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Sodium in PDB 4xav: Crystal Structure of Olfactomedin Domain From Gliomedin

Protein crystallography data

The structure of Crystal Structure of Olfactomedin Domain From Gliomedin, PDB code: 4xav was solved by S.E.Hill, E.Nguyen, R.L.Lieberman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.65 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.164, 140.643, 78.152, 90.00, 106.03, 90.00
R / Rfree (%) 16.6 / 21.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Olfactomedin Domain From Gliomedin (pdb code 4xav). 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 Olfactomedin Domain From Gliomedin, PDB code: 4xav:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4xav

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Sodium binding site 1 out of 4 in the Crystal Structure of Olfactomedin Domain From Gliomedin


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 Olfactomedin Domain From Gliomedin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:19.0
occ:1.00
 O A:ALA472 2.3 18.3 1.0
OD1 A:ASN423 2.3 19.9 1.0
O A:LEU517 2.3 15.4 1.0
OD1 A:ASN471 2.3 15.7 1.0
O A:HOH762 2.4 16.2 1.0
CG A:ASN423 3.4 20.4 1.0
C A:LEU517 3.4 17.6 1.0
O A:HOH801 3.5 22.6 1.0
C A:ALA472 3.5 16.1 1.0
CG A:ASN471 3.5 21.1 1.0
N A:ALA472 3.8 15.3 1.0
N A:LEU517 3.8 18.6 1.0
CB A:LEU517 3.9 16.4 1.0
CA A:LEU517 3.9 17.3 1.0
ND2 A:ASN423 3.9 19.7 1.0
ND2 A:ASN471 4.1 21.1 1.0
CA A:ALA472 4.2 14.5 1.0
O A:HOH800 4.3 22.1 1.0
O A:HOH815 4.3 22.6 1.0
CE2 A:PHE415 4.5 14.7 1.0
N A:PHE473 4.5 15.9 1.0
N A:SER518 4.5 13.1 1.0
CB A:ASN423 4.6 15.9 1.0
CB A:ASN471 4.7 18.1 1.0
CG A:LEU517 4.7 18.7 1.0
CA A:PHE473 4.8 15.2 1.0
C A:ASN471 4.9 18.1 1.0
CD2 A:PHE415 4.9 18.7 1.0
CA A:SER518 5.0 18.4 1.0
CB A:ALA472 5.0 15.0 1.0

Sodium binding site 2 out of 4 in 4xav

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Sodium binding site 2 out of 4 in the Crystal Structure of Olfactomedin Domain From Gliomedin


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 Olfactomedin Domain From Gliomedin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na603

b:19.6
occ:1.00
 OD1 B:ASN423 2.2 18.7 1.0
OD1 B:ASN471 2.3 14.4 1.0
O B:ALA472 2.4 18.3 1.0
O B:LEU517 2.4 17.9 1.0
O B:HOH745 2.6 17.1 1.0
CG B:ASN423 3.3 18.7 1.0
O B:HOH763 3.4 20.8 1.0
C B:LEU517 3.5 17.5 1.0
CG B:ASN471 3.5 19.7 1.0
C B:ALA472 3.5 19.0 1.0
N B:ALA472 3.8 19.2 1.0
CB B:LEU517 3.9 14.8 1.0
ND2 B:ASN423 3.9 20.8 1.0
N B:LEU517 3.9 19.2 1.0
CA B:LEU517 4.0 17.0 1.0
ND2 B:ASN471 4.2 15.4 1.0
CA B:ALA472 4.3 17.9 1.0
O B:HOH780 4.3 22.9 1.0
O B:HOH757 4.4 22.0 1.0
CE2 B:PHE415 4.4 13.6 1.0
CB B:ASN423 4.6 15.2 1.0
N B:PHE473 4.6 19.6 1.0
CB B:ASN471 4.6 17.1 1.0
N B:SER518 4.6 15.0 1.0
CG B:LEU517 4.8 17.1 1.0
CA B:PHE473 4.8 16.4 1.0
CD2 B:PHE415 4.9 16.9 1.0
C B:ASN471 4.9 18.5 1.0

Sodium binding site 3 out of 4 in 4xav

Go back to Sodium Binding Sites List in 4xav
Sodium binding site 3 out of 4 in the Crystal Structure of Olfactomedin Domain From Gliomedin


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 Olfactomedin Domain From Gliomedin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na601

b:18.6
occ:1.00
 OD1 C:ASN423 2.2 19.6 1.0
OD1 C:ASN471 2.4 17.5 1.0
O C:LEU517 2.4 14.9 1.0
O C:ALA472 2.5 16.6 1.0
O C:HOH758 2.5 18.7 1.0
CG C:ASN423 3.2 21.4 1.0
O C:HOH781 3.3 24.0 1.0
C C:LEU517 3.5 14.9 1.0
CG C:ASN471 3.5 17.9 1.0
C C:ALA472 3.6 16.5 1.0
ND2 C:ASN423 3.7 27.6 1.0
N C:ALA472 3.9 16.6 1.0
N C:LEU517 3.9 15.8 1.0
CB C:LEU517 4.0 13.8 1.0
CA C:LEU517 4.0 15.0 1.0
ND2 C:ASN471 4.2 18.3 1.0
O C:HOH837 4.2 25.9 1.0
O C:HOH805 4.3 23.0 1.0
CA C:ALA472 4.3 15.1 1.0
CE2 C:PHE415 4.4 15.3 1.0
CB C:ASN423 4.5 15.3 1.0
N C:SER518 4.6 15.0 1.0
N C:PHE473 4.7 15.9 1.0
CB C:ASN471 4.7 17.8 1.0
CG C:LEU517 4.8 16.3 1.0
CA C:PHE473 4.9 13.2 1.0
CD2 C:PHE415 4.9 16.1 1.0
CA C:SER518 5.0 18.3 1.0

Sodium binding site 4 out of 4 in 4xav

Go back to Sodium Binding Sites List in 4xav
Sodium binding site 4 out of 4 in the Crystal Structure of Olfactomedin Domain From Gliomedin


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 Olfactomedin Domain From Gliomedin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na601

b:18.7
occ:1.00
 OD1 D:ASN471 2.3 16.4 1.0
OD1 D:ASN423 2.3 18.0 1.0
O D:ALA472 2.3 17.9 1.0
O D:LEU517 2.4 16.6 1.0
O D:HOH769 2.5 18.0 1.0
CG D:ASN423 3.4 20.8 1.0
CG D:ASN471 3.4 17.4 1.0
C D:LEU517 3.4 15.0 1.0
O D:HOH785 3.5 23.2 1.0
C D:ALA472 3.5 16.7 1.0
N D:ALA472 3.7 14.0 1.0
CB D:LEU517 3.8 15.0 1.0
N D:LEU517 3.8 16.8 1.0
CA D:LEU517 3.9 14.9 1.0
ND2 D:ASN423 3.9 29.8 1.0
ND2 D:ASN471 4.1 19.3 1.0
CA D:ALA472 4.2 13.4 1.0
O D:HOH854 4.3 26.3 1.0
CE2 D:PHE415 4.3 13.8 1.0
N D:PHE473 4.6 16.0 1.0
CB D:ASN423 4.6 16.0 1.0
CB D:ASN471 4.6 14.9 1.0
N D:SER518 4.6 12.4 1.0
CG D:LEU517 4.6 18.6 1.0
CA D:PHE473 4.8 14.5 1.0
C D:ASN471 4.9 15.0 1.0
CD2 D:PHE415 4.9 16.3 1.0
CB D:ALA472 4.9 14.5 1.0

Reference:

S.E.Hill, R.K.Donegan, E.Nguyen, T.M.Desai, R.L.Lieberman. Molecular Details of Olfactomedin Domains Provide Pathway to Structure-Function Studies. Plos One V. 10 30888 2015.
ISSN: ESSN 1932-6203
PubMed: 26121352
DOI: 10.1371/JOURNAL.PONE.0130888
Page generated: Mon Oct 7 19:01:53 2024

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