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Sodium in PDB 5swz: Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex

Protein crystallography data

The structure of Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex, PDB code: 5swz was solved by S.Gras, C.M.Del Campo, C.Farenc, T.M.Josephs, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.80 / 2.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.231, 100.185, 469.456, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 24.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex (pdb code 5swz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex, PDB code: 5swz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5swz

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Sodium binding site 1 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np 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 NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:50.5
occ:1.00
 O E:GLY111 2.6 40.0 1.0
OG E:SER107 2.6 51.6 1.0
O E:ASP113 3.0 42.5 1.0
OH E:TYR40 3.2 46.5 1.0
OD1 E:ASP109 3.3 52.0 1.0
O E:ASP109 3.3 41.4 1.0
CB E:SER107 3.4 41.3 1.0
N E:GLY111 3.5 37.8 1.0
C E:GLY111 3.5 41.9 1.0
CA E:GLY111 4.0 38.3 1.0
C E:ASP113 4.1 44.3 1.0
C E:ASP109 4.1 42.8 1.0
N E:ASP113 4.2 42.2 1.0
CZ E:TYR40 4.3 44.5 1.0
CG E:ASP109 4.4 53.3 1.0
C E:LEU110 4.5 41.7 1.0
CA D:TRP113 4.5 40.3 1.0
CE1 E:TYR40 4.5 38.4 1.0
N E:ARG112 4.5 40.4 1.0
O D:TRP113 4.5 43.2 1.0
CA E:ASP113 4.5 42.4 1.0
CA E:LEU110 4.6 37.8 1.0
CG E:GLN115 4.6 43.9 1.0
C E:ARG112 4.6 44.9 1.0
N E:LEU110 4.7 39.2 1.0
O E:THR114 4.7 42.0 1.0
CA E:SER107 4.8 38.3 1.0
OE1 E:GLN115 4.8 52.0 1.0
CB E:ASP113 4.8 45.2 1.0
CB D:TRP113 5.0 39.9 1.0

Sodium binding site 2 out of 6 in 5swz

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Sodium binding site 2 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np 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 NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Na301

b:48.8
occ:1.00
 OE1 I:GLN1 2.4 0.9 1.0
OE2 L:GLU36 3.3 86.2 1.0
CD I:GLN1 3.6 0.2 1.0
CG L:LYS83 3.6 58.9 1.0
CD2 L:HIS34 3.7 60.6 1.0
O L:LYS83 3.9 48.0 1.0
CA L:HIS84 4.0 46.4 1.0
C L:LYS83 4.1 48.9 1.0
C L:HIS84 4.1 52.6 1.0
N L:HIS84 4.2 46.1 1.0
O L:HIS34 4.2 55.3 1.0
CD L:GLU36 4.3 90.6 1.0
N L:ALA85 4.3 50.7 1.0
NE2 L:HIS34 4.4 60.7 1.0
CG I:GLN1 4.4 92.4 1.0
CD L:LYS83 4.5 65.5 1.0
NE2 I:GLN1 4.5 0.3 1.0
CG L:GLU36 4.6 66.4 1.0
O L:HIS84 4.7 52.9 1.0
C L:HIS34 4.7 55.4 1.0
CB L:LYS83 4.7 47.8 1.0
CG L:HIS34 4.7 58.3 1.0
CA L:ILE35 4.8 50.7 1.0
N L:GLU36 4.9 51.8 1.0
N L:ILE35 4.9 51.4 1.0

Sodium binding site 3 out of 6 in 5swz

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Sodium binding site 3 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na301

b:38.7
occ:1.00
 OH J:TYR40 2.5 56.6 1.0
OD1 J:ASP109 2.8 75.8 1.0
O J:ASP109 2.9 65.7 1.0
O J:GLY111 3.0 62.4 1.0
N J:GLY111 3.1 61.3 1.0
CB J:SER107 3.5 66.2 1.0
C J:ASP109 3.5 68.5 1.0
CZ J:TYR40 3.7 54.4 1.0
OG J:SER107 3.7 76.3 1.0
CA J:LEU110 3.7 62.6 1.0
C J:GLY111 3.8 64.5 1.0
C J:LEU110 3.8 65.6 1.0
CG J:ASP109 3.9 77.8 1.0
N J:LEU110 3.9 65.1 1.0
CA J:GLY111 4.0 61.2 1.0
CA I:TRP113 4.0 52.1 1.0
CE1 J:TYR40 4.0 48.6 1.0
CB I:TRP113 4.1 51.0 1.0
O J:ASP113 4.2 68.4 1.0
O I:TRP113 4.2 55.5 1.0
NE2 J:GLN115 4.5 80.5 1.0
CA J:ASP109 4.5 68.2 1.0
OG1 J:THR31 4.6 63.2 1.0
C I:TRP113 4.6 55.6 1.0
OD2 J:ASP109 4.7 84.0 1.0
CB J:THR31 4.7 60.6 1.0
N J:ASP109 4.7 68.0 1.0
CB J:ASP109 4.7 71.5 1.0
CG2 J:THR31 4.8 56.6 1.0
CG J:GLN115 4.8 71.0 1.0
CE2 J:TYR40 4.9 45.8 1.0
CA J:SER107 4.9 63.1 1.0

Sodium binding site 4 out of 6 in 5swz

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Sodium binding site 4 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na302

b:79.8
occ:1.00
 C K:LYS253 2.7 0.6 1.0
O K:LYS253 2.9 0.6 1.0
CB K:ASN256 2.9 0.4 1.0
CA K:LYS253 3.0 0.8 1.0
N K:ASN256 3.1 98.2 1.0
N K:GLU254 3.1 98.0 1.0
ND2 K:ASN256 3.2 0.2 0.9
CA K:ASN256 3.4 98.6 1.0
CD2 K:TYR257 3.5 99.5 1.0
CG K:ASN256 3.5 0.2 0.1
CE2 K:TYR257 3.7 0.9 1.0
CA K:GLU254 3.8 95.8 1.0
N K:LYS253 3.8 0.2 1.0
N K:GLN255 3.8 97.0 1.0
C K:GLU254 3.9 99.0 1.0
C K:ASN256 3.9 0.5 1.0
CB K:LYS253 4.2 0.6 1.0
N K:TYR257 4.2 95.1 1.0
C K:GLN255 4.3 0.9 1.0
O K:ASN256 4.6 0.6 1.0
CA K:GLN255 4.6 96.7 1.0
O K:GLU254 4.6 97.0 1.0
CG K:TYR257 4.7 96.8 1.0
OD1 K:ASN256 4.8 0.2 0.8
CG K:LYS253 4.8 0.3 1.0

Sodium binding site 5 out of 6 in 5swz

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Sodium binding site 5 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na302

b:42.7
occ:1.00
 OG T:SER107 2.5 58.0 1.0
O T:GLY111 2.6 47.1 1.0
O T:ASP113 2.9 49.3 1.0
OD1 T:ASP109 3.1 61.2 1.0
O T:ASP109 3.3 48.5 1.0
CB T:SER107 3.3 48.5 1.0
OH T:TYR40 3.4 54.5 1.0
N T:GLY111 3.5 43.1 1.0
C T:GLY111 3.5 48.1 1.0
C T:ASP113 3.9 51.3 1.0
C T:ASP109 4.0 49.4 1.0
CA T:GLY111 4.0 43.7 1.0
N T:ASP113 4.1 48.5 1.0
CG T:ASP109 4.3 61.9 1.0
CA T:ASP113 4.4 49.0 1.0
CZ T:TYR40 4.4 53.0 1.0
C T:LEU110 4.5 46.2 1.0
N T:ARG112 4.5 46.4 1.0
CA T:LEU110 4.6 43.1 1.0
C T:ARG112 4.6 52.0 1.0
N T:LEU110 4.6 44.8 1.0
CE1 T:TYR40 4.6 46.3 1.0
O T:THR114 4.6 46.9 1.0
CB T:ASP113 4.7 51.2 1.0
CG T:GLN115 4.7 50.7 1.0
CA T:SER107 4.7 46.1 1.0
CA S:TRP113 4.8 44.0 1.0
O S:TRP113 4.8 48.1 1.0
N T:ASP109 4.8 48.8 1.0
O T:HOH430 4.9 34.4 1.0
CA T:ASP109 4.9 47.9 1.0
OE1 T:GLN115 5.0 58.5 1.0
OD2 T:ASP109 5.0 69.7 1.0

Sodium binding site 6 out of 6 in 5swz

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Sodium binding site 6 out of 6 in the Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of NP1-B17 Tcr-H2DB-Np Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Na303

b:49.4
occ:1.00
 O P:HOH338 2.9 42.6 1.0
O T:HOH426 3.2 29.7 1.0
N T:LEU110 3.5 44.8 1.0
CB T:LEU110 3.8 42.3 1.0
O T:LEU110 4.0 45.4 1.0
OE1 P:GLN72 4.0 61.9 1.0
CA T:LEU110 4.1 43.1 1.0
CB T:ASP109 4.2 51.0 1.0
NH1 P:ARG75 4.3 57.8 1.0
C T:LEU110 4.3 46.2 1.0
CD P:GLN72 4.4 68.5 1.0
C T:ASP109 4.5 49.4 1.0
CA T:ASP109 4.6 47.9 1.0
NE2 P:GLN72 4.6 60.4 1.0
CE1 T:TYR57 4.7 50.0 1.0
OE2 P:GLU19 4.7 67.1 0.5
OH T:TYR57 4.8 59.5 1.0
CG T:ASP109 5.0 61.9 1.0

Reference:

S.Gras, J.Chadderton, C.M.Del Campo, C.Farenc, F.Wiede, T.M.Josephs, X.Y.Sng, M.Mirams, K.A.Watson, T.Tiganis, K.M.Quinn, J.Rossjohn, N.L.La Gruta. Reversed T Cell Receptor Docking on A Major Histocompatibility Class I Complex Limits Involvement in the Immune Response. Immunity V. 45 749 2016.
ISSN: ISSN 1074-7613
PubMed: 27717799
DOI: 10.1016/J.IMMUNI.2016.09.007
Page generated: Tue Dec 15 11:33:33 2020

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