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Sodium in PDB 5l2k: Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex

Protein crystallography data

The structure of Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex, PDB code: 5l2k was solved by S.Gras, A.Shahine, J.Le Nours, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.73 / 3.20
Space group P 64 2 2
Cell size a, b, c (Å), α, β, γ (°) 174.998, 174.998, 170.869, 90.00, 90.00, 120.00
R / Rfree (%) 21.8 / 23.9

Other elements in 5l2k:

The structure of Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex also contains other interesting chemical elements:

Caesium (Cs) 1 atom
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex (pdb code 5l2k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex, PDB code: 5l2k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5l2k

Go back to Sodium Binding Sites List in 5l2k
Sodium binding site 1 out of 2 in the Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex


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 GEM42 Tcr-CD1B-Gmm Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na410

b:65.0
occ:1.00
NH1 A:ARG246 3.1 0.3 1.0
OG1 A:THR248 3.3 0.9 1.0
O A:ARG246 3.6 92.1 1.0
O A:GLN231 3.6 93.4 1.0
CZ A:ARG246 3.7 0.6 1.0
CG2 A:THR248 3.9 0.1 1.0
N A:GLY233 3.9 85.4 1.0
CA A:GLY233 4.0 84.6 1.0
CB A:THR248 4.1 0.1 1.0
CG A:ARG246 4.2 95.8 1.0
NH2 A:ARG246 4.2 0.7 1.0
C A:LEU232 4.3 90.2 1.0
C A:ARG246 4.4 92.3 1.0
N A:THR248 4.4 95.1 1.0
NE A:ARG246 4.4 0.2 1.0
C A:GLN231 4.5 94.0 1.0
O A:LEU232 4.7 89.8 1.0
CD A:ARG246 4.7 0.1 1.0
CB A:ARG246 4.8 86.0 1.0
CA A:LEU232 4.9 87.8 1.0
CA A:THR248 4.9 95.7 1.0
CA A:ALA247 5.0 91.1 1.0
N A:ALA247 5.0 90.5 1.0

Sodium binding site 2 out of 2 in 5l2k

Go back to Sodium Binding Sites List in 5l2k
Sodium binding site 2 out of 2 in the Crystal Structure of GEM42 Tcr-CD1B-Gmm Complex


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 GEM42 Tcr-CD1B-Gmm Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:43.8
occ:1.00
N E:HIS179 3.6 76.2 1.0
N E:SER180 3.8 79.9 1.0
CB E:SER180 4.2 84.0 1.0
CA E:VAL178 4.3 72.2 1.0
CB E:HIS179 4.4 77.7 1.0
CA E:HIS179 4.4 76.8 1.0
C E:VAL178 4.4 78.1 1.0
CD2 E:HIS179 4.6 83.0 1.0
C E:HIS179 4.6 82.2 1.0
CA E:SER180 4.7 80.1 1.0
CB E:VAL178 4.7 76.0 1.0
O E:GLU177 4.8 73.4 1.0
CG1 E:VAL178 4.9 75.9 1.0
CG E:HIS179 4.9 81.2 1.0

Reference:

S.Gras, I.Van Rhijn, A.Shahine, T.Y.Cheng, M.Bhati, L.L.Tan, H.Halim, K.D.Tuttle, L.Gapin, J.Le Nours, D.B.Moody, J.Rossjohn. T Cell Receptor Recognition of CD1B Presenting A Mycobacterial Glycolipid. Nat Commun V. 7 13257 2016.
ISSN: ESSN 2041-1723
PubMed: 27807341
DOI: 10.1038/NCOMMS13257
Page generated: Tue Dec 15 11:12:25 2020

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