Iron in PDB 6rpe: Structure of 5% Reduced Kpdyp in Complex with Cyanide

The structure of Structure of 5% Reduced Kpdyp in Complex with Cyanide, PDB code: 6rpe 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)	36.31 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.853, 76.592, 76.308, 90.00, 107.87, 90.00
R / Rfree (%)	17.2 / 19.7

The structure of Structure of 5% Reduced 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 5% Reduced Kpdyp in Complex with Cyanide (pdb code 6rpe). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of 5% Reduced Kpdyp in Complex with Cyanide, PDB code: 6rpe:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of 5% Reduced 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 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:3.0 occ:0.05 FE A:HEM401 0.0 3.0 0.1 FE A:HEM401 0.0 3.1 0.9 ND A:HEM401 1.9 3.0 0.9 NB A:HEM401 2.0 3.0 0.1 ND A:HEM401 2.0 3.0 0.1 NA A:HEM401 2.0 3.0 0.1 NC A:HEM401 2.0 3.0 0.1 NA A:HEM401 2.0 3.0 0.9 NB A:HEM401 2.1 3.0 0.9 NE2 A:HIS215 2.1 3.7 1.0 NC A:HEM401 2.1 3.0 0.9 C A:CYN404 2.2 3.0 1.0 C1D A:HEM401 2.9 3.0 0.9 C4D A:HEM401 2.9 3.0 0.9 C4D A:HEM401 3.0 3.0 0.1 C4B A:HEM401 3.0 3.0 0.1 C4B A:HEM401 3.0 3.0 0.9 C1A A:HEM401 3.0 3.0 0.9 C1D A:HEM401 3.0 3.0 0.1 C1B A:HEM401 3.0 3.0 0.1 C1A A:HEM401 3.0 3.0 0.1 C4C A:HEM401 3.0 3.0 0.9 C1B A:HEM401 3.0 3.0 0.9 C4A A:HEM401 3.0 3.0 0.1 C4A A:HEM401 3.0 3.0 0.9 C4C A:HEM401 3.0 3.0 0.1 C1C A:HEM401 3.0 3.0 0.1 CE1 A:HIS215 3.1 3.0 1.0 C1C A:HEM401 3.1 3.0 0.9 CD2 A:HIS215 3.1 3.1 1.0 N A:CYN404 3.2 5.8 1.0 HE1 A:HIS215 3.3 3.0 1.0 CHD A:HEM401 3.3 3.4 0.9 CHA A:HEM401 3.4 3.3 0.9 CHA A:HEM401 3.4 3.3 0.1 HD2 A:HIS215 3.4 3.0 1.0 CHB A:HEM401 3.4 3.4 0.9 CHC A:HEM401 3.4 3.4 0.9 CHC A:HEM401 3.4 3.5 0.1 CHD A:HEM401 3.4 3.4 0.1 CHB A:HEM401 3.4 3.4 0.1 HG21 A:VAL219 3.8 3.0 1.0 HE1 A:PHE248 3.9 3.0 1.0 HE1 A:MET276 3.9 3.0 1.0 HH11 A:ARG232 4.0 3.0 1.0 ND1 A:HIS215 4.2 3.1 1.0 C2D A:HEM401 4.2 3.0 0.9 CG A:HIS215 4.2 3.3 1.0 C3D A:HEM401 4.2 3.0 0.9 C3A A:HEM401 4.2 3.1 0.9 C2A A:HEM401 4.2 3.0 0.9 C2A A:HEM401 4.2 3.0 0.1 C3D A:HEM401 4.3 3.0 0.1 C3A A:HEM401 4.3 3.1 0.1 C3C A:HEM401 4.3 3.1 0.9 C3B A:HEM401 4.3 3.1 0.1 C3B A:HEM401 4.3 3.1 0.9 C2B A:HEM401 4.3 3.0 0.9 C2B A:HEM401 4.3 3.0 0.1 C2D A:HEM401 4.3 3.0 0.1 C2C A:HEM401 4.3 3.0 0.1 C3C A:HEM401 4.3 3.1 0.1 C2C A:HEM401 4.3 3.0 0.9 HHA A:HEM401 4.3 3.0 0.1 HD3 A:ARG232 4.3 3.0 1.0 HHC A:HEM401 4.4 3.0 0.1 HHD A:HEM401 4.4 3.0 0.1 HHD A:HEM401 4.4 3.0 0.9 HHB A:HEM401 4.4 3.0 0.1 HHA A:HEM401 4.4 3.0 0.9 NH1 A:ARG232 4.5 3.0 1.0 HHC A:HEM401 4.5 3.0 0.9 HHB A:HEM401 4.5 3.0 0.9 HD2 A:ARG232 4.5 3.0 1.0 OD2 A:ASP143 4.6 14.8 0.3 OD1 A:ASP143 4.6 13.8 0.3 HG11 A:VAL219 4.7 3.0 1.0 CE1 A:PHE248 4.7 3.0 1.0 HH12 A:ARG232 4.8 3.0 1.0 CG2 A:VAL219 4.8 3.0 1.0 CD A:ARG232 4.9 3.1 1.0 HD1 A:PHE248 4.9 3.0 1.0 CE A:MET276 5.0 3.0 1.0

Iron binding site 2 out of 4 in the Structure of 5% Reduced 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 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:3.1 occ:0.95 FE A:HEM401 0.0 3.1 0.9 FE A:HEM401 0.0 3.0 0.1 ND A:HEM401 1.9 3.0 0.9 ND A:HEM401 1.9 3.0 0.1 NB A:HEM401 2.0 3.0 0.1 NA A:HEM401 2.0 3.0 0.1 NC A:HEM401 2.0 3.0 0.1 NA A:HEM401 2.0 3.0 0.9 NC A:HEM401 2.1 3.0 0.9 NB A:HEM401 2.1 3.0 0.9 NE2 A:HIS215 2.1 3.7 1.0 C A:CYN404 2.1 3.0 1.0 C1D A:HEM401 2.9 3.0 0.9 C4D A:HEM401 2.9 3.0 0.9 C4D A:HEM401 3.0 3.0 0.1 C1D A:HEM401 3.0 3.0 0.1 C1A A:HEM401 3.0 3.0 0.9 C4B A:HEM401 3.0 3.0 0.1 C1A A:HEM401 3.0 3.0 0.1 C4B A:HEM401 3.0 3.0 0.9 C4C A:HEM401 3.0 3.0 0.9 C1B A:HEM401 3.0 3.0 0.1 C4C A:HEM401 3.0 3.0 0.1 C4A A:HEM401 3.0 3.0 0.1 C4A A:HEM401 3.0 3.0 0.9 C1B A:HEM401 3.0 3.0 0.9 C1C A:HEM401 3.1 3.0 0.1 CE1 A:HIS215 3.1 3.0 1.0 C1C A:HEM401 3.1 3.0 0.9 CD2 A:HIS215 3.1 3.1 1.0 N A:CYN404 3.2 5.8 1.0 HE1 A:HIS215 3.3 3.0 1.0 CHD A:HEM401 3.3 3.4 0.9 CHA A:HEM401 3.3 3.3 0.9 CHA A:HEM401 3.4 3.3 0.1 HD2 A:HIS215 3.4 3.0 1.0 CHD A:HEM401 3.4 3.4 0.1 CHB A:HEM401 3.4 3.4 0.9 CHC A:HEM401 3.4 3.4 0.9 CHC A:HEM401 3.4 3.5 0.1 CHB A:HEM401 3.4 3.4 0.1 HG21 A:VAL219 3.8 3.0 1.0 HE1 A:PHE248 3.9 3.0 1.0 HE1 A:MET276 3.9 3.0 1.0 HH11 A:ARG232 4.0 3.0 1.0 C2D A:HEM401 4.2 3.0 0.9 C3D A:HEM401 4.2 3.0 0.9 ND1 A:HIS215 4.2 3.1 1.0 CG A:HIS215 4.2 3.3 1.0 C2A A:HEM401 4.2 3.0 0.9 C3D A:HEM401 4.2 3.0 0.1 C3A A:HEM401 4.2 3.1 0.9 C2A A:HEM401 4.2 3.0 0.1 C3C A:HEM401 4.3 3.1 0.9 C3A A:HEM401 4.3 3.1 0.1 C2D A:HEM401 4.3 3.0 0.1 C3B A:HEM401 4.3 3.1 0.1 C3C A:HEM401 4.3 3.1 0.1 C3B A:HEM401 4.3 3.1 0.9 C2B A:HEM401 4.3 3.0 0.9 C2B A:HEM401 4.3 3.0 0.1 C2C A:HEM401 4.3 3.0 0.1 C2C A:HEM401 4.3 3.0 0.9 HHA A:HEM401 4.3 3.0 0.1 HD3 A:ARG232 4.3 3.0 1.0 HHC A:HEM401 4.4 3.0 0.1 HHD A:HEM401 4.4 3.0 0.1 HHD A:HEM401 4.4 3.0 0.9 NH1 A:ARG232 4.4 3.0 1.0 HHA A:HEM401 4.4 3.0 0.9 HHB A:HEM401 4.4 3.0 0.1 HD2 A:ARG232 4.5 3.0 1.0 HHB A:HEM401 4.5 3.0 0.9 HHC A:HEM401 4.5 3.0 0.9 OD1 A:ASP143 4.6 13.8 0.3 OD2 A:ASP143 4.6 14.8 0.3 CE1 A:PHE248 4.7 3.0 1.0 HG11 A:VAL219 4.7 3.0 1.0 HH12 A:ARG232 4.7 3.0 1.0 CG2 A:VAL219 4.8 3.0 1.0 CD A:ARG232 4.8 3.1 1.0 HD1 A:PHE248 4.9 3.0 1.0 CE A:MET276 5.0 3.0 1.0

Iron binding site 3 out of 4 in the Structure of 5% Reduced 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 3 of Structure of 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:3.0 occ:0.05 FE B:HEM401 0.0 3.0 0.1 FE B:HEM401 0.0 3.2 0.9 ND B:HEM401 1.9 3.0 0.9 NB B:HEM401 1.9 3.0 0.1 NA B:HEM401 2.0 3.0 0.1 ND B:HEM401 2.0 3.0 0.1 NC B:HEM401 2.0 3.0 0.1 NA B:HEM401 2.0 3.1 0.9 NE2 B:HIS215 2.1 3.8 1.0 NB B:HEM401 2.1 3.0 0.9 NC B:HEM401 2.1 3.0 0.9 C B:CYN404 2.1 4.7 1.0 C4D B:HEM401 2.9 3.0 0.9 C1D B:HEM401 2.9 3.0 0.9 C4B B:HEM401 3.0 3.0 0.1 C1A B:HEM401 3.0 3.0 0.9 C4B B:HEM401 3.0 3.0 0.9 C4D B:HEM401 3.0 3.0 0.1 C1B B:HEM401 3.0 3.0 0.1 C1B B:HEM401 3.0 3.0 0.9 C1D B:HEM401 3.0 3.1 0.1 C4C B:HEM401 3.0 3.0 0.1 C1A B:HEM401 3.0 3.0 0.1 C4C B:HEM401 3.0 3.0 0.9 C1C B:HEM401 3.0 3.0 0.1 C4A B:HEM401 3.0 3.0 0.9 C4A B:HEM401 3.0 3.0 0.1 CE1 B:HIS215 3.0 3.0 1.0 CD2 B:HIS215 3.1 3.1 1.0 C1C B:HEM401 3.1 3.0 0.9 N B:CYN404 3.2 8.5 1.0 HE1 B:HIS215 3.3 3.0 1.0 CHA B:HEM401 3.3 3.4 0.9 HD2 B:HIS215 3.4 3.1 1.0 CHD B:HEM401 3.4 3.4 0.9 CHA B:HEM401 3.4 3.4 0.1 CHC B:HEM401 3.4 3.5 0.1 CHB B:HEM401 3.4 3.3 0.9 CHC B:HEM401 3.4 3.5 0.9 CHB B:HEM401 3.4 3.4 0.1 CHD B:HEM401 3.4 3.4 0.1 HG21 B:VAL219 3.8 3.1 1.0 HE1 B:MET276 3.9 3.0 1.0 HE1 B:PHE248 3.9 3.0 1.0 HH11 B:ARG232 4.1 3.0 1.0 ND1 B:HIS215 4.2 3.2 1.0 CG B:HIS215 4.2 3.8 1.0 C3D B:HEM401 4.2 3.1 0.9 C2D B:HEM401 4.2 3.1 0.9 C2A B:HEM401 4.2 3.2 0.9 C3A B:HEM401 4.2 3.2 0.9 C2A B:HEM401 4.2 3.2 0.1 C3B B:HEM401 4.2 3.1 0.1 C3A B:HEM401 4.3 3.2 0.1 C3B B:HEM401 4.3 3.2 0.9 C2B B:HEM401 4.3 3.0 0.9 C2C B:HEM401 4.3 3.0 0.1 C3C B:HEM401 4.3 3.1 0.1 C2B B:HEM401 4.3 3.0 0.1 C3D B:HEM401 4.3 3.1 0.1 C3C B:HEM401 4.3 3.1 0.9 C2C B:HEM401 4.3 3.0 0.9 C2D B:HEM401 4.3 3.1 0.1 HHA B:HEM401 4.3 3.3 0.1 HHC B:HEM401 4.4 3.0 0.1 HD3 B:ARG232 4.4 3.0 1.0 HHA B:HEM401 4.4 3.3 0.9 HHD B:HEM401 4.4 3.0 0.1 HHB B:HEM401 4.4 3.0 0.1 HHD B:HEM401 4.5 3.0 0.9 HHB B:HEM401 4.5 3.0 0.9 HHC B:HEM401 4.5 3.0 0.9 NH1 B:ARG232 4.5 3.1 1.0 OD1 B:ASP143 4.6 20.6 0.5 HD2 B:ARG232 4.6 3.0 1.0 HG11 B:VAL219 4.7 3.0 1.0 CE1 B:PHE248 4.7 3.0 1.0 OD2 B:ASP143 4.8 29.1 0.5 HH12 B:ARG232 4.8 3.1 1.0 CG2 B:VAL219 4.8 3.2 1.0 HD1 B:PHE248 4.9 3.0 1.0 CD B:ARG232 4.9 3.0 1.0 CE B:MET276 5.0 3.0 1.0

Iron binding site 4 out of 4 in the Structure of 5% Reduced 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 4 of Structure of 5% Reduced Kpdyp in Complex with Cyanide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:3.2 occ:0.95 FE B:HEM401 0.0 3.2 0.9 FE B:HEM401 0.0 3.0 0.1 ND B:HEM401 1.9 3.0 0.9 NB B:HEM401 2.0 3.0 0.1 ND B:HEM401 2.0 3.0 0.1 NA B:HEM401 2.0 3.0 0.1 NC B:HEM401 2.0 3.0 0.1 NA B:HEM401 2.0 3.1 0.9 NE2 B:HIS215 2.1 3.8 1.0 NB B:HEM401 2.1 3.0 0.9 NC B:HEM401 2.1 3.0 0.9 C B:CYN404 2.1 4.7 1.0 C4D B:HEM401 2.9 3.0 0.9 C1D B:HEM401 2.9 3.0 0.9 C1A B:HEM401 3.0 3.0 0.9 C4D B:HEM401 3.0 3.0 0.1 C4B B:HEM401 3.0 3.0 0.1 C1D B:HEM401 3.0 3.1 0.1 C4B B:HEM401 3.0 3.0 0.9 C1B B:HEM401 3.0 3.0 0.1 C4C B:HEM401 3.0 3.0 0.1 C1A B:HEM401 3.0 3.0 0.1 C4C B:HEM401 3.0 3.0 0.9 C1B B:HEM401 3.0 3.0 0.9 C4A B:HEM401 3.0 3.0 0.9 C4A B:HEM401 3.0 3.0 0.1 C1C B:HEM401 3.0 3.0 0.1 CE1 B:HIS215 3.1 3.0 1.0 CD2 B:HIS215 3.1 3.1 1.0 C1C B:HEM401 3.1 3.0 0.9 N B:CYN404 3.2 8.5 1.0 HE1 B:HIS215 3.3 3.0 1.0 CHA B:HEM401 3.3 3.4 0.9 CHD B:HEM401 3.4 3.4 0.9 CHA B:HEM401 3.4 3.4 0.1 HD2 B:HIS215 3.4 3.1 1.0 CHC B:HEM401 3.4 3.5 0.1 CHD B:HEM401 3.4 3.4 0.1 CHB B:HEM401 3.4 3.3 0.9 CHC B:HEM401 3.4 3.5 0.9 CHB B:HEM401 3.4 3.4 0.1 HG21 B:VAL219 3.8 3.1 1.0 HE1 B:PHE248 3.9 3.0 1.0 HE1 B:MET276 3.9 3.0 1.0 HH11 B:ARG232 4.1 3.0 1.0 C3D B:HEM401 4.2 3.1 0.9 ND1 B:HIS215 4.2 3.2 1.0 C2D B:HEM401 4.2 3.1 0.9 CG B:HIS215 4.2 3.8 1.0 C2A B:HEM401 4.2 3.2 0.9 C3A B:HEM401 4.2 3.2 0.9 C2A B:HEM401 4.2 3.2 0.1 C3A B:HEM401 4.3 3.2 0.1 C3D B:HEM401 4.3 3.1 0.1 C3B B:HEM401 4.3 3.1 0.1 C3C B:HEM401 4.3 3.1 0.1 C2C B:HEM401 4.3 3.0 0.1 C2B B:HEM401 4.3 3.0 0.9 C3B B:HEM401 4.3 3.2 0.9 C3C B:HEM401 4.3 3.1 0.9 C2D B:HEM401 4.3 3.1 0.1 C2B B:HEM401 4.3 3.0 0.1 C2C B:HEM401 4.3 3.0 0.9 HHA B:HEM401 4.3 3.3 0.1 HD3 B:ARG232 4.4 3.0 1.0 HHC B:HEM401 4.4 3.0 0.1 HHA B:HEM401 4.4 3.3 0.9 HHD B:HEM401 4.4 3.0 0.1 HHB B:HEM401 4.4 3.0 0.1 HHD B:HEM401 4.4 3.0 0.9 NH1 B:ARG232 4.5 3.1 1.0 HHB B:HEM401 4.5 3.0 0.9 HHC B:HEM401 4.5 3.0 0.9 OD1 B:ASP143 4.5 20.6 0.5 HD2 B:ARG232 4.5 3.0 1.0 HG11 B:VAL219 4.7 3.0 1.0 CE1 B:PHE248 4.7 3.0 1.0 OD2 B:ASP143 4.7 29.1 0.5 HH12 B:ARG232 4.8 3.1 1.0 CG2 B:VAL219 4.8 3.2 1.0 HD1 B:PHE248 4.9 3.0 1.0 CD B:ARG232 4.9 3.0 1.0 CE B:MET276 5.0 3.0 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