Iron in PDB 3by0: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin, PDB code: 3by0 was solved by M.C.Clifton, J.C.Pizzaro, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.59 / 2.57
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.358, 114.358, 119.042, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 26.2

The binding sites of Iron atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin (pdb code 3by0). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin, PDB code: 3by0:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe401 b:57.6 occ:1.00 O3 A:DBH193 1.7 85.7 1.0 O6 A:DBH192 2.1 0.4 1.0 O1 A:DBS191 2.1 53.1 1.0 O4 A:DBS191 2.2 52.2 1.0 O3 A:DBH192 2.6 0.5 1.0 C3 A:DBH193 2.7 85.6 1.0 O6 A:DBH193 2.8 85.2 1.0 C1 A:DBS191 2.9 53.3 1.0 C4 A:DBS191 3.0 52.9 1.0 C6 A:DBH192 3.0 0.6 1.0 C6 A:DBH193 3.1 85.5 1.0 C3 A:DBH192 3.3 0.6 1.0 NZ A:LYS134 3.8 38.9 1.0 C18 A:DBH193 3.9 85.7 1.0 OH A:TYR106 4.1 38.1 1.0 O9 A:DBH193 4.1 85.6 1.0 O A:HOH615 4.1 48.5 1.0 C16 A:DBS191 4.3 54.2 1.0 C7 A:DBS191 4.3 52.7 1.0 C9 A:DBH192 4.3 0.6 1.0 C21 A:DBH193 4.3 85.8 1.0 C9 A:DBH193 4.5 85.6 1.0 NZ A:LYS125 4.5 38.4 1.0 CE A:LYS134 4.6 38.4 1.0 C18 A:DBH192 4.6 0.7 1.0 N1 A:DBS191 4.7 57.3 1.0 CE2 A:TYR106 4.7 39.5 1.0 CZ A:TYR106 4.9 39.2 1.0 C19 A:DBS191 5.0 55.8 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe402 b:0.6 occ:1.00 O3 B:DBH201 2.2 85.3 1.0 O6 B:DBH201 2.4 84.6 1.0 C3 B:DBH201 3.1 85.1 1.0 C6 B:DBH201 3.2 84.9 1.0 NZ B:LYS125 4.3 89.4 1.0 NZ B:LYS134 4.4 90.4 1.0 C18 B:DBH201 4.4 85.2 1.0 C9 B:DBH201 4.5 84.9 1.0 OH B:TYR106 4.7 81.9 1.0 O9 B:DBH201 4.9 85.4 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) W79A-R81A Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe403 b:54.8 occ:1.00 O1 C:DBS302 1.8 69.0 1.0 O1 C:DBS301 2.1 47.9 1.0 O6 C:DBH303 2.2 85.4 1.0 O3 C:DBH303 2.2 85.5 1.0 O4 C:DBS301 2.3 46.9 1.0 O4 C:DBS302 2.5 69.0 1.0 C1 C:DBS302 2.7 69.2 1.0 C1 C:DBS301 3.0 47.3 1.0 C6 C:DBH303 3.0 85.8 1.0 C3 C:DBH303 3.0 86.0 1.0 C4 C:DBS302 3.0 69.1 1.0 C4 C:DBS301 3.0 47.5 1.0 C16 C:DBS302 4.0 69.6 1.0 NZ C:LYS134 4.0 35.3 1.0 N1 C:DBS302 4.1 70.6 1.0 C16 C:DBS301 4.3 47.5 1.0 O13 C:DBS302 4.3 70.9 1.0 OH C:TYR106 4.3 31.3 1.0 C9 C:DBH303 4.3 85.8 1.0 C18 C:DBH303 4.3 86.2 1.0 NZ C:LYS125 4.4 32.5 1.0 C7 C:DBS302 4.4 69.2 1.0 C7 C:DBS301 4.4 47.2 1.0 C19 C:DBS302 4.5 70.2 1.0 N1 C:DBS301 4.6 48.8 1.0 CE C:LYS125 4.8 32.2 1.0 CE C:LYS134 4.8 34.2 1.0 CE2 C:TYR106 4.9 30.8 1.0 C19 C:DBS301 4.9 47.8 1.0 O15 C:DBS302 5.0 70.8 1.0

R.J.Abergel, M.C.Clifton, J.C.Pizarro, J.A.Warner, D.K.Shuh, R.K.Strong, K.N.Raymond. The Siderocalin/Enterobactin Interaction: A Link Between Mammalian Immunity and Bacterial Iron Transport. J.Am.Chem.Soc. V. 130 11524 2008.
ISSN: ISSN 0002-7863
PubMed: 18680288
DOI: 10.1021/JA803524W