Sodium in PDB 1qhu: Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem

The structure of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem, PDB code: 1qhu was solved by M.Paoli, H.M.Baker, W.T.Morgan, A.Smith, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.680, 61.950, 83.290, 90.00, 93.21, 90.00
R / Rfree (%)	20.7 / 28.9

The structure of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem also contains other interesting chemical elements:

Iron	(Fe)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem (pdb code 1qhu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem, PDB code: 1qhu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range: probe atom residue distance (Å) B Occ A:Na436 b:33.2 occ:1.00 O A:ASP34 2.3 30.7 1.0 O A:ASP121 2.4 40.4 1.0 O A:THR166 2.4 32.5 1.0 O A:HOH526 2.5 33.7 1.0 O A:ASP75 2.6 28.7 1.0 C A:THR166 3.4 32.3 1.0 C A:ASP121 3.4 38.7 1.0 C A:ASP34 3.5 30.1 1.0 C A:ASP75 3.7 30.2 1.0 CA A:ASP121 4.1 39.3 1.0 CA A:ASP34 4.2 29.2 1.0 CA A:THR166 4.2 31.8 1.0 N A:SER167 4.3 30.8 1.0 CA A:ASP75 4.4 32.5 1.0 N A:ALA122 4.4 36.7 1.0 CA A:SER167 4.5 30.0 1.0 N A:ALA35 4.5 30.4 1.0 O A:HOH598 4.5 38.3 1.0 CA A:ALA35 4.6 30.2 1.0 CA A:ALA122 4.6 35.4 1.0 CB A:ALA35 4.7 29.7 1.0 N A:ALA76 4.8 28.4 1.0 CB A:SER167 4.8 29.3 1.0 O A:VAL74 4.8 36.8 1.0 O A:LEU120 4.9 36.6 1.0 CB A:ASP121 4.9 40.6 1.0 CB A:ASP34 4.9 28.7 1.0 CB A:ALA122 5.0 34.0 1.0 CA A:ALA76 5.0 27.1 1.0

Sodium binding site 2 out of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range: probe atom residue distance (Å) B Occ A:Na437 b:32.4 occ:1.00 O A:ALA168 2.2 23.7 1.0 O A:ALA123 2.4 30.4 1.0 O A:THR36 2.4 28.8 1.0 O A:ALA77 2.5 26.3 1.0 O A:HOH502 2.6 23.5 1.0 CL A:CL435 3.1 26.7 1.0 C A:ALA168 3.4 23.7 1.0 C A:THR36 3.6 27.0 1.0 C A:ALA77 3.6 26.7 1.0 C A:ALA123 3.6 31.4 1.0 OG1 A:THR36 4.0 23.2 1.0 N A:ALA168 4.2 28.0 1.0 CA A:ALA168 4.2 25.6 1.0 N A:LEU169 4.2 25.1 1.0 N A:THR36 4.3 27.6 1.0 CA A:LEU169 4.3 23.5 1.0 CB A:ALA168 4.4 25.1 1.0 N A:ALA123 4.4 32.9 1.0 CA A:VAL124 4.4 30.3 1.0 CA A:PHE78 4.4 30.5 1.0 N A:ALA77 4.5 25.1 1.0 CA A:THR36 4.5 27.2 1.0 N A:VAL124 4.5 29.5 1.0 N A:PHE78 4.5 29.6 1.0 N A:THR37 4.5 26.1 1.0 CG1 A:VAL124 4.5 29.1 1.0 CB A:PHE78 4.5 31.0 1.0 CA A:ALA77 4.6 25.2 1.0 CB A:THR37 4.6 25.1 1.0 CA A:THR37 4.6 25.8 1.0 CA A:ALA123 4.6 31.9 1.0 CB A:LEU169 4.6 23.1 1.0 CB A:THR36 4.8 26.3 1.0 CB A:ALA77 4.9 22.9 1.0 CB A:VAL124 4.9 28.6 1.0

Sodium binding site 3 out of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range: probe atom residue distance (Å) B Occ A:Na438 b:26.0 occ:1.00 O A:ALA283 2.2 22.5 1.0 O A:ALA378 2.3 19.9 1.0 O A:MET238 2.4 23.1 1.0 O A:ALA335 2.4 18.6 1.0 CL A:CL439 2.9 20.4 1.0 O4 A:PO4441 2.9 19.7 0.5 O2 A:PO4441 3.2 20.9 0.5 C A:ALA283 3.4 23.0 1.0 C A:ALA378 3.4 18.1 1.0 C A:MET238 3.5 22.1 1.0 C A:ALA335 3.6 20.1 1.0 P A:PO4441 3.8 20.9 0.5 N A:MET238 3.9 22.6 1.0 N A:ALA378 4.1 15.6 1.0 N A:ALA283 4.2 22.4 1.0 CA A:MET238 4.2 22.2 1.0 CA A:ALA378 4.2 17.2 1.0 CA A:ALA283 4.3 23.1 1.0 N A:LEU379 4.3 19.0 1.0 N A:PHE284 4.4 22.0 1.0 N A:VAL239 4.4 22.0 1.0 N A:ALA335 4.4 20.6 1.0 CA A:LEU379 4.4 21.1 1.0 CB A:MET238 4.4 22.5 1.0 CA A:ALA335 4.5 21.0 1.0 N A:PHE336 4.5 21.9 1.0 CA A:PHE284 4.5 20.0 1.0 CB A:ALA378 4.6 12.8 1.0 O3 A:PO4441 4.6 20.0 0.5 CA A:PHE336 4.6 21.5 1.0 CA A:VAL239 4.7 22.8 1.0 CB A:ALA283 4.8 22.5 1.0 CG A:MET238 4.8 24.3 1.0 CB A:LEU379 4.8 23.9 1.0 CB A:PHE284 4.9 19.0 1.0 CB A:ALA335 4.9 22.3 1.0 O1 A:PO4441 5.0 18.3 0.5 CD1 A:LEU379 5.0 21.5 1.0

Sodium binding site 4 out of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range: probe atom residue distance (Å) B Occ A:Na440 b:27.7 occ:1.00 O A:SER236 2.2 20.6 1.0 O A:ASP333 2.3 22.4 1.0 O A:ASP376 2.3 21.2 1.0 O A:HOH619 2.3 34.6 1.0 O A:ASP281 2.3 26.4 1.0 C A:SER236 3.2 20.4 1.0 C A:ASP376 3.3 22.3 1.0 C A:ASP333 3.3 23.9 1.0 C A:ASP281 3.3 25.5 1.0 CA A:SER236 3.8 20.8 1.0 CA A:ASP333 3.9 25.4 1.0 CA A:ASP281 4.0 23.8 1.0 CA A:ASP376 4.1 22.3 1.0 N A:GLY377 4.2 21.6 1.0 N A:ALA237 4.2 21.6 1.0 CB A:SER236 4.2 19.6 1.0 CA A:GLY377 4.3 19.1 1.0 N A:ALA334 4.3 22.4 1.0 N A:ALA282 4.3 25.3 1.0 CA A:ALA237 4.5 21.3 1.0 CA A:ALA282 4.6 23.0 1.0 CA A:ALA334 4.6 21.2 1.0 CB A:ASP333 4.7 22.7 1.0 CB A:ALA282 4.7 20.5 1.0 CB A:ALA237 4.8 24.4 1.0 CB A:ASP281 4.8 24.2 1.0 O A:VAL280 4.9 21.3 1.0 CB A:ASP376 5.0 20.9 1.0

M.Paoli, B.F.Anderson, H.M.Baker, W.T.Morgan, A.Smith, E.N.Baker. Crystal Structure of Hemopexin Reveals A Novel High-Affinity Heme Site Formed Between Two Beta-Propeller Domains. Nat.Struct.Biol. V. 6 926 1999.
ISSN: ISSN 1072-8368
PubMed: 10504726
DOI: 10.1038/13294