Sodium in PDB 7li0: Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation

The structure of Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation, PDB code: 7li0 was solved by C.Chan, D.Ng, M.E.Fraser, A.B.Schryvers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.61 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	62.06, 67.83, 73.53, 91.28, 91.59, 105.82
R / Rfree (%)	19.3 / 22.3

The binding sites of Sodium atom in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation (pdb code 7li0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation, PDB code: 7li0:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation


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 Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.3 occ:1.00 OD1 A:ASN152 2.7 24.6 1.0 OD1 A:ASP288 2.7 24.4 1.0 CD A:LYS223 3.0 47.7 1.0 O A:HOH676 3.0 39.2 1.0 CG A:ASP288 3.6 24.0 1.0 CG A:ASN152 3.6 24.4 1.0 CB A:ILE290 3.6 21.8 1.0 OD2 A:ASP288 3.6 23.6 1.0 ND2 A:ASN152 3.8 21.3 1.0 CB A:LYS223 3.9 39.1 1.0 CG A:LYS223 4.0 43.5 1.0 N A:ILE290 4.1 23.0 1.0 CA A:ILE290 4.2 22.1 1.0 SD D:MET304 4.3 31.6 1.0 O A:HOH523 4.3 30.5 1.0 CD1 A:ILE290 4.3 22.9 1.0 CG1 A:ILE290 4.3 23.6 1.0 CE D:MET304 4.4 31.4 1.0 CG2 A:ILE290 4.4 22.9 1.0 CB A:ASN152 4.9 21.9 1.0 N A:PHE289 5.0 24.6 1.0 CB A:ASP288 5.0 22.6 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation


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 Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:47.2 occ:1.00 O A:HOH545 2.6 40.9 1.0 OG A:SER118 2.7 22.7 1.0 OD2 A:ASP122 2.8 33.0 1.0 O A:GLU116 3.1 25.8 1.0 O A:HOH579 3.3 35.0 1.0 CB A:SER118 3.4 20.9 1.0 CG A:ASP122 3.5 32.8 1.0 O A:HOH546 3.6 47.4 1.0 N A:SER118 3.7 19.2 1.0 C A:LEU117 3.7 22.0 1.0 C A:GLU116 3.8 23.9 1.0 O A:LEU117 4.0 20.8 1.0 CA A:LEU117 4.1 23.2 1.0 CB A:ASP122 4.1 27.8 1.0 N A:LEU117 4.1 22.7 1.0 NZ A:LYS127 4.1 29.9 1.0 CA A:SER118 4.2 20.3 1.0 O A:HOH610 4.3 22.9 1.0 OD1 A:ASP122 4.3 34.7 1.0 O A:HOH590 4.4 39.7 1.0 CA A:GLU116 4.8 25.7 1.0 CE A:LYS127 4.8 31.3 1.0 O A:SER115 4.9 25.9 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation


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 Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:55.5 occ:1.00 O A:HOH521 2.5 43.8 1.0 O A:ALA124 2.8 31.2 1.0 O A:GLY164 3.2 29.2 1.0 OD1 A:ASN168 3.3 32.6 1.0 CA A:GLY164 3.5 28.5 1.0 ND2 A:ASN168 3.5 25.5 1.0 CG A:ASN168 3.6 28.9 1.0 C A:GLY164 3.7 28.1 1.0 CB A:ALA167 3.8 30.2 1.0 C A:ALA124 3.8 30.0 1.0 CA A:ALA124 4.4 29.2 1.0 N A:PRO126 4.4 34.6 1.0 CA A:PRO126 4.5 34.6 1.0 C A:ASP125 4.5 32.9 1.0 O A:ASP125 4.5 32.8 1.0 N A:ASN168 4.7 32.1 1.0 CB A:ALA124 4.7 28.0 1.0 CB A:ASN168 4.8 27.4 1.0 N A:GLY164 4.8 28.5 1.0 CA A:ALA167 4.9 30.9 1.0 CD A:PRO126 4.9 35.0 1.0 C A:ALA167 4.9 31.6 1.0 N A:ASP125 4.9 28.0 1.0 N A:TRP165 4.9 27.9 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation


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 Apo Moraxella Catarrhalis Ferric Binding Protein A in An Open Conformation within 5.0Å range: probe atom residue distance (Å) B Occ C:Na403 b:45.6 occ:1.00 O C:HOH623 2.5 31.9 1.0 O C:HOH659 2.8 30.9 1.0 O D:HOH667 2.9 40.7 1.0 O C:LYS81 2.9 32.4 1.0 O C:ILE84 3.3 29.2 1.0 O C:SER82 3.6 33.9 1.0 CA C:PRO85 3.8 26.4 1.0 C C:ILE84 3.9 27.3 1.0 NH2 C:ARG89 3.9 34.8 1.0 C C:LYS81 4.1 33.3 1.0 N C:PRO85 4.1 26.0 1.0 O C:HOH555 4.1 48.7 1.0 C C:SER82 4.1 34.5 1.0 CG D:GLU46 4.1 32.7 1.0 O D:HOH551 4.3 28.3 1.0 CA C:SER82 4.4 35.8 1.0 N C:SER86 4.4 29.2 1.0 C C:PRO85 4.5 30.8 1.0 O C:HOH661 4.5 28.3 1.0 N C:ILE84 4.7 28.6 1.0 N C:SER82 4.7 36.2 1.0 O D:HOH586 4.8 40.3 1.0 OE2 D:GLU46 4.8 32.5 1.0 CD D:GLU46 4.9 34.6 1.0 CB C:PRO85 4.9 24.2 1.0 CZ C:ARG89 5.0 34.7 1.0 CA C:ILE84 5.0 26.0 1.0

C.Chan, D.Ng, M.E.Fraser, A.B.Schryvers. Structural and Functional Insights Into Iron Acquisition From Lactoferrin and Transferrin in Gram-Negative Bacterial Pathogens. Biometals 2022.
ISSN: ESSN 1572-8773
PubMed: 36418809
DOI: 10.1007/S10534-022-00466-6