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Sodium in PDB 5gzc: Crystal Structure of Galectin-8 N-Crd with Part of Linker

Protein crystallography data

The structure of Crystal Structure of Galectin-8 N-Crd with Part of Linker, PDB code: 5gzc was solved by J.Y.Su, Y.L.Si, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.52 / 1.08
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.557, 49.376, 76.684, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 16.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Galectin-8 N-Crd with Part of Linker (pdb code 5gzc). 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 Crystal Structure of Galectin-8 N-Crd with Part of Linker, PDB code: 5gzc:

Sodium binding site 1 out of 1 in 5gzc

Go back to Sodium Binding Sites List in 5gzc
Sodium binding site 1 out of 1 in the Crystal Structure of Galectin-8 N-Crd with Part of Linker


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 Galectin-8 N-Crd with Part of Linker within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:21.8
occ:1.00
HH22 A:ARG66 2.2 20.8 1.0
HE22 A:GLN54 2.3 12.3 1.0
HH12 A:ARG66 2.6 22.8 1.0
H2 A:HOH457 2.9 27.5 0.0
O A:HOH457 2.9 22.9 1.0
NH2 A:ARG66 2.9 17.3 1.0
H2 A:HOH502 3.0 35.1 0.0
O A:HOH502 3.0 29.2 1.0
HZ2 A:TRP93 3.0 12.9 1.0
H1 A:HOH502 3.0 35.1 0.0
NE2 A:GLN54 3.1 10.2 1.0
NH1 A:ARG66 3.3 19.0 1.0
CZ A:ARG66 3.5 17.2 1.0
HH21 A:ARG66 3.6 20.8 1.0
HE21 A:GLN54 3.7 12.3 1.0
OE1 A:GLN54 3.7 11.1 1.0
H1 A:HOH457 3.8 27.5 0.0
H2 A:HOH513 3.8 33.5 0.0
O A:HOH513 3.9 27.9 1.0
CD A:GLN54 3.9 9.2 1.0
HE1 A:HIS72 3.9 9.1 1.0
CZ2 A:TRP93 3.9 10.8 1.0
H32 A:GOL201 4.0 12.8 1.0
H31 A:GOL201 4.0 12.8 1.0
HH11 A:ARG66 4.0 22.8 1.0
HH22 A:ARG52 4.1 12.3 1.0
H1 A:HOH485 4.2 30.8 0.0
HH21 A:ARG52 4.2 12.3 1.0
HO3 A:GOL201 4.3 11.1 1.0
H2 A:HOH485 4.3 30.8 0.0
H1 A:HOH513 4.3 33.5 0.0
HE1 A:TRP93 4.4 15.6 1.0
C3 A:GOL201 4.4 10.7 1.0
CE1 A:HIS72 4.4 7.5 1.0
NH2 A:ARG52 4.4 10.2 1.0
O A:HOH485 4.5 25.6 1.0
HH2 A:TRP93 4.6 12.1 1.0
CH2 A:TRP93 4.7 10.1 1.0
CE2 A:TRP93 4.8 10.7 1.0
O3 A:GOL201 4.8 9.2 1.0
NE A:ARG66 4.8 18.1 1.0
NE1 A:TRP93 4.9 13.0 1.0
HD1 A:HIS72 5.0 9.1 1.0
ND1 A:HIS72 5.0 7.6 1.0

Reference:

Y.L.Si, Y.Wang, J.Gao, C.Song, S.Feng, Y.Zhou, G.Tai, J.Y.Su. Crystallization of Galectin-8 Linker Reveals Intricate Relationship Between the N-Terminal Tail and the Linker Int J Mol Sci V. 17 2088 2016.
ISSN: ESSN 1422-0067
DOI: 10.3390/IJMS17122088
Page generated: Tue Dec 15 11:02:09 2020

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