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Sodium in PDB 6lt9: The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain

Protein crystallography data

The structure of The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain, PDB code: 6lt9 was solved by Y.Zhou, L.Lin, Z.Yuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.94 / 1.80
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 64.893, 64.893, 95.767, 90, 90, 90
R / Rfree (%) 18.7 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain (pdb code 6lt9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain, PDB code: 6lt9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6lt9

Go back to Sodium Binding Sites List in 6lt9
Sodium binding site 1 out of 2 in the The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na902

b:30.0
occ:1.00
SG F:CYS839 2.4 15.0 1.0
CB F:CYS839 3.2 15.2 1.0
O B:HOH1061 3.8 12.9 1.0
NH2 B:ARG655 3.8 12.8 1.0
H31 F:GOL901 4.0 20.0 1.0
HO1 F:GOL901 4.2 20.0 1.0
CZ F:PHE840 4.2 21.0 1.0
CZ B:PHE659 4.2 14.6 1.0
SG F:CYS837 4.3 12.3 1.0
SD F:MET787 4.5 25.2 1.0
CE2 F:PHE840 4.6 18.9 1.0
O1 F:GOL901 4.6 20.0 1.0
CB F:CYS837 4.6 15.5 1.0
CA F:CYS839 4.7 15.9 1.0
CE2 B:PHE659 4.7 11.9 1.0
CG F:MET787 4.8 12.9 1.0
O B:HOH1024 4.8 11.7 1.0
OD1 B:ASN657 4.9 17.4 1.0
CE1 F:PHE840 4.9 20.0 1.0
CA F:GLY661 4.9 10.1 1.0
N F:GLY661 5.0 11.2 1.0
CZ B:ARG655 5.0 13.5 1.0
C3 F:GOL901 5.0 20.0 1.0

Sodium binding site 2 out of 2 in 6lt9

Go back to Sodium Binding Sites List in 6lt9
Sodium binding site 2 out of 2 in the The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na904

b:30.0
occ:1.00
SG B:CYS839 2.4 26.6 1.0
CB B:CYS839 3.2 19.6 1.0
O F:HOH1048 3.7 15.3 1.0
NH1 F:ARG655 3.8 12.6 1.0
CZ B:PHE840 4.2 21.6 1.0
CZ F:PHE659 4.2 12.8 1.0
SG B:CYS837 4.3 15.3 1.0
SD B:MET787 4.5 26.3 1.0
H31 B:GOL901 4.5 20.0 1.0
CE2 B:PHE840 4.6 19.3 1.0
CB B:CYS837 4.6 12.4 1.0
CA B:CYS839 4.6 12.9 1.0
CE2 F:PHE659 4.7 12.5 1.0
H12 B:GOL901 4.7 20.0 1.0
CG B:MET787 4.8 13.7 1.0
OD1 F:ASN657 4.8 13.7 1.0
O F:HOH1014 4.8 15.1 1.0
CE1 B:PHE840 4.8 16.5 1.0
CA B:GLY661 4.9 10.8 1.0
CZ F:ARG655 4.9 17.2 1.0
N B:GLY661 4.9 11.0 1.0

Reference:

B.Nayak, Y.Zhou, N.Salauddin, L.Lin, M.You, S.You, Z.Yuchi. The Crystal Structure of Diamondback Moth Ryanodine Receptor SPRY1 Domain To Be Published.
Page generated: Wed Mar 3 15:25:42 2021

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