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Sodium in PDB 3lp9: Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus

Protein crystallography data

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9 was solved by V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.63 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.170, 88.140, 154.530, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 26.6

Other elements in 3lp9:

The structure of Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Calcium (Ca) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus (pdb code 3lp9). 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 LS24, A Seed Albumin From Lathyrus Sativus, PDB code: 3lp9:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3lp9

Go back to Sodium Binding Sites List in 3lp9
Sodium binding site 1 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na318

b:17.1
occ:1.00
OD1 A:ASP69 2.8 15.4 1.0
O A:HOH242 3.0 15.8 1.0
N A:ARG125 3.0 16.1 1.0
N A:ALA179 3.0 15.1 1.0
CA A:TYR124 3.4 15.2 1.0
CA A:PHE178 3.6 15.2 1.0
CB A:ARG125 3.6 16.5 1.0
CB A:ALA179 3.7 14.1 1.0
CB A:TYR124 3.7 15.1 1.0
C A:TYR124 3.7 15.3 1.0
CG A:ASP69 3.8 15.5 1.0
C A:PHE178 3.8 14.8 1.0
CB A:PHE178 3.9 15.3 1.0
CA A:ALA179 3.9 15.2 1.0
CA A:ARG125 4.0 16.3 1.0
OD2 A:ASP69 4.1 14.1 1.0
N A:ARG11 4.4 15.8 1.0
O A:ALA179 4.4 15.6 1.0
N A:ASP69 4.5 15.9 1.0
CB A:PHE68 4.5 15.6 1.0
O A:ALA123 4.6 15.3 1.0
N A:TYR124 4.6 15.3 1.0
CA A:PHE68 4.6 15.7 1.0
CB A:ARG11 4.7 15.3 1.0
C A:ALA179 4.7 16.1 1.0
CA A:PHE10 4.7 15.6 1.0
N A:PHE178 4.8 15.3 1.0
O A:ARG125 4.8 15.8 1.0
C A:ARG125 4.9 15.9 1.0
O A:TYR124 5.0 15.4 1.0
O A:PHE178 5.0 14.7 1.0

Sodium binding site 2 out of 4 in 3lp9

Go back to Sodium Binding Sites List in 3lp9
Sodium binding site 2 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na319

b:17.6
occ:1.00
OD1 B:ASP69 2.7 16.5 1.0
N B:ALA179 3.0 16.1 1.0
N B:ARG125 3.1 15.9 1.0
O B:HOH321 3.1 16.3 1.0
CB B:ARG125 3.4 15.7 1.0
CG B:ASP69 3.6 17.1 1.0
CB B:ALA179 3.7 15.4 1.0
CA B:PHE178 3.7 16.3 1.0
C B:PHE178 3.8 15.7 1.0
CA B:ARG125 3.9 16.1 1.0
CA B:TYR124 3.9 16.2 1.0
CA B:ALA179 3.9 15.3 1.0
OD2 B:ASP69 3.9 16.7 1.0
C B:TYR124 4.0 16.2 1.0
CB B:PHE178 4.0 15.9 1.0
N B:ARG11 4.1 15.9 1.0
O B:ALA179 4.3 16.1 1.0
CB B:TYR124 4.3 15.6 1.0
CB B:ARG11 4.4 15.9 1.0
N B:ASP69 4.4 16.3 1.0
CA B:PHE10 4.5 16.0 1.0
C B:ALA179 4.6 15.9 1.0
O B:ARG125 4.7 15.8 1.0
CA B:PHE68 4.8 16.0 1.0
C B:ARG125 4.8 15.8 1.0
CG B:ARG125 4.8 17.0 1.0
C B:PHE10 4.8 15.9 1.0
CB B:PHE68 4.8 15.7 1.0
CA B:ARG11 4.9 16.1 1.0
CB B:ASP69 4.9 16.1 1.0
CB B:PHE10 5.0 15.8 1.0
NH2 B:ARG11 5.0 18.6 1.0
O B:ALA123 5.0 16.4 1.0

Sodium binding site 3 out of 4 in 3lp9

Go back to Sodium Binding Sites List in 3lp9
Sodium binding site 3 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na320

b:17.0
occ:1.00
OD1 C:ASP69 2.7 17.5 1.0
O C:HOH326 2.9 17.7 1.0
N C:ALA179 3.0 16.5 1.0
N C:ARG125 3.0 16.4 1.0
CA C:TYR124 3.6 15.4 1.0
CB C:ARG125 3.6 15.9 1.0
CA C:PHE178 3.6 16.6 1.0
CB C:ALA179 3.7 15.4 1.0
CG C:ASP69 3.7 16.6 1.0
C C:TYR124 3.8 16.3 1.0
C C:PHE178 3.8 16.6 1.0
CA C:ARG125 3.9 15.6 1.0
CA C:ALA179 3.9 16.0 1.0
CB C:TYR124 4.0 14.7 1.0
CB C:PHE178 4.0 16.1 1.0
OD2 C:ASP69 4.1 16.4 1.0
N C:ARG11 4.2 15.8 1.0
N C:ASP69 4.3 15.7 1.0
CA C:PHE10 4.5 15.7 1.0
O C:ALA179 4.5 17.3 1.0
CA C:PHE68 4.5 16.2 1.0
CB C:PHE68 4.6 15.7 1.0
O C:ALA123 4.6 15.5 1.0
CB C:ARG11 4.7 16.2 1.0
O C:ARG125 4.7 15.9 1.0
C C:ALA179 4.8 16.3 1.0
N C:TYR124 4.8 15.2 1.0
C C:ARG125 4.9 15.9 1.0
C C:PHE10 4.9 15.3 1.0
CB C:PHE10 4.9 15.4 1.0
N C:PHE178 4.9 16.3 1.0
C C:PHE68 5.0 16.0 1.0
O C:TYR124 5.0 15.9 1.0
O C:PHE178 5.0 17.1 1.0
CG C:ARG125 5.0 14.9 1.0

Sodium binding site 4 out of 4 in 3lp9

Go back to Sodium Binding Sites List in 3lp9
Sodium binding site 4 out of 4 in the Crystal Structure of LS24, A Seed Albumin From Lathyrus Sativus


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 LS24, A Seed Albumin From Lathyrus Sativus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na321

b:16.5
occ:1.00
OD2 D:ASP69 2.7 15.7 1.0
O D:HOH455 3.0 16.3 1.0
N D:ARG125 3.1 16.8 1.0
N D:ALA179 3.2 16.7 1.0
CA D:TYR124 3.5 16.0 1.0
CA D:PHE178 3.6 16.2 1.0
CG D:ASP69 3.7 15.9 1.0
CB D:ARG125 3.8 16.2 1.0
C D:TYR124 3.8 16.6 1.0
CB D:PHE178 3.9 15.7 1.0
CB D:ALA179 3.9 15.9 1.0
CB D:TYR124 3.9 15.9 1.0
C D:PHE178 3.9 16.1 1.0
OD1 D:ASP69 4.0 15.3 1.0
CA D:ARG125 4.1 16.6 1.0
CA D:ALA179 4.1 16.3 1.0
N D:ARG11 4.1 15.9 1.0
N D:ASP69 4.2 16.4 1.0
CA D:PHE68 4.5 16.0 1.0
CA D:PHE10 4.5 15.8 1.0
O D:ALA123 4.5 15.3 1.0
O D:ALA179 4.5 16.9 1.0
CB D:PHE68 4.5 15.6 1.0
CB D:ARG11 4.7 16.2 1.0
N D:TYR124 4.7 15.5 1.0
C D:PHE10 4.8 15.8 1.0
C D:ALA179 4.9 16.6 1.0
N D:PHE178 4.9 15.9 1.0
CB D:PHE10 4.9 15.3 1.0
O D:ARG125 4.9 17.1 1.0
C D:PHE68 4.9 16.2 1.0
CB D:ASP69 4.9 16.1 1.0
O D:ALA177 5.0 17.1 1.0
CG D:ARG125 5.0 18.0 1.0

Reference:

V.Gaur, I.A.Qureshi, A.Singh, V.Chanana, D.M.Salunke. Crystal Structure and Functional Insights of Hemopexin Fold Protein From Grass Pea Plant Physiol. V. 152 1842 2010.
ISSN: ISSN 0032-0889
PubMed: 20147493
DOI: 10.1104/PP.109.150680
Page generated: Tue Dec 15 06:16:55 2020

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