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Sodium in PDB 1qjs: Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem

Protein crystallography data

The structure of Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem, PDB code: 1qjs 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 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.900, 69.900, 151.810, 90.00, 108.16, 90.00
R / Rfree (%) 25.5 / 31.2

Other elements in 1qjs:

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

Iron (Fe) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem (pdb code 1qjs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem, PDB code: 1qjs:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 1qjs

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Sodium binding site 1 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na512

b:33.2
occ:1.00
 O A:THR166 2.3 35.3 1.0
O A:ASP121 2.3 40.2 1.0
O A:ASP34 2.4 37.9 1.0
O A:ASP75 2.6 33.7 1.0
C A:ASP121 3.3 39.3 1.0
C A:THR166 3.4 35.5 1.0
C A:ASP34 3.5 38.1 1.0
C A:ASP75 3.8 35.4 1.0
CA A:ASP121 3.8 39.2 1.0
CA A:ASP34 4.1 36.1 1.0
N A:SER167 4.4 34.7 1.0
N A:ALA122 4.4 38.1 1.0
CA A:THR166 4.4 36.1 1.0
CA A:ASP75 4.4 39.0 1.0
CA A:SER167 4.4 34.5 1.0
N A:ALA35 4.5 39.8 1.0
CB A:SER167 4.5 23.1 1.0
O A:LEU120 4.6 39.3 1.0
CB A:ASP121 4.6 49.9 1.0
CA A:ALA35 4.7 39.0 1.0
CA A:ALA122 4.7 37.1 1.0
CB A:ASP34 4.8 47.4 1.0
N A:ALA76 4.8 31.3 1.0
O A:VAL74 4.9 42.0 1.0
O A:PHE33 4.9 37.8 1.0
N A:ASP121 4.9 40.5 1.0
CB A:THR166 5.0 29.1 1.0
CB A:ALA35 5.0 35.2 1.0

Sodium binding site 2 out of 8 in 1qjs

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Sodium binding site 2 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na513

b:32.4
occ:1.00
 O A:ALA168 2.0 28.6 1.0
O A:ALA77 2.2 31.9 1.0
O A:ALA123 2.4 34.0 1.0
O A:THR36 2.6 33.7 1.0
CL A:CL511 3.1 26.7 1.0
C A:ALA168 3.2 31.4 1.0
C A:ALA77 3.5 31.5 1.0
C A:ALA123 3.6 34.0 1.0
C A:THR36 3.9 35.1 1.0
N A:ALA168 4.1 33.5 1.0
N A:LEU169 4.2 31.9 1.0
CA A:ALA168 4.2 31.1 1.0
OG1 A:THR36 4.2 17.6 1.0
CA A:LEU169 4.3 31.4 1.0
N A:ALA123 4.3 35.3 1.0
N A:ALA77 4.3 29.7 1.0
N A:PHE78 4.4 32.2 1.0
CA A:ALA77 4.4 29.8 1.0
N A:VAL124 4.5 33.1 1.0
CA A:VAL124 4.5 32.9 1.0
CA A:PHE78 4.5 34.5 1.0
CA A:ALA123 4.5 34.7 1.0
N A:THR36 4.5 41.0 1.0
CB A:LEU169 4.6 24.1 1.0
CB A:THR37 4.6 24.7 1.0
CA A:THR37 4.7 30.7 1.0
CB A:PHE78 4.7 37.7 1.0
CA A:THR36 4.7 35.1 1.0
CB A:ALA168 4.7 46.2 1.0
N A:THR37 4.8 33.9 1.0
CB A:ALA77 4.9 18.2 1.0
CB A:ALA123 5.0 35.4 1.0

Sodium binding site 3 out of 8 in 1qjs

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Sodium binding site 3 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na522

b:26.0
occ:1.00
 O A:ALA379 2.2 24.3 1.0
O A:ALA336 2.3 33.9 1.0
O A:ALA284 2.4 22.1 1.0
O A:MET239 2.6 25.4 1.0
CL A:CL521 2.9 20.4 1.0
O4 A:PO4501 2.9 19.7 0.5
O2 A:PO4501 3.2 20.9 0.5
C A:ALA379 3.4 26.7 1.0
C A:ALA336 3.5 27.9 1.0
C A:ALA284 3.6 25.5 1.0
C A:MET239 3.7 24.9 1.0
P A:PO4501 3.8 20.9 0.5
N A:MET239 4.1 26.0 1.0
N A:ALA379 4.2 22.5 1.0
N A:ALA336 4.3 29.7 1.0
CA A:ALA379 4.3 24.3 1.0
N A:LEU380 4.3 26.5 1.0
CA A:MET239 4.3 22.4 1.0
CB A:MET239 4.4 10.3 1.0
CA A:ALA336 4.4 28.4 1.0
N A:ALA284 4.4 28.8 1.0
CA A:LEU380 4.4 27.9 1.0
N A:PHE337 4.5 27.8 1.0
N A:PHE285 4.5 23.2 1.0
CA A:ALA284 4.5 26.3 1.0
CA A:PHE337 4.5 25.1 1.0
CA A:PHE285 4.6 25.1 1.0
N A:VAL240 4.6 27.7 1.0
O3 A:PO4501 4.6 20.0 0.5
CB A:PHE337 4.7 27.2 1.0
CA A:VAL240 4.7 25.8 1.0
CB A:ALA379 4.8 20.0 1.0
CB A:ALA336 4.8 21.9 1.0
CB A:ALA284 4.9 33.6 1.0
CB A:PHE285 4.9 12.5 1.0
O1 A:PO4501 5.0 18.3 0.5

Sodium binding site 4 out of 8 in 1qjs

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Sodium binding site 4 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na523

b:27.7
occ:1.00
 O A:ASP334 2.0 29.0 1.0
O A:ASP282 2.1 21.7 1.0
O A:SER237 2.3 27.7 1.0
O A:ASP377 2.6 22.1 1.0
C A:ASP334 3.1 29.9 1.0
C A:ASP282 3.2 27.9 1.0
C A:SER237 3.3 24.3 1.0
C A:ASP377 3.6 27.6 1.0
CA A:ASP334 3.7 30.9 1.0
CA A:ASP282 3.8 26.3 1.0
CA A:SER237 3.8 22.4 1.0
N A:ALA335 4.2 30.0 1.0
CB A:SER237 4.2 16.1 1.0
N A:ALA283 4.3 30.7 1.0
N A:ALA238 4.4 25.4 1.0
CA A:ASP377 4.4 27.0 1.0
N A:GLY378 4.5 27.5 1.0
CA A:ALA335 4.5 28.2 1.0
CB A:ASP282 4.5 24.3 1.0
CA A:GLY378 4.5 24.9 1.0
O A:VAL333 4.6 26.9 1.0
CA A:ALA283 4.6 30.1 1.0
CB A:ASP334 4.7 36.1 1.0
CA A:ALA238 4.7 23.3 1.0
N A:ASP334 4.8 32.6 1.0
CB A:ALA283 5.0 18.2 1.0

Sodium binding site 5 out of 8 in 1qjs

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Sodium binding site 5 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 5 of Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na512

b:33.2
occ:1.00
 O B:THR166 2.2 34.5 1.0
O B:ASP34 2.4 38.0 1.0
O B:ASP121 2.4 40.0 1.0
O B:ASP75 2.8 33.8 1.0
C B:ASP121 3.3 39.0 1.0
C B:THR166 3.4 35.4 1.0
C B:ASP34 3.5 38.1 1.0
CA B:ASP121 3.8 39.1 1.0
C B:ASP75 3.9 35.2 1.0
CA B:ASP34 4.1 35.5 1.0
CA B:THR166 4.3 35.8 1.0
N B:SER167 4.3 34.6 1.0
N B:ALA122 4.4 38.1 1.0
CA B:SER167 4.4 34.0 1.0
CA B:ASP75 4.5 38.6 1.0
N B:ALA35 4.5 39.9 1.0
CB B:SER167 4.6 27.3 1.0
CB B:ASP121 4.7 40.9 1.0
O B:LEU120 4.7 39.1 1.0
CA B:ALA35 4.7 38.6 1.0
CB B:ASP34 4.8 30.3 1.0
CA B:ALA122 4.8 36.8 1.0
O B:PHE33 4.9 37.3 1.0
CB B:THR166 4.9 25.4 1.0
O B:VAL74 4.9 41.5 1.0
N B:ALA76 4.9 31.0 1.0
CB B:ALA35 5.0 29.3 1.0
N B:ASP121 5.0 40.3 1.0

Sodium binding site 6 out of 8 in 1qjs

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Sodium binding site 6 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 6 of Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na513

b:32.4
occ:1.00
 O B:ALA168 2.0 28.6 1.0
O B:ALA77 2.3 31.1 1.0
O B:ALA123 2.4 33.7 1.0
O B:THR36 2.6 33.3 1.0
CL B:CL511 3.1 26.7 1.0
C B:ALA168 3.3 31.4 1.0
C B:ALA77 3.4 30.7 1.0
C B:ALA123 3.6 33.4 1.0
C B:THR36 3.8 35.0 1.0
N B:ALA168 4.1 33.8 1.0
OG1 B:THR36 4.2 26.1 1.0
CA B:ALA168 4.2 31.3 1.0
N B:LEU169 4.2 31.9 1.0
N B:ALA77 4.3 29.5 1.0
N B:ALA123 4.3 34.6 1.0
CA B:LEU169 4.3 31.3 1.0
CA B:ALA77 4.4 29.3 1.0
N B:PHE78 4.4 32.0 1.0
N B:THR36 4.4 41.0 1.0
CA B:PHE78 4.5 34.0 1.0
CA B:ALA123 4.5 34.1 1.0
N B:VAL124 4.5 33.0 1.0
CA B:VAL124 4.5 32.7 1.0
CB B:THR37 4.6 25.1 1.0
CA B:THR36 4.6 35.2 1.0
CB B:LEU169 4.7 16.0 1.0
CA B:THR37 4.7 30.4 1.0
N B:THR37 4.7 33.8 1.0
CB B:ALA168 4.8 24.0 1.0
CB B:PHE78 4.8 25.6 1.0
CB B:ALA77 4.8 12.5 1.0

Sodium binding site 7 out of 8 in 1qjs

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Sodium binding site 7 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 7 of Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na522

b:26.0
occ:1.00
 O B:ALA379 2.2 24.6 1.0
O B:ALA336 2.2 34.1 1.0
O B:ALA284 2.4 22.6 1.0
O B:MET239 2.7 25.5 1.0
CL B:CL521 2.9 20.4 1.0
O4 B:PO4501 2.9 19.7 0.5
O2 B:PO4501 3.2 20.9 0.5
C B:ALA379 3.4 26.8 1.0
C B:ALA336 3.4 27.8 1.0
C B:ALA284 3.6 25.4 1.0
C B:MET239 3.7 24.8 1.0
P B:PO4501 3.8 20.9 0.5
N B:ALA379 4.2 22.7 1.0
N B:ALA336 4.2 29.7 1.0
N B:MET239 4.2 25.7 1.0
CA B:ALA379 4.3 24.5 1.0
CA B:ALA336 4.3 28.1 1.0
N B:LEU380 4.3 26.4 1.0
N B:ALA284 4.4 29.0 1.0
N B:PHE337 4.4 27.7 1.0
CA B:MET239 4.4 22.5 1.0
CB B:MET239 4.4 18.2 1.0
CA B:LEU380 4.5 28.0 1.0
CA B:PHE337 4.5 24.5 1.0
N B:PHE285 4.5 23.5 1.0
CA B:ALA284 4.5 26.2 1.0
CA B:PHE285 4.5 25.5 1.0
CB B:PHE337 4.6 25.0 1.0
O3 B:PO4501 4.6 20.0 0.5
N B:VAL240 4.6 27.6 1.0
CB B:ALA336 4.7 18.2 1.0
CB B:ALA379 4.7 10.5 1.0
CA B:VAL240 4.8 25.9 1.0
CB B:ALA284 4.8 22.1 1.0
CB B:PHE285 4.8 20.5 1.0
O1 B:PO4501 5.0 18.3 0.5

Sodium binding site 8 out of 8 in 1qjs

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Sodium binding site 8 out of 8 in the Mammalian Blood Serum Haemopexin Glycosylated-Native Protein 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 8 of Mammalian Blood Serum Haemopexin Glycosylated-Native Protein and in Complex with Its Ligand Haem within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na523

b:27.7
occ:1.00
 O B:ASP334 2.0 29.5 1.0
O B:ASP282 2.2 21.9 1.0
O B:SER237 2.3 26.7 1.0
O B:ASP377 2.5 22.8 1.0
C B:ASP334 3.1 30.2 1.0
C B:ASP282 3.2 28.0 1.0
C B:SER237 3.3 24.2 1.0
C B:ASP377 3.5 27.6 1.0
CA B:SER237 3.7 22.8 1.0
CA B:ASP334 3.8 30.7 1.0
CA B:ASP282 3.9 26.3 1.0
CB B:SER237 4.1 23.2 1.0
N B:ALA335 4.2 29.8 1.0
N B:ALA283 4.3 31.2 1.0
CA B:ASP377 4.3 27.3 1.0
N B:ALA238 4.3 25.6 1.0
N B:GLY378 4.4 27.2 1.0
CA B:GLY378 4.5 24.8 1.0
CA B:ALA335 4.5 27.8 1.0
CB B:ASP282 4.6 24.4 1.0
CA B:ALA283 4.7 30.4 1.0
O B:VAL333 4.7 27.2 1.0
CA B:ALA238 4.7 23.7 1.0
CB B:ASP334 4.7 25.6 1.0
N B:ASP334 4.9 32.5 1.0

Reference:

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
Page generated: Sun Oct 6 21:31:41 2024

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