Atomistry » Sodium » PDB 1ph7-1qsx » 1qjs
Atomistry »
  Sodium »
    PDB 1ph7-1qsx »
      1qjs »

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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Go back to Sodium Binding Sites List in 1qjs
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy