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Sodium in PDB 4lfh: Crystal Structure of 9C2 Tcr

Protein crystallography data

The structure of Crystal Structure of 9C2 Tcr, PDB code: 4lfh was solved by A.P.Uldrich, J.Le Nours, D.G.Pellicci, S.Gras, J.Rossjohn, D.I.Godfrey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.71 / 2.30
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.534, 118.534, 89.127, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 9C2 Tcr (pdb code 4lfh). 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 9C2 Tcr, PDB code: 4lfh:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4lfh

Go back to Sodium Binding Sites List in 4lfh
Sodium binding site 1 out of 2 in the Crystal Structure of 9C2 Tcr


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 9C2 Tcr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na302

b:35.8
occ:1.00
N G:TRP79 3.2 37.4 1.0
NH1 G:ARG78 3.5 36.6 1.0
OG1 G:THR75 3.6 52.8 1.0
NE1 G:TRP81 3.8 37.1 1.0
CD G:ARG78 3.8 34.2 1.0
O G:HOH458 3.8 43.7 1.0
CA G:TRP79 3.8 37.0 1.0
CG1 G:VAL55 3.9 37.3 1.0
CD1 G:TRP79 3.9 39.6 1.0
CA G:ARG78 4.2 37.5 1.0
C G:ARG78 4.2 42.1 1.0
CZ2 G:TRP81 4.3 36.6 1.0
CE2 G:TRP81 4.3 38.0 1.0
CZ G:ARG78 4.5 48.6 1.0
NE G:ARG78 4.6 36.3 1.0
CB G:THR75 4.7 49.0 1.0
CG G:TRP79 4.7 37.1 1.0
O G:ARG77 4.7 39.4 1.0
N G:SER80 4.7 36.8 1.0
CG G:ARG78 4.7 41.5 1.0
NE1 G:TRP79 4.8 39.9 1.0
CD1 G:TRP81 4.8 37.0 1.0
C G:TRP79 4.9 40.0 1.0
CB G:TRP79 4.9 36.4 1.0

Sodium binding site 2 out of 2 in 4lfh

Go back to Sodium Binding Sites List in 4lfh
Sodium binding site 2 out of 2 in the Crystal Structure of 9C2 Tcr


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 9C2 Tcr within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na303

b:78.8
occ:1.00
ND2 G:ASN91 3.5 71.6 1.0
O G:ASN91 3.8 42.0 1.0
O G:HOH421 4.2 39.4 1.0
O G:HOH438 4.2 48.0 1.0
O G:HOH412 4.3 36.2 1.0
OD2 G:ASP92 4.5 42.5 1.0
C G:ASN91 4.6 43.5 1.0
CG G:ASN91 4.6 82.6 1.0
CD1 G:LEU40 4.7 37.5 1.0
OH G:TYR71 4.8 47.9 1.0
O G:HOH469 4.9 69.1 1.0
CB G:ASN91 4.9 53.2 1.0

Reference:

A.P.Uldrich, J.Le Nours, D.G.Pellicci, N.A.Gherardin, K.G.Mcpherson, R.T.Lim, O.Patel, T.Beddoe, S.Gras, J.Rossjohn, D.I.Godfrey. CD1D-Lipid Antigen Recognition By the Gamma Delta Tcr. Nat.Immunol. V. 14 1137 2013.
ISSN: ISSN 1529-2908
PubMed: 24076636
DOI: 10.1038/NI.2713
Page generated: Mon Oct 7 16:44:47 2024

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