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Sodium in PDB 6puc: Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru

Protein crystallography data

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru, PDB code: 6puc was solved by W.Awad, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.34 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 217.967, 70.248, 143.634, 90.00, 104.81, 90.00
R / Rfree (%) 15.9 / 17.8

Other elements in 6puc:

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru (pdb code 6puc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru, PDB code: 6puc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6puc

Go back to Sodium Binding Sites List in 6puc
Sodium binding site 1 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na102

b:39.3
occ:0.88
O F:LEU87 2.3 38.8 1.0
O F:HOH286 2.3 43.0 1.0
O F:HIS84 2.4 32.6 1.0
O F:HOH249 2.4 45.6 1.0
O F:HOH270 2.5 44.0 1.0
OD1 F:ASN83 2.5 41.8 1.0
C F:HIS84 3.3 36.7 1.0
C F:LEU87 3.4 36.5 1.0
CG F:ASN83 3.5 47.1 1.0
N F:HIS84 3.8 32.7 1.0
ND2 F:ASN83 4.0 52.8 1.0
N F:LEU87 4.0 36.1 1.0
CA F:VAL85 4.1 34.8 1.0
CA F:LEU87 4.1 32.1 1.0
N F:VAL85 4.1 36.2 1.0
CB F:LEU87 4.2 32.0 1.0
CA F:HIS84 4.3 34.1 1.0
C F:VAL85 4.3 38.1 1.0
O F:VAL85 4.3 37.4 1.0
N F:SER88 4.5 39.4 1.0
C F:SER88 4.6 40.2 1.0
O F:SER88 4.6 45.1 1.0
CA F:SER88 4.7 41.1 0.4
CA F:SER88 4.7 40.7 0.6
CB F:ASN83 4.7 40.6 1.0
C F:ASN83 4.8 30.1 1.0
N F:THR86 5.0 33.5 1.0
N F:GLN89 5.0 38.8 1.0

Sodium binding site 2 out of 2 in 6puc

Go back to Sodium Binding Sites List in 6puc
Sodium binding site 2 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-5-Op-Ru within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na301

b:33.2
occ:1.00
O H:HOH503 2.4 32.8 1.0
O H:TYR64 2.4 31.4 1.0
O H:HOH512 2.4 34.1 1.0
O H:HOH543 2.5 38.7 1.0
O H:PRO61 2.5 26.2 1.0
OH H:TYR47 2.6 32.9 1.0
C H:PRO61 3.4 28.8 1.0
C H:TYR64 3.6 28.7 1.0
CZ H:TYR47 3.6 31.8 1.0
CE1 H:TYR47 3.7 31.1 1.0
N H:TYR64 3.8 27.9 1.0
CA H:ASN62 4.0 34.2 1.0
N H:ASN62 4.1 28.1 1.0
CB H:PRO61 4.1 28.6 1.0
N H:GLY63 4.1 30.2 1.0
O H:HOH728 4.2 48.7 1.0
OD1 H:ASN65 4.2 40.3 0.6
CA H:TYR64 4.3 24.5 1.0
CA H:PRO61 4.3 27.6 1.0
C H:ASN62 4.4 33.2 1.0
O H:HOH670 4.5 37.4 1.0
CG H:ASN65 4.5 43.7 0.6
OD1 H:ASN62 4.6 39.0 1.0
N H:ASN65 4.6 26.9 1.0
O H:HOH709 4.7 51.4 1.0
ND2 H:ASN65 4.7 49.6 0.6
C H:GLY63 4.8 30.7 1.0
CA H:ASN65 4.9 31.8 0.4
CB H:TYR64 4.9 24.5 1.0
CE2 H:TYR47 4.9 28.7 1.0
CA H:ASN65 4.9 32.4 0.6

Reference:

W.Awad, J.Rossjohn. The Molecular Basis Underpinning the Potency and Specificity of Mait Cell Antigens To Be Published.
Page generated: Tue Dec 15 12:46:33 2020

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