Sodium in PDB 3hwd: Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin

The structure of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin, PDB code: 3hwd was solved by M.C.Clifton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.95
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	115.825, 115.825, 119.316, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 30.3

The binding sites of Sodium atom in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin (pdb code 3hwd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin, PDB code: 3hwd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant 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) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na179 b:22.4 occ:1.00 CB A:ALA134 4.3 26.3 1.0 CB A:PHE123 4.3 26.1 1.0 CB A:ALA125 4.6 28.9 1.0 N A:ALA134 4.8 26.8 1.0 CE2 A:TYR106 4.9 30.3 1.0 OH A:TYR106 4.9 30.7 1.0 CB A:TYR132 4.9 29.7 1.0

Sodium binding site 2 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant 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) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na179 b:44.7 occ:1.00 NZ C:LYS75 3.7 38.7 1.0 CE C:LYS75 4.2 39.1 1.0

Sodium binding site 3 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant 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) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na180 b:38.1 occ:1.00 NE2 C:HIS165 3.7 34.5 1.0 CD2 C:HIS165 4.1 34.5 1.0 CG C:PRO162 4.6 33.8 1.0 OD1 C:ASN164 4.7 36.7 1.0 ND2 C:ASN164 4.8 36.1 1.0 CD1 C:ILE8 5.0 34.3 1.0 CE1 C:HIS165 5.0 34.2 1.0

Sodium binding site 4 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant 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) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na181 b:44.5 occ:1.00 O C:ASN129 3.5 34.2 1.0 CG1 C:VAL126 3.9 30.1 1.0 C C:ASN129 4.0 34.3 1.0 CA C:ASN129 4.5 34.5 1.0 CG2 C:VAL126 4.5 30.3 1.0 CB C:GLU131 4.5 31.9 1.0 N C:GLU131 4.6 32.4 1.0 N C:ARG130 4.7 34.0 1.0 CB C:VAL126 4.9 30.3 1.0 CB C:ASN129 5.0 34.7 1.0 C C:ARG130 5.0 33.0 1.0 CA C:GLU131 5.0 31.9 1.0

Sodium binding site 5 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant 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) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na182 b:43.8 occ:1.00 NZ C:LYS149 4.2 38.5 1.0 CB C:PHE168 4.4 31.2 1.0 O C:HOH186 4.4 23.5 1.0 CD1 C:PHE168 4.5 30.6 1.0 CG C:PHE168 4.8 31.0 1.0

Sodium binding site 6 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na183 b:46.8 occ:1.00 N C:LYS73 4.2 37.5 1.0 CA C:ARG72 4.8 37.0 1.0 CA C:LYS73 5.0 37.7 1.0

Sodium binding site 7 out of 7 in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A-K134A Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ C:Na184 b:64.8 occ:0.50 OE2 C:GLU91 3.5 28.7 1.0 OE1 C:GLU91 3.8 29.9 1.0 CD C:GLU91 4.1 28.9 1.0 CB C:SER87 4.2 29.1 1.0 CG C:GLN88 4.4 31.6 1.0 NE2 C:GLN88 4.6 34.3 1.0 OG C:SER87 4.6 28.5 1.0 NH2 C:ARG109 4.7 26.8 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.