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Sodium in PDB 6qhj: High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain

Protein crystallography data

The structure of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain, PDB code: 6qhj was solved by M.F.Pronker, H.G.Van Den Hoek, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.73 / 1.25
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 61.794, 79.631, 111.719, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14.1

Other elements in 6qhj:

The structure of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain (pdb code 6qhj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain, PDB code: 6qhj:

Sodium binding site 1 out of 1 in 6qhj

Go back to Sodium Binding Sites List in 6qhj
Sodium binding site 1 out of 1 in the High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High-Resolution Crystal Structure of Calcium- and Sodium-Bound Mouse Olfactomedin-1 Beta-Propeller Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:9.6
occ:1.00
O A:LEU357 2.2 8.4 1.0
OD1 A:ASP356 2.3 8.3 1.0
OD2 A:ASP453 2.3 11.3 1.0
O A:HOH667 2.4 8.8 1.0
O A:GLY302 2.9 9.1 1.0
HA2 A:GLY302 2.9 8.8 1.0
O A:GLN303 3.0 7.7 1.0
C A:GLY302 3.2 7.7 1.0
H A:LEU357 3.2 8.5 1.0
CG A:ASP453 3.3 9.0 1.0
C A:LEU357 3.3 7.9 1.0
CG A:ASP356 3.5 7.6 1.0
CA A:GLY302 3.5 7.3 1.0
HB3 A:MET358 3.5 11.8 1.0
OD1 A:ASP453 3.6 8.4 1.0
N A:LEU357 3.6 7.1 1.0
O A:HOH651 3.7 12.0 1.0
HB A:VAL304 3.7 9.6 1.0
HA3 A:GLY302 3.8 8.8 1.0
C A:GLN303 3.8 7.1 1.0
O A:HOH628 3.8 8.0 1.0
HE1 A:MET358 3.9 13.6 1.0
N A:GLN303 3.9 7.4 1.0
HA A:ASP356 4.0 8.3 1.0
HA A:MET358 4.0 10.1 1.0
CA A:LEU357 4.1 7.2 1.0
OD2 A:ASP356 4.2 7.6 1.0
C A:ASP356 4.2 7.7 1.0
HB2 A:LEU357 4.3 10.3 1.0
N A:MET358 4.4 7.6 1.0
CB A:MET358 4.4 9.9 1.0
CA A:ASP356 4.4 7.0 1.0
H A:GLN303 4.4 8.9 1.0
CA A:GLN303 4.4 7.1 1.0
CA A:MET358 4.5 8.4 1.0
CA A:CA505 4.5 7.4 1.0
CB A:ASP356 4.5 7.2 1.0
CB A:ASP453 4.6 9.1 1.0
HB2 A:ASP453 4.6 10.9 1.0
O A:THR301 4.6 7.6 1.0
CB A:VAL304 4.6 8.0 1.0
N A:VAL304 4.7 7.4 1.0
N A:GLY302 4.8 7.1 1.0
HA A:GLN303 4.8 8.5 1.0
HB2 A:MET358 4.8 11.8 1.0
CE A:MET358 4.8 11.4 1.0
CB A:LEU357 4.8 8.6 1.0
HA A:LEU357 4.9 8.6 1.0
HA A:VAL304 4.9 8.2 1.0
HB3 A:ASP453 4.9 10.9 1.0
HE3 A:MET358 4.9 13.6 1.0

Reference:

M.F.Pronker, H.Van Den Hoek, B.J.C.Janssen. Design and Structural Characterisation of Olfactomedin-1 Variants As Tools For Functional Studies. Bmc Mol Cell Biol V. 20 50 2019.
ISSN: ISSN 2661-8850
PubMed: 31726976
DOI: 10.1186/S12860-019-0232-1
Page generated: Tue Dec 15 12:49:40 2020

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