Iron in PDB 3bng: W. Succinogenes Nrfa Y218F

All present enzymatic activity of W. Succinogenes Nrfa Y218F:
1.7.2.2;

The structure of W. Succinogenes Nrfa Y218F, PDB code: 3bng was solved by P.Lukat, O.Einsle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.45 / 1.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	120.030, 120.030, 186.276, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.5

The structure of W. Succinogenes Nrfa Y218F also contains other interesting chemical elements:

Yttrium	(Y)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the W. Succinogenes Nrfa Y218F (pdb code 3bng). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the W. Succinogenes Nrfa Y218F, PDB code: 3bng:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe513 b:16.5 occ:1.00 FE A:HEM513 0.0 16.5 1.0 NA A:HEM513 2.0 15.8 1.0 NB A:HEM513 2.0 15.7 1.0 ND A:HEM513 2.0 14.9 1.0 NC A:HEM513 2.1 15.0 1.0 NZ A:LYS134 2.1 15.6 1.0 O A:HOH1047 2.2 19.2 1.0 C4A A:HEM513 3.0 15.9 1.0 C1A A:HEM513 3.0 15.2 1.0 C1B A:HEM513 3.0 16.4 1.0 C4B A:HEM513 3.0 15.4 1.0 C1D A:HEM513 3.0 15.2 1.0 C4D A:HEM513 3.1 15.7 1.0 C1C A:HEM513 3.1 14.8 1.0 C4C A:HEM513 3.1 14.7 1.0 CE A:LYS134 3.1 17.2 1.0 CHB A:HEM513 3.4 15.7 1.0 CHD A:HEM513 3.4 15.6 1.0 CHA A:HEM513 3.4 15.8 1.0 CHC A:HEM513 3.4 16.0 1.0 NE2 A:HIS277 4.1 16.5 1.0 O A:HOH581 4.2 16.6 1.0 C2A A:HEM513 4.2 14.8 1.0 C3A A:HEM513 4.2 14.7 1.0 C3B A:HEM513 4.3 15.8 1.0 C2B A:HEM513 4.3 18.4 1.0 O A:HOH519 4.3 23.7 1.0 C3C A:HEM513 4.3 14.2 1.0 C2D A:HEM513 4.3 15.8 1.0 C2C A:HEM513 4.3 14.0 1.0 C3D A:HEM513 4.3 15.4 1.0 CD A:LYS134 4.5 16.1 1.0 O A:HOH569 4.6 20.5 1.0 CD2 A:HIS277 4.8 16.7 1.0 CMD A:HEM515 4.8 15.4 1.0

Iron binding site 2 out of 5 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe514 b:20.4 occ:1.00 FE A:HEM514 0.0 20.4 1.0 NE2 A:HIS172 2.0 20.4 1.0 NC A:HEM514 2.0 18.3 1.0 NB A:HEM514 2.0 19.5 1.0 ND A:HEM514 2.0 20.0 1.0 NA A:HEM514 2.0 19.1 1.0 NE2 A:HIS313 2.0 19.6 1.0 CE1 A:HIS172 2.9 20.1 1.0 CD2 A:HIS313 3.0 19.1 1.0 C1B A:HEM514 3.0 20.1 1.0 C4B A:HEM514 3.0 18.3 1.0 C4C A:HEM514 3.0 18.7 1.0 CD2 A:HIS172 3.0 19.2 1.0 C1D A:HEM514 3.0 19.4 1.0 C4A A:HEM514 3.0 19.8 1.0 C4D A:HEM514 3.0 20.2 1.0 C1C A:HEM514 3.1 18.0 1.0 CE1 A:HIS313 3.1 19.4 1.0 C1A A:HEM514 3.1 20.4 1.0 CHB A:HEM514 3.4 19.6 1.0 CHA A:HEM514 3.4 21.1 1.0 CHD A:HEM514 3.4 19.6 1.0 CHC A:HEM514 3.4 18.7 1.0 ND1 A:HIS172 4.1 19.4 1.0 CG A:HIS172 4.1 18.2 1.0 ND1 A:HIS313 4.2 18.5 1.0 CG A:HIS313 4.2 18.0 1.0 C3B A:HEM514 4.3 18.0 1.0 C3C A:HEM514 4.3 18.2 1.0 C2B A:HEM514 4.3 19.3 1.0 C2D A:HEM514 4.3 19.9 1.0 C3A A:HEM514 4.3 19.2 1.0 C3D A:HEM514 4.3 21.8 1.0 C2C A:HEM514 4.3 16.3 1.0 C2A A:HEM514 4.3 19.9 1.0 CE A:MET300 4.5 20.4 1.0

Iron binding site 3 out of 5 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe515 b:16.4 occ:1.00 FE A:HEM515 0.0 16.4 1.0 ND A:HEM515 2.0 15.7 1.0 NA A:HEM515 2.0 14.7 1.0 NB A:HEM515 2.0 16.3 1.0 NC A:HEM515 2.0 15.1 1.0 NE2 A:HIS215 2.0 15.2 1.0 NE2 A:HIS102 2.1 14.1 1.0 CE1 A:HIS215 3.0 15.3 1.0 CE1 A:HIS102 3.0 15.2 1.0 C1D A:HEM515 3.0 17.0 1.0 C4C A:HEM515 3.0 15.3 1.0 C1B A:HEM515 3.0 15.8 1.0 C4A A:HEM515 3.0 15.7 1.0 C4D A:HEM515 3.0 15.3 1.0 C4B A:HEM515 3.0 16.5 1.0 C1C A:HEM515 3.0 16.4 1.0 C1A A:HEM515 3.0 15.3 1.0 CD2 A:HIS215 3.1 15.8 1.0 CD2 A:HIS102 3.1 15.4 1.0 CHD A:HEM515 3.4 16.2 1.0 CHB A:HEM515 3.4 16.9 1.0 CHC A:HEM515 3.4 16.7 1.0 CHA A:HEM515 3.4 15.4 1.0 ND1 A:HIS215 4.1 14.6 1.0 ND1 A:HIS102 4.1 15.6 1.0 CG A:HIS215 4.2 14.6 1.0 CG A:HIS102 4.2 14.7 1.0 C2C A:HEM515 4.2 17.2 1.0 C3C A:HEM515 4.3 15.0 1.0 C3B A:HEM515 4.3 15.6 1.0 C2D A:HEM515 4.3 17.0 1.0 C3D A:HEM515 4.3 15.5 1.0 C2A A:HEM515 4.3 14.9 1.0 C2B A:HEM515 4.3 16.9 1.0 C3A A:HEM515 4.3 16.4 1.0 CD1 A:ILE166 4.8 22.1 1.0 CG1 A:VAL315 5.0 17.1 1.0

Iron binding site 4 out of 5 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe516 b:17.6 occ:1.00 FE A:HEM516 0.0 17.6 1.0 NB A:HEM516 2.0 15.1 1.0 ND A:HEM516 2.0 17.0 1.0 NA A:HEM516 2.0 16.6 1.0 NC A:HEM516 2.0 16.8 1.0 NE2 A:HIS299 2.1 16.0 1.0 NE2 A:HIS405 2.1 16.1 1.0 C1B A:HEM516 3.0 15.2 1.0 C1D A:HEM516 3.0 16.7 1.0 C4B A:HEM516 3.0 16.4 1.0 C4A A:HEM516 3.0 16.5 1.0 C4D A:HEM516 3.0 15.9 1.0 CE1 A:HIS405 3.0 16.8 1.0 C4C A:HEM516 3.0 17.9 1.0 C1C A:HEM516 3.0 16.0 1.0 C1A A:HEM516 3.0 15.9 1.0 CD2 A:HIS299 3.0 15.7 1.0 CE1 A:HIS299 3.1 16.9 1.0 CD2 A:HIS405 3.2 15.8 1.0 CHB A:HEM516 3.4 17.1 1.0 CHD A:HEM516 3.4 17.5 1.0 CHC A:HEM516 3.4 17.2 1.0 CHA A:HEM516 3.4 16.6 1.0 ND1 A:HIS405 4.2 15.3 1.0 ND1 A:HIS299 4.2 16.9 1.0 C3B A:HEM516 4.2 14.3 1.0 CG A:HIS299 4.2 16.4 1.0 C2B A:HEM516 4.2 16.4 1.0 C3C A:HEM516 4.2 16.1 1.0 C2D A:HEM516 4.2 16.5 1.0 C3D A:HEM516 4.2 18.2 1.0 C3A A:HEM516 4.3 16.2 1.0 C2A A:HEM516 4.3 16.6 1.0 C2C A:HEM516 4.3 16.7 1.0 CG A:HIS405 4.3 15.1 1.0

Iron binding site 5 out of 5 in the W. Succinogenes Nrfa Y218F


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of W. Succinogenes Nrfa Y218F within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe517 b:21.1 occ:1.00 FE A:HEM517 0.0 21.1 1.0 NA A:HEM517 2.0 19.6 1.0 NE2 A:HIS288 2.0 18.1 1.0 NB A:HEM517 2.0 20.4 1.0 NC A:HEM517 2.0 20.4 1.0 NE2 A:HIS330 2.0 19.7 1.0 ND A:HEM517 2.0 20.4 1.0 CE1 A:HIS330 2.9 22.3 1.0 CE1 A:HIS288 3.0 18.3 1.0 C4C A:HEM517 3.0 21.8 1.0 C1A A:HEM517 3.0 21.6 1.0 C4A A:HEM517 3.0 20.7 1.0 C4B A:HEM517 3.0 20.5 1.0 C1D A:HEM517 3.0 22.3 1.0 CD2 A:HIS288 3.0 16.9 1.0 C1B A:HEM517 3.0 20.8 1.0 C1C A:HEM517 3.1 20.4 1.0 C4D A:HEM517 3.1 22.9 1.0 CD2 A:HIS330 3.2 20.5 1.0 CHD A:HEM517 3.4 23.0 1.0 CHC A:HEM517 3.4 21.7 1.0 CHB A:HEM517 3.4 21.6 1.0 CHA A:HEM517 3.4 22.7 1.0 ND1 A:HIS330 4.1 22.9 1.0 ND1 A:HIS288 4.1 17.6 1.0 CG A:HIS288 4.2 16.1 1.0 CG A:HIS330 4.2 23.6 1.0 C2A A:HEM517 4.2 21.6 1.0 C3A A:HEM517 4.3 22.4 1.0 C3C A:HEM517 4.3 22.6 1.0 C3B A:HEM517 4.3 19.5 1.0 C2B A:HEM517 4.3 19.7 1.0 C2C A:HEM517 4.3 20.2 1.0 C2D A:HEM517 4.3 24.0 1.0 C3D A:HEM517 4.3 24.0 1.0 CBC A:HEM516 4.8 17.0 1.0

P.Lukat, M.Rudolf, P.Stach, A.Messerschmidt, P.M.H.Kroneck, J.Simon, O.Einsle. Binding and Reduction of Sulfite By Cytochrome C Nitrite Reductase Biochemistry V. 47 2080 2008.
ISSN: ISSN 0006-2960
PubMed: 18201106
DOI: 10.1021/BI7021415