Sodium in PDB 3cbc: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin, PDB code: 3cbc was solved by M.C.Clifton, J.C.Pizaro, R.K.Strong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.17
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	114.809, 114.809, 118.695, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 25.6

The binding sites of Sodium atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin (pdb code 3cbc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin, PDB code: 3cbc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na180 b:34.6 occ:1.00 O A:HOH400 2.4 48.2 1.0 OH A:TYR138 2.9 26.8 1.0 OG1 A:THR54 3.0 27.7 1.0 CZ A:TYR138 3.8 27.5 1.0 CB A:THR54 3.8 28.0 1.0 CE1 A:TYR138 3.9 27.3 1.0 CG2 A:THR54 4.0 27.5 1.0 OG A:SER68 4.1 30.9 1.0 CE2 A:TYR52 4.1 30.4 1.0 OH A:TYR52 4.2 31.3 1.0 CG2 A:VAL33 4.5 27.7 1.0 CZ A:PHE123 4.6 27.5 1.0 NH2 A:ARG81 4.6 41.8 1.0 CZ A:TYR52 4.6 30.9 1.0 CG2 A:THR136 4.7 28.0 1.0 NZ A:LYS134 4.8 32.3 1.0 OH A:TYR56 4.8 28.6 1.0 CE2 A:PHE123 5.0 27.5 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na180 b:53.5 occ:1.00 O B:HOH353 2.8 46.8 1.0 OH B:TYR138 2.9 46.5 1.0 OG1 B:THR54 3.5 55.7 1.0 CZ B:TYR138 4.0 46.3 1.0 OH B:TYR52 4.1 57.3 1.0 CE2 B:TYR52 4.2 57.3 1.0 CE1 B:TYR138 4.3 46.6 1.0 CG2 B:THR54 4.3 55.7 1.0 CB B:THR54 4.3 55.9 1.0 OG B:SER68 4.4 55.2 0.5 CZ B:PHE123 4.5 39.1 1.0 CG2 B:VAL33 4.7 47.0 1.0 CZ B:TYR52 4.7 57.3 1.0 NZ B:LYS134 4.8 43.4 1.0 OG1 B:THR136 4.8 43.3 0.5 CE2 B:PHE123 4.9 39.0 1.0 OH B:TYR56 4.9 53.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na182 b:60.4 occ:1.00 OD2 C:ASP61 3.0 35.4 1.0 NZ C:LYS59 3.1 38.2 1.0 OG C:SER63 3.4 34.9 1.0 CG2 C:THR82 3.9 29.5 1.0 CG C:ASP61 4.0 35.9 1.0 CB C:SER63 4.1 33.3 1.0 CE C:LYS59 4.1 37.9 1.0 OD1 C:ASP61 4.3 35.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na183 b:62.9 occ:1.00 N C:LYS73 4.1 38.4 1.0 OD1 C:ASP47 4.2 48.1 1.0 CG C:LYS73 4.8 40.0 1.0 CA C:LYS73 4.8 38.8 1.0 CA C:ARG72 4.9 37.2 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) Y106F Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na184 b:36.9 occ:1.00 OH C:TYR138 2.9 24.3 1.0 OG1 C:THR54 3.0 25.3 1.0 CZ C:TYR138 3.9 25.1 1.0 CB C:THR54 3.9 25.4 1.0 CE1 C:TYR138 3.9 24.4 1.0 OH C:TYR52 4.0 29.0 1.0 CE2 C:TYR52 4.0 28.0 1.0 CG2 C:THR54 4.1 25.1 1.0 OG C:SER68 4.2 29.1 1.0 CZ C:PHE123 4.2 19.8 1.0 CG2 C:THR136 4.3 22.4 1.0 CZ C:TYR52 4.5 28.5 1.0 CG2 C:VAL33 4.5 22.6 1.0 NZ C:LYS134 4.5 27.7 1.0 CE2 C:PHE123 4.6 20.9 1.0 OH C:TYR56 4.8 24.7 1.0 CE1 C:PHE123 4.9 20.5 1.0 OG1 C:THR136 5.0 22.9 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