Sodium 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:

Iron

(Fe)

3 atoms

The binding sites of Sodium 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 Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Siderocalin (Ngal, Lipocalin 2) K125A Mutant Complexed with Ferric Enterobactin, PDB code: 3cmp:
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 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 Mutant Complexed with Ferric Enterobactin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na180 b:34.8 occ:1.00 O10 A:EB4183 3.2 61.9 1.0 NZ A:LYS134 3.3 23.1 1.0 OH A:TYR52 3.6 27.1 1.0 C6 A:EB4183 3.9 63.1 1.0 C9 A:EB4183 4.0 63.2 1.0 CD1 A:LEU36 4.1 23.8 1.0 C3 A:EB4183 4.2 63.2 1.0 C12 A:EB4183 4.2 63.4 1.0 CD A:LYS134 4.4 22.7 1.0 O6 A:EB4183 4.4 62.7 1.0 O1 A:EB4183 4.4 57.1 1.0 CD1 A:ILE41 4.4 32.5 1.0 CE A:LYS134 4.4 23.0 1.0 C25 A:EB4183 4.4 61.6 1.0 C18 A:EB4183 4.4 63.3 1.0 C15 A:EB4183 4.5 63.3 1.0 CD2 A:LEU36 4.5 24.2 1.0 CZ A:TYR52 4.6 26.7 1.0 O4 A:SO4181 4.8 62.0 1.0 O3 A:EB4183 4.8 63.1 1.0 CE1 A:TYR52 4.9 26.6 1.0 CG A:LEU36 4.9 23.8 1.0

Sodium binding site 2 out of 7 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 Sodium with other atoms in the Na 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:Na180 b:34.2 occ:1.00 OG1 B:THR54 3.1 63.1 1.0 CB B:THR54 3.9 63.2 1.0 CG2 B:THR54 4.3 63.1 1.0 CZ B:PHE123 4.5 61.4 1.0 CE2 B:PHE123 4.6 61.4 1.0 CG2 B:THR136 4.7 62.2 1.0 OG1 B:THR136 4.8 62.4 1.0 OG B:SER68 4.8 66.2 1.0

Sodium binding site 3 out of 7 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 Sodium with other atoms in the Na 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:Na180 b:24.3 occ:1.00 OH C:TYR138 2.9 20.4 1.0 OG1 C:THR54 3.3 24.3 1.0 CZ C:TYR138 3.9 20.9 1.0 OH C:TYR52 4.0 26.6 1.0 NH2 C:ARG81 4.0 31.2 1.0 CE1 C:TYR138 4.0 20.8 1.0 CE2 C:TYR52 4.1 26.0 1.0 CG2 C:THR136 4.2 21.0 1.0 C8 C:EB4186 4.2 53.1 1.0 CZ C:PHE123 4.2 21.5 1.0 CB C:THR54 4.3 24.5 1.0 OG C:SER68 4.3 26.5 1.0 NZ C:LYS134 4.4 22.9 1.0 CG2 C:THR54 4.5 23.7 1.0 CG2 C:VAL33 4.5 19.3 1.0 CZ C:TYR52 4.5 26.1 1.0 CE2 C:PHE123 4.7 21.6 1.0 CE C:LYS134 4.8 22.7 1.0 CE1 C:PHE123 4.8 21.4 1.0 OG1 C:THR136 4.9 22.0 1.0 CB C:THR136 4.9 21.0 1.0 OH C:TYR56 4.9 25.0 1.0 O5 C:EB4186 5.0 52.5 1.0

Sodium binding site 4 out of 7 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 Sodium with other atoms in the Na binding site number 4 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:Na181 b:31.7 occ:1.00 NZ C:LYS134 3.2 22.9 1.0 OH C:TYR52 3.5 26.6 1.0 CD1 C:LEU36 3.9 23.6 1.0 C17 C:EB4186 4.0 53.9 1.0 C2 C:EB4186 4.1 53.5 1.0 C14 C:EB4186 4.1 53.7 1.0 C5 C:EB4186 4.1 53.1 1.0 C11 C:EB4186 4.2 53.3 1.0 C8 C:EB4186 4.2 53.1 1.0 CD C:LYS134 4.2 22.5 1.0 CE C:LYS134 4.3 22.7 1.0 CZ C:TYR52 4.4 26.1 1.0 O3 C:EB4186 4.4 47.3 1.0 CD1 C:ILE41 4.5 32.6 1.0 N2 C:EB4186 4.7 55.2 1.0 O2 C:EB4186 4.7 53.4 1.0 CD2 C:LEU36 4.7 23.9 1.0 C20 C:EB4186 4.7 54.5 1.0 CG C:LEU36 4.8 23.5 1.0 O5 C:EB4186 4.8 52.5 1.0 CE1 C:TYR52 4.8 26.2 1.0 O14 C:EB4186 4.9 54.8 1.0

Sodium binding site 5 out of 7 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 Sodium with other atoms in the Na binding site number 5 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:Na182 b:41.1 occ:1.00 ND2 C:ASN114 3.9 23.6 1.0 CB C:ASN114 4.1 22.6 1.0 NE2 C:HIS118 4.5 25.1 1.0 CG C:ASN114 4.6 23.0 1.0 NE2 A:GLN117 4.7 27.8 1.0

Sodium binding site 6 out of 7 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 Sodium with other atoms in the Na binding site number 6 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:Na183 b:48.6 occ:1.00 CG C:ARG72 4.1 33.9 1.0 N C:LYS73 4.2 31.7 1.0 CA C:ARG72 4.4 31.5 1.0 OD2 C:ASP47 4.6 41.3 1.0 O C:PHE71 4.7 30.0 1.0 C C:ARG72 4.8 31.6 1.0 CB C:ARG72 4.9 31.9 1.0

Sodium binding site 7 out of 7 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 Sodium with other atoms in the Na binding site number 7 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:Na184 b:52.7 occ:1.00 CD1 C:PHE168 4.2 24.6 1.0 CB C:PHE168 4.4 24.6 1.0 O C:HOH207 4.4 33.0 1.0 CG C:PHE168 4.6 24.4 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.