Iron in PDB 3lf5: Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution

All present enzymatic activity of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution:
1.6.2.2;

The structure of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution, PDB code: 3lf5 was solved by B.Deng, S.Parthasarathy, W.Wang, B.R.Gibney, K.P.Battaile, S.Lovell, D.R.Benson, H.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.91 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	38.480, 56.370, 42.560, 90.00, 100.67, 90.00
R / Rfree (%)	14.7 / 17.3

The binding sites of Iron atom in the Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution (pdb code 3lf5). 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 Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution, PDB code: 3lf5:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1 b:9.5 occ:0.50 FE A:HEM1 0.0 9.5 0.5 FE A:HEM1 0.2 8.3 0.5 NA A:HEM1 1.9 8.3 0.5 NC A:HEM1 1.9 9.5 0.5 NE2 A:HIS112 2.0 7.8 1.0 NA A:HEM1 2.0 9.4 0.5 NB A:HEM1 2.0 9.0 0.5 NB A:HEM1 2.1 7.8 0.5 ND A:HEM1 2.1 10.1 0.5 NE2 A:HIS89 2.1 8.4 1.0 NC A:HEM1 2.1 8.5 0.5 ND A:HEM1 2.1 8.2 0.5 C4A A:HEM1 2.9 7.4 0.5 C4C A:HEM1 2.9 9.8 0.5 CE1 A:HIS112 3.0 8.7 1.0 C1A A:HEM1 3.0 8.0 0.5 C1B A:HEM1 3.0 9.3 0.5 CD2 A:HIS112 3.0 8.2 1.0 C1C A:HEM1 3.0 9.3 0.5 C4A A:HEM1 3.0 8.8 0.5 C1D A:HEM1 3.0 9.3 0.5 CD2 A:HIS89 3.0 8.3 1.0 C1A A:HEM1 3.0 10.4 0.5 C4B A:HEM1 3.1 9.9 0.5 C4B A:HEM1 3.1 8.8 0.5 C1B A:HEM1 3.1 9.2 0.5 C4D A:HEM1 3.1 10.1 0.5 CE1 A:HIS89 3.1 10.0 1.0 C1C A:HEM1 3.1 9.4 0.5 C4D A:HEM1 3.1 8.9 0.5 C1D A:HEM1 3.2 9.3 0.5 C4C A:HEM1 3.2 9.4 0.5 CHB A:HEM1 3.3 9.5 0.5 CHD A:HEM1 3.3 9.4 0.5 CHA A:HEM1 3.4 8.0 0.5 CHC A:HEM1 3.4 9.1 0.5 CHB A:HEM1 3.4 8.7 0.5 CHA A:HEM1 3.4 9.6 0.5 CHC A:HEM1 3.4 9.9 0.5 CHD A:HEM1 3.5 9.6 0.5 ND1 A:HIS112 4.1 8.8 1.0 C3A A:HEM1 4.1 7.7 0.5 CG A:HIS112 4.1 9.2 1.0 C2A A:HEM1 4.1 8.8 0.5 C3C A:HEM1 4.1 9.6 0.5 C2C A:HEM1 4.2 9.1 0.5 ND1 A:HIS89 4.2 9.7 1.0 CG A:HIS89 4.2 9.7 1.0 C2B A:HEM1 4.2 9.8 0.5 C2A A:HEM1 4.2 10.2 0.5 C3A A:HEM1 4.2 8.9 0.5 C3B A:HEM1 4.3 10.0 0.5 C2D A:HEM1 4.3 11.1 0.5 C3D A:HEM1 4.3 10.3 0.5 C3B A:HEM1 4.3 9.1 0.5 C2B A:HEM1 4.3 9.5 0.5 C2C A:HEM1 4.3 10.5 0.5 C3D A:HEM1 4.4 9.2 0.5 C3C A:HEM1 4.4 10.9 0.5 C2D A:HEM1 4.4 9.3 0.5 CG1 A:VAL111 4.8 14.1 1.0 N A:GLY91 4.9 12.4 1.0

Iron binding site 2 out of 4 in the Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe1 b:8.3 occ:0.50 FE A:HEM1 0.0 8.3 0.5 FE A:HEM1 0.2 9.5 0.5 NA A:HEM1 1.9 9.4 0.5 NB A:HEM1 1.9 7.8 0.5 NE2 A:HIS89 2.0 8.4 1.0 NA A:HEM1 2.0 8.3 0.5 NC A:HEM1 2.0 8.5 0.5 NC A:HEM1 2.0 9.5 0.5 ND A:HEM1 2.0 8.2 0.5 NB A:HEM1 2.1 9.0 0.5 NE2 A:HIS112 2.1 7.8 1.0 ND A:HEM1 2.2 10.1 0.5 C4A A:HEM1 2.9 8.8 0.5 C1B A:HEM1 3.0 9.2 0.5 CE1 A:HIS89 3.0 10.0 1.0 CD2 A:HIS89 3.0 8.3 1.0 C4B A:HEM1 3.0 8.8 0.5 C4A A:HEM1 3.0 7.4 0.5 C1A A:HEM1 3.0 10.4 0.5 C1A A:HEM1 3.0 8.0 0.5 C1C A:HEM1 3.0 9.4 0.5 C4C A:HEM1 3.0 9.4 0.5 C1C A:HEM1 3.0 9.3 0.5 C1D A:HEM1 3.0 9.3 0.5 C4C A:HEM1 3.0 9.8 0.5 C4D A:HEM1 3.1 8.9 0.5 CE1 A:HIS112 3.1 8.7 1.0 C4B A:HEM1 3.1 9.9 0.5 C1B A:HEM1 3.1 9.3 0.5 CD2 A:HIS112 3.1 8.2 1.0 C1D A:HEM1 3.2 9.3 0.5 C4D A:HEM1 3.2 10.1 0.5 CHB A:HEM1 3.3 8.7 0.5 CHC A:HEM1 3.4 9.1 0.5 CHA A:HEM1 3.4 8.0 0.5 CHD A:HEM1 3.4 9.6 0.5 CHB A:HEM1 3.4 9.5 0.5 CHC A:HEM1 3.4 9.9 0.5 CHA A:HEM1 3.5 9.6 0.5 CHD A:HEM1 3.5 9.4 0.5 ND1 A:HIS89 4.1 9.7 1.0 CG A:HIS89 4.1 9.7 1.0 C3A A:HEM1 4.2 8.9 0.5 C2A A:HEM1 4.2 10.2 0.5 ND1 A:HIS112 4.2 8.8 1.0 C2B A:HEM1 4.2 9.5 0.5 C3B A:HEM1 4.2 9.1 0.5 C3C A:HEM1 4.2 9.6 0.5 C3A A:HEM1 4.2 7.7 0.5 CG A:HIS112 4.2 9.2 1.0 C2A A:HEM1 4.2 8.8 0.5 C2C A:HEM1 4.2 9.1 0.5 C2C A:HEM1 4.2 10.5 0.5 C3C A:HEM1 4.2 10.9 0.5 C2D A:HEM1 4.3 9.3 0.5 C3D A:HEM1 4.3 9.2 0.5 C3B A:HEM1 4.3 10.0 0.5 C2B A:HEM1 4.3 9.8 0.5 C3D A:HEM1 4.4 10.3 0.5 C2D A:HEM1 4.4 11.1 0.5 CG1 A:VAL111 4.8 14.1 1.0 N A:GLY91 4.8 12.4 1.0

Iron binding site 3 out of 4 in the Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2 b:9.0 occ:0.50 FE B:HEM2 0.0 9.0 0.5 FE B:HEM2 0.2 9.1 0.5 NC B:HEM2 1.9 8.3 0.5 NA B:HEM2 2.0 10.1 0.5 ND B:HEM2 2.0 9.7 0.5 NE2 B:HIS89 2.0 8.6 1.0 NC B:HEM2 2.0 9.8 0.5 NB B:HEM2 2.0 8.6 0.5 NE2 B:HIS112 2.1 8.5 1.0 ND B:HEM2 2.1 8.2 0.5 NB B:HEM2 2.1 8.7 0.5 NA B:HEM2 2.2 8.9 0.5 C4C B:HEM2 2.8 8.7 0.5 C1C B:HEM2 2.9 8.9 0.5 C1D B:HEM2 2.9 8.7 0.5 CD2 B:HIS89 3.0 9.8 1.0 C1A B:HEM2 3.0 9.2 0.5 CE1 B:HIS112 3.0 9.1 1.0 C4A B:HEM2 3.0 9.2 0.5 CE1 B:HIS89 3.0 9.4 1.0 C4B B:HEM2 3.0 8.1 0.5 C1C B:HEM2 3.0 8.9 0.5 C4C B:HEM2 3.0 9.1 0.5 C4D B:HEM2 3.1 8.7 0.5 C4D B:HEM2 3.1 9.4 0.5 CD2 B:HIS112 3.1 9.5 1.0 C1D B:HEM2 3.1 9.4 0.5 C1B B:HEM2 3.1 8.9 0.5 C4B B:HEM2 3.1 9.5 0.5 C1B B:HEM2 3.1 8.7 0.5 C1A B:HEM2 3.2 9.7 0.5 C4A B:HEM2 3.2 8.8 0.5 CHD B:HEM2 3.2 8.1 0.5 CHC B:HEM2 3.3 8.3 0.5 CHA B:HEM2 3.4 8.2 0.5 CHB B:HEM2 3.4 7.8 0.5 CHC B:HEM2 3.4 9.3 0.5 CHD B:HEM2 3.4 9.9 0.5 CHA B:HEM2 3.5 8.6 0.5 CHB B:HEM2 3.5 9.3 0.5 C3C B:HEM2 4.1 11.5 0.5 C2C B:HEM2 4.1 9.9 0.5 ND1 B:HIS112 4.1 9.7 1.0 ND1 B:HIS89 4.1 9.9 1.0 CG B:HIS89 4.1 9.6 1.0 C2A B:HEM2 4.2 9.2 0.5 CG B:HIS112 4.2 9.6 1.0 C2D B:HEM2 4.2 9.3 0.5 C3A B:HEM2 4.2 10.4 0.5 C2C B:HEM2 4.2 8.9 0.5 C3C B:HEM2 4.3 9.5 0.5 C3D B:HEM2 4.3 10.6 0.5 C3B B:HEM2 4.3 8.4 0.5 C3D B:HEM2 4.3 10.0 0.5 C2B B:HEM2 4.3 8.3 0.5 C3B B:HEM2 4.3 10.9 0.5 C2D B:HEM2 4.3 10.4 0.5 C2B B:HEM2 4.3 8.9 0.5 C2A B:HEM2 4.4 10.3 0.5 C3A B:HEM2 4.4 9.4 0.5 CG1 B:VAL111 4.9 15.1 1.0 N B:GLY91 4.9 12.2 1.0

Iron binding site 4 out of 4 in the Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Human Nadh Cytochrome B5 Oxidoreductase (NCB5OR) B5 Domain to 1.25A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe2 b:9.1 occ:0.50 FE B:HEM2 0.0 9.1 0.5 FE B:HEM2 0.2 9.0 0.5 ND B:HEM2 1.9 8.2 0.5 NC B:HEM2 2.0 9.8 0.5 NB B:HEM2 2.0 8.6 0.5 NC B:HEM2 2.0 8.3 0.5 NE2 B:HIS112 2.0 8.5 1.0 ND B:HEM2 2.0 9.7 0.5 NA B:HEM2 2.0 8.9 0.5 NA B:HEM2 2.0 10.1 0.5 NE2 B:HIS89 2.1 8.6 1.0 NB B:HEM2 2.2 8.7 0.5 C1D B:HEM2 2.9 9.4 0.5 C4D B:HEM2 2.9 8.7 0.5 C4C B:HEM2 2.9 9.1 0.5 C4C B:HEM2 3.0 8.7 0.5 C1A B:HEM2 3.0 9.2 0.5 CE1 B:HIS112 3.0 9.1 1.0 C1B B:HEM2 3.0 8.7 0.5 CD2 B:HIS112 3.0 9.5 1.0 C1C B:HEM2 3.0 8.9 0.5 C1D B:HEM2 3.0 8.7 0.5 CE1 B:HIS89 3.0 9.4 1.0 C4B B:HEM2 3.0 8.1 0.5 C1C B:HEM2 3.0 8.9 0.5 C1A B:HEM2 3.1 9.7 0.5 C4A B:HEM2 3.1 8.8 0.5 C4D B:HEM2 3.1 9.4 0.5 CD2 B:HIS89 3.1 9.8 1.0 C4A B:HEM2 3.1 9.2 0.5 C4B B:HEM2 3.2 9.5 0.5 C1B B:HEM2 3.2 8.9 0.5 CHD B:HEM2 3.3 9.9 0.5 CHA B:HEM2 3.3 8.2 0.5 CHD B:HEM2 3.4 8.1 0.5 CHC B:HEM2 3.4 8.3 0.5 CHB B:HEM2 3.4 9.3 0.5 CHA B:HEM2 3.4 8.6 0.5 CHC B:HEM2 3.5 9.3 0.5 CHB B:HEM2 3.5 7.8 0.5 ND1 B:HIS112 4.1 9.7 1.0 CG B:HIS112 4.1 9.6 1.0 ND1 B:HIS89 4.2 9.9 1.0 C3D B:HEM2 4.2 10.0 0.5 C2D B:HEM2 4.2 10.4 0.5 C3C B:HEM2 4.2 9.5 0.5 C3C B:HEM2 4.2 11.5 0.5 CG B:HIS89 4.2 9.6 1.0 C2C B:HEM2 4.2 8.9 0.5 C2A B:HEM2 4.2 9.2 0.5 C2C B:HEM2 4.2 9.9 0.5 C2B B:HEM2 4.2 8.3 0.5 C3B B:HEM2 4.2 8.4 0.5 C2A B:HEM2 4.3 10.3 0.5 C3A B:HEM2 4.3 9.4 0.5 C3D B:HEM2 4.3 10.6 0.5 C2D B:HEM2 4.3 9.3 0.5 C3A B:HEM2 4.3 10.4 0.5 C3B B:HEM2 4.4 10.9 0.5 C2B B:HEM2 4.5 8.9 0.5 CG1 B:VAL111 4.7 15.1 1.0 N B:GLY91 4.9 12.2 1.0

B.Deng, S.Parthasarathy, W.Wang, B.R.Gibney, K.P.Battaile, S.Lovell, D.R.Benson, H.Zhu. Study of the Individual Cytochrome B5 and Cytochrome B5 Reductase Domains of NCB5OR Reveals A Unique Heme Pocket and A Possible Role of the Cs Domain. J.Biol.Chem. V. 285 30181 2010.
ISSN: ISSN 0021-9258
PubMed: 20630863
DOI: 10.1074/JBC.M110.120329