Iron in PDB 6rr4: Structure of 25% Reduced Kpdyp

The structure of Structure of 25% Reduced Kpdyp, PDB code: 6rr4 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)	48.40 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.889, 76.647, 76.579, 90.00, 108.01, 90.00
R / Rfree (%)	16.9 / 18.1

The structure of Structure of 25% Reduced Kpdyp also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Iron atom in the Structure of 25% Reduced Kpdyp (pdb code 6rr4). 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 25% Reduced Kpdyp, PDB code: 6rr4:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:3.1 occ:0.25 FE A:HEM401 0.0 3.1 0.2 FE A:HEM401 0.1 3.2 0.8 NC A:HEM401 2.0 3.0 0.2 ND A:HEM401 2.0 3.0 0.2 ND A:HEM401 2.0 3.0 0.8 NA A:HEM401 2.0 3.0 0.2 NB A:HEM401 2.0 3.0 0.2 NC A:HEM401 2.1 3.0 0.8 NA A:HEM401 2.1 3.0 0.8 NB A:HEM401 2.1 3.0 0.8 NE2 A:HIS215 2.2 3.9 1.0 O A:HOH508 2.6 35.6 1.0 C4D A:HEM401 3.0 3.0 0.8 C4B A:HEM401 3.0 3.0 0.8 C1D A:HEM401 3.0 3.0 0.8 C4C A:HEM401 3.0 3.0 0.2 C4D A:HEM401 3.0 3.0 0.2 C4C A:HEM401 3.0 3.0 0.8 C1D A:HEM401 3.0 3.0 0.2 C1B A:HEM401 3.0 3.0 0.8 C4B A:HEM401 3.0 3.0 0.2 C1C A:HEM401 3.0 3.0 0.8 C1B A:HEM401 3.0 3.0 0.2 CD2 A:HIS215 3.0 3.2 1.0 C1A A:HEM401 3.0 3.0 0.2 C1A A:HEM401 3.0 3.0 0.8 C4A A:HEM401 3.0 3.0 0.2 C4A A:HEM401 3.0 3.0 0.8 C1C A:HEM401 3.1 3.0 0.2 CE1 A:HIS215 3.1 3.0 1.0 HD2 A:HIS215 3.1 3.0 1.0 HE1 A:HIS215 3.3 3.0 1.0 CHC A:HEM401 3.4 3.5 0.8 CHD A:HEM401 3.4 3.4 0.8 CHA A:HEM401 3.4 3.3 0.8 CHB A:HEM401 3.4 3.4 0.8 CHA A:HEM401 3.4 3.3 0.2 CHD A:HEM401 3.4 3.4 0.2 CHC A:HEM401 3.4 3.5 0.2 CHB A:HEM401 3.4 3.4 0.2 HH11 A:ARG232 3.9 3.0 1.0 HE1 A:PHE248 4.0 3.0 1.0 HG21 A:VAL219 4.0 3.0 1.0 HE1 A:MET276 4.0 3.0 1.0 CG A:HIS215 4.2 3.9 1.0 ND1 A:HIS215 4.2 3.2 1.0 C3C A:HEM401 4.2 3.1 0.8 C3C A:HEM401 4.3 3.1 0.2 C2C A:HEM401 4.3 3.0 0.8 C3D A:HEM401 4.3 3.0 0.2 C2C A:HEM401 4.3 3.0 0.2 C3D A:HEM401 4.3 3.0 0.8 C2B A:HEM401 4.3 3.0 0.8 C3A A:HEM401 4.3 3.1 0.8 C3B A:HEM401 4.3 3.2 0.8 C3A A:HEM401 4.3 3.1 0.2 C2A A:HEM401 4.3 3.0 0.2 C2A A:HEM401 4.3 3.0 0.8 C2D A:HEM401 4.3 3.0 0.2 C2D A:HEM401 4.3 3.0 0.8 C2B A:HEM401 4.3 3.0 0.2 NH1 A:ARG232 4.3 3.0 1.0 C3B A:HEM401 4.3 3.1 0.2 HHA A:HEM401 4.3 3.0 0.2 HHC A:HEM401 4.4 3.0 0.2 HD3 A:ARG232 4.4 3.0 1.0 HHC A:HEM401 4.4 3.0 0.8 HHD A:HEM401 4.4 3.0 0.2 HHD A:HEM401 4.4 3.0 0.8 HHB A:HEM401 4.5 3.0 0.2 HHA A:HEM401 4.5 3.0 0.8 HHB A:HEM401 4.5 3.0 0.8 HH12 A:ARG232 4.5 3.0 1.0 HD2 A:ARG232 4.5 3.0 1.0 HG11 A:VAL219 4.6 3.0 1.0 O A:HOH526 4.6 27.4 1.0 OD1 A:ASP143 4.7 14.5 1.0 CE1 A:PHE248 4.7 3.0 1.0 CD A:ARG232 4.9 3.1 1.0 CG2 A:VAL219 4.9 3.0 1.0 CE A:MET276 5.0 3.0 1.0 HD1 A:PHE248 5.0 3.0 1.0

Iron binding site 2 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:3.2 occ:0.75 FE A:HEM401 0.0 3.2 0.8 FE A:HEM401 0.1 3.1 0.2 ND A:HEM401 1.9 3.0 0.2 ND A:HEM401 2.0 3.0 0.8 NA A:HEM401 2.0 3.0 0.2 NC A:HEM401 2.0 3.0 0.2 NB A:HEM401 2.0 3.0 0.2 NA A:HEM401 2.1 3.0 0.8 NC A:HEM401 2.1 3.0 0.8 NB A:HEM401 2.1 3.0 0.8 NE2 A:HIS215 2.2 3.9 1.0 O A:HOH508 2.6 35.6 1.0 C4D A:HEM401 2.9 3.0 0.8 C4D A:HEM401 3.0 3.0 0.2 C1D A:HEM401 3.0 3.0 0.8 C1D A:HEM401 3.0 3.0 0.2 C1A A:HEM401 3.0 3.0 0.2 C1A A:HEM401 3.0 3.0 0.8 C4C A:HEM401 3.0 3.0 0.2 C4C A:HEM401 3.0 3.0 0.8 C4B A:HEM401 3.0 3.0 0.8 C4A A:HEM401 3.0 3.0 0.2 C1B A:HEM401 3.0 3.0 0.8 C4A A:HEM401 3.0 3.0 0.8 C1B A:HEM401 3.0 3.0 0.2 C4B A:HEM401 3.1 3.0 0.2 CD2 A:HIS215 3.1 3.2 1.0 C1C A:HEM401 3.1 3.0 0.8 C1C A:HEM401 3.1 3.0 0.2 HD2 A:HIS215 3.2 3.0 1.0 CE1 A:HIS215 3.2 3.0 1.0 CHA A:HEM401 3.3 3.3 0.8 CHA A:HEM401 3.3 3.3 0.2 CHD A:HEM401 3.4 3.4 0.8 CHB A:HEM401 3.4 3.4 0.8 HE1 A:HIS215 3.4 3.0 1.0 CHC A:HEM401 3.4 3.5 0.8 CHD A:HEM401 3.4 3.4 0.2 CHB A:HEM401 3.4 3.4 0.2 CHC A:HEM401 3.5 3.5 0.2 HH11 A:ARG232 3.9 3.0 1.0 HE1 A:PHE248 4.0 3.0 1.0 HG21 A:VAL219 4.0 3.0 1.0 HE1 A:MET276 4.1 3.0 1.0 C3D A:HEM401 4.2 3.0 0.2 C3D A:HEM401 4.2 3.0 0.8 CG A:HIS215 4.2 3.9 1.0 C3A A:HEM401 4.3 3.1 0.8 C2A A:HEM401 4.3 3.0 0.2 C3A A:HEM401 4.3 3.1 0.2 NH1 A:ARG232 4.3 3.0 1.0 C2A A:HEM401 4.3 3.0 0.8 C2D A:HEM401 4.3 3.0 0.2 C3C A:HEM401 4.3 3.1 0.8 C2D A:HEM401 4.3 3.0 0.8 ND1 A:HIS215 4.3 3.2 1.0 C3C A:HEM401 4.3 3.1 0.2 C2C A:HEM401 4.3 3.0 0.8 C2B A:HEM401 4.3 3.0 0.8 C2C A:HEM401 4.3 3.0 0.2 HHA A:HEM401 4.3 3.0 0.2 C3B A:HEM401 4.3 3.2 0.8 C2B A:HEM401 4.3 3.0 0.2 HD3 A:ARG232 4.4 3.0 1.0 C3B A:HEM401 4.4 3.1 0.2 HHA A:HEM401 4.4 3.0 0.8 HHC A:HEM401 4.4 3.0 0.2 HHD A:HEM401 4.4 3.0 0.2 HHD A:HEM401 4.4 3.0 0.8 HH12 A:ARG232 4.4 3.0 1.0 HHB A:HEM401 4.4 3.0 0.2 HHB A:HEM401 4.5 3.0 0.8 HD2 A:ARG232 4.5 3.0 1.0 HHC A:HEM401 4.5 3.0 0.8 O A:HOH526 4.6 27.4 1.0 HG11 A:VAL219 4.6 3.0 1.0 OD1 A:ASP143 4.7 14.5 1.0 CE1 A:PHE248 4.7 3.0 1.0 CD A:ARG232 4.8 3.1 1.0 CG2 A:VAL219 4.9 3.0 1.0 CZ A:ARG232 5.0 12.4 1.0 HD1 A:PHE248 5.0 3.0 1.0

Iron binding site 3 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:3.1 occ:0.25 FE B:HEM401 0.0 3.1 0.2 FE B:HEM401 0.0 3.3 0.8 NC B:HEM401 2.0 3.0 0.2 NA B:HEM401 2.0 3.0 0.2 NB B:HEM401 2.0 3.0 0.2 ND B:HEM401 2.0 3.0 0.8 ND B:HEM401 2.0 3.0 0.2 NA B:HEM401 2.0 3.1 0.8 NB B:HEM401 2.1 3.0 0.8 NE2 B:HIS215 2.1 3.6 1.0 NC B:HEM401 2.1 3.0 0.8 O B:HOH501 2.6 25.5 1.0 C4D B:HEM401 3.0 3.0 0.8 C1D B:HEM401 3.0 3.0 0.8 C4B B:HEM401 3.0 3.0 0.8 C1B B:HEM401 3.0 3.0 0.2 C1A B:HEM401 3.0 3.0 0.8 C4B B:HEM401 3.0 3.0 0.2 C1B B:HEM401 3.0 3.0 0.8 C4C B:HEM401 3.0 3.0 0.2 C1D B:HEM401 3.0 3.0 0.2 CE1 B:HIS215 3.0 3.0 1.0 C4D B:HEM401 3.0 3.0 0.2 C4A B:HEM401 3.0 3.0 0.8 C4A B:HEM401 3.0 3.0 0.2 C1A B:HEM401 3.0 3.0 0.2 C4C B:HEM401 3.0 3.0 0.8 CD2 B:HIS215 3.0 3.1 1.0 C1C B:HEM401 3.1 3.0 0.2 C1C B:HEM401 3.1 3.0 0.8 HE1 B:HIS215 3.2 3.0 1.0 HD2 B:HIS215 3.2 3.0 1.0 CHA B:HEM401 3.4 3.3 0.8 CHD B:HEM401 3.4 3.4 0.8 CHA B:HEM401 3.4 3.3 0.2 CHD B:HEM401 3.4 3.4 0.2 CHB B:HEM401 3.4 3.4 0.2 CHC B:HEM401 3.4 3.5 0.2 CHB B:HEM401 3.4 3.4 0.8 CHC B:HEM401 3.5 3.5 0.8 HG21 B:VAL219 3.9 3.0 1.0 HE1 B:PHE248 3.9 3.0 1.0 HH11 B:ARG232 3.9 3.0 1.0 OD2 B:ASP143 4.1 22.6 0.5 ND1 B:HIS215 4.1 3.2 1.0 CG B:HIS215 4.2 3.9 1.0 C3A B:HEM401 4.2 3.1 0.8 HE1 B:MET276 4.2 3.0 1.0 C3D B:HEM401 4.2 3.0 0.8 C2A B:HEM401 4.2 3.1 0.8 C2D B:HEM401 4.2 3.0 0.8 C3B B:HEM401 4.2 3.1 0.8 C2B B:HEM401 4.3 3.0 0.8 C3C B:HEM401 4.3 3.1 0.2 C3C B:HEM401 4.3 3.1 0.8 C3A B:HEM401 4.3 3.1 0.2 C2C B:HEM401 4.3 3.0 0.2 C3D B:HEM401 4.3 3.0 0.2 C2B B:HEM401 4.3 3.0 0.2 C2A B:HEM401 4.3 3.1 0.2 C2C B:HEM401 4.3 3.0 0.8 C3B B:HEM401 4.3 3.1 0.2 C2D B:HEM401 4.3 3.0 0.2 NH1 B:ARG232 4.3 3.0 1.0 HHA B:HEM401 4.4 3.0 0.2 HHC B:HEM401 4.4 3.0 0.2 HD3 B:ARG232 4.4 3.0 1.0 HHB B:HEM401 4.4 3.0 0.2 HHD B:HEM401 4.5 3.0 0.2 HHA B:HEM401 4.5 3.0 0.8 HHD B:HEM401 4.5 3.0 0.8 HH12 B:ARG232 4.5 3.0 1.0 HHB B:HEM401 4.5 3.0 0.8 HHC B:HEM401 4.5 3.0 0.8 OD1 B:ASP143 4.6 9.0 0.5 HG11 B:VAL219 4.6 3.0 1.0 CE1 B:PHE248 4.6 3.1 1.0 HD2 B:ARG232 4.6 3.0 1.0 O B:HOH525 4.8 21.0 1.0 CG2 B:VAL219 4.8 3.0 1.0 HD1 B:HIS215 4.9 3.0 1.0 CD B:ARG232 4.9 3.0 1.0 HG23 B:VAL219 4.9 3.0 1.0 CZ B:ARG232 5.0 8.5 1.0

Iron binding site 4 out of 4 in the Structure of 25% Reduced Kpdyp


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of 25% Reduced Kpdyp within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe401 b:3.3 occ:0.75 FE B:HEM401 0.0 3.3 0.8 FE B:HEM401 0.0 3.1 0.2 ND B:HEM401 1.9 3.0 0.8 NC B:HEM401 2.0 3.0 0.2 ND B:HEM401 2.0 3.0 0.2 NA B:HEM401 2.0 3.0 0.2 NB B:HEM401 2.0 3.0 0.2 NA B:HEM401 2.0 3.1 0.8 NB B:HEM401 2.1 3.0 0.8 NC B:HEM401 2.1 3.0 0.8 NE2 B:HIS215 2.1 3.6 1.0 O B:HOH501 2.6 25.5 1.0 C4D B:HEM401 2.9 3.0 0.8 C1D B:HEM401 2.9 3.0 0.8 C1D B:HEM401 3.0 3.0 0.2 C1A B:HEM401 3.0 3.0 0.8 C4D B:HEM401 3.0 3.0 0.2 C4C B:HEM401 3.0 3.0 0.2 C4B B:HEM401 3.0 3.0 0.8 C1B B:HEM401 3.0 3.0 0.2 C1A B:HEM401 3.0 3.0 0.2 C4B B:HEM401 3.0 3.0 0.2 C4C B:HEM401 3.0 3.0 0.8 C1B B:HEM401 3.0 3.0 0.8 C4A B:HEM401 3.0 3.0 0.8 C4A B:HEM401 3.0 3.0 0.2 CE1 B:HIS215 3.1 3.0 1.0 C1C B:HEM401 3.1 3.0 0.2 CD2 B:HIS215 3.1 3.1 1.0 C1C B:HEM401 3.1 3.0 0.8 HE1 B:HIS215 3.2 3.0 1.0 HD2 B:HIS215 3.2 3.0 1.0 CHA B:HEM401 3.4 3.3 0.8 CHD B:HEM401 3.4 3.4 0.8 CHA B:HEM401 3.4 3.3 0.2 CHD B:HEM401 3.4 3.4 0.2 CHB B:HEM401 3.4 3.4 0.2 CHC B:HEM401 3.4 3.5 0.2 CHB B:HEM401 3.5 3.4 0.8 CHC B:HEM401 3.5 3.5 0.8 HG21 B:VAL219 3.9 3.0 1.0 HE1 B:PHE248 3.9 3.0 1.0 HH11 B:ARG232 3.9 3.0 1.0 OD2 B:ASP143 4.1 22.6 0.5 ND1 B:HIS215 4.2 3.2 1.0 C3D B:HEM401 4.2 3.0 0.8 C2D B:HEM401 4.2 3.0 0.8 CG B:HIS215 4.2 3.9 1.0 C3A B:HEM401 4.2 3.1 0.8 C2A B:HEM401 4.2 3.1 0.8 C3C B:HEM401 4.2 3.1 0.2 C3C B:HEM401 4.3 3.1 0.8 C3D B:HEM401 4.3 3.0 0.2 HE1 B:MET276 4.3 3.0 1.0 C3A B:HEM401 4.3 3.1 0.2 C3B B:HEM401 4.3 3.1 0.8 C2C B:HEM401 4.3 3.0 0.2 C2B B:HEM401 4.3 3.0 0.8 NH1 B:ARG232 4.3 3.0 1.0 C2D B:HEM401 4.3 3.0 0.2 C2A B:HEM401 4.3 3.1 0.2 C2C B:HEM401 4.3 3.0 0.8 C2B B:HEM401 4.3 3.0 0.2 C3B B:HEM401 4.3 3.1 0.2 HHA B:HEM401 4.3 3.0 0.2 HD3 B:ARG232 4.4 3.0 1.0 HHC B:HEM401 4.4 3.0 0.2 HHD B:HEM401 4.4 3.0 0.2 HHB B:HEM401 4.4 3.0 0.2 HHA B:HEM401 4.4 3.0 0.8 HHD B:HEM401 4.5 3.0 0.8 HH12 B:ARG232 4.5 3.0 1.0 HHB B:HEM401 4.5 3.0 0.8 HHC B:HEM401 4.6 3.0 0.8 OD1 B:ASP143 4.6 9.0 0.5 HD2 B:ARG232 4.6 3.0 1.0 CE1 B:PHE248 4.6 3.1 1.0 HG11 B:VAL219 4.6 3.0 1.0 O B:HOH525 4.8 21.0 1.0 CG2 B:VAL219 4.8 3.0 1.0 CD B:ARG232 4.9 3.0 1.0 HG23 B:VAL219 4.9 3.0 1.0 HD1 B:HIS215 5.0 3.0 1.0 CZ B:ARG232 5.0 8.5 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