Iron in PDB 3cmp: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant Complexed with Ferric Enterobactin

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant Complexed with Ferric Enterobactin, PDB code: 3cmp was solved by M.C.Clifton, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.96 / 2.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.908, 114.908, 118.832, 90.00, 90.00, 90.00
R / Rfree (%)	24.8 / 30.4

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant Complexed with Ferric Enterobactin also contains other interesting chemical elements:

Sodium

(Na)

7 atoms

The binding sites of Iron atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant Complexed with Ferric Enterobactin (pdb code 3cmp). 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) K125A Mutant Complexed with Ferric Enterobactin, PDB code: 3cmp:
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) K125A Mutant 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) K125A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe179 b:60.0 occ:1.00 O3 A:EB4183 1.9 63.1 1.0 O1 A:EB4183 2.1 57.1 1.0 O5 A:EB4183 2.3 59.8 1.0 O4 A:EB4183 2.3 56.5 1.0 O2 A:EB4183 2.3 58.8 1.0 O6 A:EB4183 2.7 62.7 1.0 C1 A:EB4183 3.0 57.0 1.0 C3 A:EB4183 3.0 63.2 1.0 C4 A:EB4183 3.0 56.6 1.0 C5 A:EB4183 3.1 59.4 1.0 C2 A:EB4183 3.1 59.3 1.0 C6 A:EB4183 3.3 63.1 1.0 OH A:TYR106 4.1 22.4 1.0 NZ A:LYS134 4.2 23.1 1.0 O12 A:EB4183 4.2 63.3 1.0 C18 A:EB4183 4.2 63.3 1.0 C16 A:EB4183 4.3 57.5 1.0 C7 A:EB4183 4.4 56.7 1.0 C8 A:EB4183 4.4 59.2 1.0 C17 A:EB4183 4.5 59.6 1.0 NE1 A:TRP79 4.5 35.2 1.0 C9 A:EB4183 4.7 63.2 1.0 CE A:LYS134 4.7 23.0 1.0 C21 A:EB4183 4.7 63.4 1.0 N1 A:EB4183 4.7 59.8 1.0 CE2 A:TYR106 4.7 22.6 1.0 O10 A:EB4183 4.8 61.9 1.0 CZ A:TYR106 4.9 22.4 1.0 C19 A:EB4183 4.9 58.5 1.0 N3 A:EB4183 4.9 62.8 1.0 CZ2 A:TRP79 5.0 35.3 1.0

Iron binding site 2 out of 3 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant 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) K125A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe179 b:0.0 occ:1.00 O3 B:DBH303 2.1 60.5 1.0 O3 B:DBH304 2.3 96.5 1.0 O6 B:DBH304 2.6 96.5 1.0 O6 B:DBH303 2.7 59.8 1.0 C3 B:DBH304 3.0 96.5 1.0 C3 B:DBH303 3.1 60.4 1.0 C6 B:DBH304 3.1 96.5 1.0 C6 B:DBH303 3.3 60.1 1.0 NZ B:LYS134 3.5 61.7 1.0 C18 B:DBH304 4.3 96.5 1.0 CE B:LYS134 4.3 62.0 1.0 C18 B:DBH303 4.4 60.5 1.0 C9 B:DBH304 4.4 96.4 1.0 O17 B:DBH303 4.6 60.7 1.0 O17 B:DBH304 4.6 96.2 1.0 C9 B:DBH303 4.7 60.1 1.0 OH B:TYR106 4.7 55.6 1.0 C21 B:DBH304 4.9 96.3 1.0 C21 B:DBH303 4.9 60.7 1.0

Iron binding site 3 out of 3 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant 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) K125A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe179 b:50.0 occ:1.00 O6 C:EB4186 1.9 47.9 1.0 O1 C:EB4186 2.0 55.6 1.0 O2 C:EB4186 2.1 53.4 1.0 O5 C:EB4186 2.1 52.5 1.0 O4 C:EB4186 2.2 56.1 1.0 O3 C:EB4186 2.3 47.3 1.0 C6 C:EB4186 2.8 47.8 1.0 C1 C:EB4186 2.8 56.0 1.0 C2 C:EB4186 2.8 53.5 1.0 C5 C:EB4186 2.9 53.1 1.0 C4 C:EB4186 2.9 55.9 1.0 C3 C:EB4186 3.0 47.9 1.0 OH C:TYR106 3.9 23.1 1.0 NZ C:LYS134 4.0 22.9 1.0 C9 C:EB4186 4.1 47.9 1.0 C16 C:EB4186 4.2 56.3 1.0 C17 C:EB4186 4.2 53.9 1.0 C8 C:EB4186 4.2 53.1 1.0 C7 C:EB4186 4.3 56.0 1.0 C18 C:EB4186 4.3 48.7 1.0 CE2 C:TYR106 4.5 22.3 1.0 NE1 C:TRP79 4.5 35.0 1.0 N1 C:EB4186 4.7 57.0 1.0 CZ C:TYR106 4.7 22.4 1.0 N2 C:EB4186 4.8 55.2 1.0 CE C:LYS134 4.8 22.7 1.0 C19 C:EB4186 4.8 56.7 1.0 C20 C:EB4186 4.9 54.5 1.0 CZ2 C:TRP79 4.9 35.2 1.0

M.C.Clifton, P.B.Rupert, T.M.Hoette, K.N.Raymond, R.J.Abergel, R.K.Strong. Parsing the Functional Specificity of Siderocalin / Lipocalin 2 / Ngal For Siderophores and Related Small-Molecule Ligands To Be Published.