2 A:HIS215 2.1 15.4 1.0 C A:CYN407 2.2 19.9 1.0 C4B A:HEM401 3.0 14.8 1.0 C1B A:HEM401 3.0 15.0 1.0 C4D A:HEM401 3.0 15.5 1.0 C4A A:HEM401 3.0 15.2 1.0 C1D A:HEM401 3.0 15.4 1.0 C1A A:HEM401 3.0 15.5 1.0 C4C A:HEM401 3.0 14.9 1.0 C1C A:HEM401 3.0 14.5 1.0 CE1 A:HIS215 3.1 14.5 1.0 CD2 A:HIS215 3.1 16.0 1.0 N A:CYN407 3.3 22.4 1.0 HE1 A:HIS215 3.3 14.4 1.0 HD2 A:HIS215 3.4 15.9 1.0 CHB A:HEM401 3.4 15.5 1.0 CHA A:HEM401 3.4 15.9 1.0 CHC A:HEM401 3.4 15.1 1.0 CHD A:HEM401 3.4 15.6 1.0 HE1 A:PHE248 3.7 13.6 1.0 HG21 A:VAL219 3.8 15.2 1.0 HE1 A:MET276 3.9 17.7 1.0 HH11 A:ARG232 4.0 15.8 1.0 CG A:HIS215 4.2 15.2 1.0 ND1 A:HIS215 4.2 15.3 1.0 C3A A:HEM401 4.2 15.8 1.0 C3B A:HEM401 4.2 15.2 1.0 C2B A:HEM401 4.2 15.1 1.0 C2A A:HEM401 4.2 15.9 1.0 C2C A:HEM401 4.3 14.9 1.0 C3D A:HEM401 4.3 15.9 1.0 C3C A:HEM401 4.3 15.2 1.0 C2D A:HEM401 4.3 15.8 1.0 HD3 A:ARG232 4.3 16.1 1.0 HHA A:HEM401 4.3 15.9 1.0 NH1 A:ARG232 4.4 15.8 1.0 HHC A:HEM401 4.4 14.9 1.0 HHD A:HEM401 4.4 15.5 1.0 HHB A:HEM401 4.5 15.3 1.0 HD2 A:ARG232 4.6 16.0 1.0 CE1 A:PHE248 4.6 13.6 1.0 HH12 A:ARG232 4.7 15.9 1.0 HG11 A:VAL219 4.7 15.7 1.0 HD1 A:PHE248 4.8 14.0 1.0 CG2 A:VAL219 4.8 15.3 1.0 OD1 A:ASP143 4.9 38.2 0.5 CD A:ARG232 4.9 16.1 1.0 CE A:MET276 5.0 17.8 1.0

Iron binding site 2 out of 2 in the Structure of Ferrous Kpdyp in Complex with Cyanide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Ferrous Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:17.2 occ:1.00 FE B:HEM401 0.0 17.2 1.0 NB B:HEM401 2.0 16.8 1.0 NA B:HEM401 2.0 17.4 1.0 NC B:HEM401 2.0 17.0 1.0 ND B:HEM401 2.0 17.2 1.0 NE2 B:HIS215 2.1 17.8 1.0 C B:CYN406 2.5 22.2 1.0 C4B B:HEM401 3.0 16.9 1.0 C1B B:HEM401 3.0 17.1 1.0 C4A B:HEM401 3.0 17.3 1.0 C4D B:HEM401 3.0 17.5 1.0 C1D B:HEM401 3.0 17.5 1.0 C4C B:HEM401 3.0 17.1 1.0 C1C B:HEM401 3.0 16.8 1.0 C1A B:HEM401 3.0 17.5 1.0 CE1 B:HIS215 3.0 17.3 1.0 CD2 B:HIS215 3.1 18.3 1.0 HE1 B:HIS215 3.3 17.3 1.0 HD2 B:HIS215 3.3 18.3 1.0 CHB B:HEM401 3.4 17.6 1.0 CHC B:HEM401 3.4 17.4 1.0 CHA B:HEM401 3.4 17.9 1.0 CHD B:HEM401 3.4 17.8 1.0 N B:CYN406 3.6 27.9 1.0 HE1 B:PHE248 3.8 16.0 1.0 HG21 B:VAL219 3.8 20.1 1.0 HE1 B:MET276 3.9 19.3 1.0 HH11 B:ARG232 4.0 16.8 1.0 CG B:HIS215 4.2 17.7 1.0 ND1 B:HIS215 4.2 18.2 1.0 C3B B:HEM401 4.2 17.4 1.0 C2B B:HEM401 4.2 17.2 1.0 C3A B:HEM401 4.2 17.9 1.0 C2C B:HEM401 4.3 17.2 1.0 C2A B:HEM401 4.3 17.9 1.0 C3C B:HEM401 4.3 17.4 1.0 C3D B:HEM401 4.3 18.0 1.0 C2D B:HEM401 4.3 17.9 1.0 HD3 B:ARG232 4.3 18.0 1.0 HHA B:HEM401 4.3 17.9 1.0 HHC B:HEM401 4.4 17.1 1.0 NH1 B:ARG232 4.4 16.9 1.0 HHD B:HEM401 4.4 17.7 1.0 HHB B:HEM401 4.5 17.4 1.0 HD2 B:ARG232 4.6 17.9 1.0 CE1 B:PHE248 4.6 16.1 1.0 HG11 B:VAL219 4.7 19.0 1.0 HH12 B:ARG232 4.7 16.9 1.0 OD1 B:ASP143 4.7 42.5 1.0 HD1 B:PHE248 4.8 16.0 1.0 CG2 B:VAL219 4.8 20.2 1.0 CD B:ARG232 4.9 18.0 1.0 CE B:MET276 5.0 19.5 1.0

V.Pfanzagl, J.H.Beale, H.Michlits, D.Schmidt, T.Gabler, C.Obinger, K.Djinovic-Carugo, S.Hofbauer. X-Ray-Induced Photoreduction of Heme Metal Centers Rapidly Induces Active-Site Perturbations in A Protein-Independent Manner. J.Biol.Chem. V. 295 13488 2020.
ISSN: ESSN 1083-351X
PubMed: 32723869
DOI: 10.1074/JBC.RA120.014087