Sodium in PDB 6puj: Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3`Oh- Propyl-5-Op-U

Protein crystallography data

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3`Oh- Propyl-5-Op-U, PDB code: 6puj was solved by W.Awad, A.N.Keller, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.77 / 1.92
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 218.607, 70.776, 143.802, 90.00, 104.56, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 6puj:

The structure of Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3`Oh- Propyl-5-Op-U 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 MR1-3`Oh- Propyl-5-Op-U (pdb code 6puj). 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 MR1-3`Oh- Propyl-5-Op-U, PDB code: 6puj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6puj

Go back to Sodium Binding Sites List in 6puj
Sodium binding site 1 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3`Oh- Propyl-5-Op-U


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 MR1-3`Oh- Propyl-5-Op-U within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:41.5
occ:0.72
O E:HOH471 2.3 48.6 1.0
O E:TYR64 2.5 47.5 1.0
O E:HOH475 2.5 56.4 1.0
OH E:TYR47 2.5 43.1 0.8
O E:HOH469 2.5 43.7 1.0
O E:PRO61 2.6 49.8 1.0
C E:PRO61 3.4 48.2 1.0
CZ E:TYR47 3.5 42.5 0.8
OD1 E:ASN65 3.6 47.1 0.4
C E:TYR64 3.6 45.3 1.0
CE1 E:TYR47 3.7 41.5 1.0
N E:TYR64 3.9 47.9 1.0
CB E:PRO61 4.0 47.5 1.0
CA E:ASN62 4.1 53.0 1.0
O E:HOH509 4.1 63.5 1.0
N E:ASN62 4.1 51.9 1.0
N E:GLY63 4.2 54.3 1.0
CA E:PRO61 4.3 46.4 1.0
CA E:TYR64 4.4 44.8 1.0
CG E:ASN65 4.4 49.5 0.4
C E:ASN62 4.5 51.8 1.0
OE1 E:GLU79 4.5 55.1 1.0
N E:ASN65 4.7 42.4 1.0
CE2 E:TYR47 4.8 43.7 0.8
OD1 E:ASN62 4.8 59.9 1.0
C E:GLY63 4.9 51.5 1.0
ND2 E:ASN65 4.9 54.7 0.4
CG E:PRO61 4.9 49.4 1.0
CA E:ASN65 4.9 46.6 0.6
CA E:ASN65 5.0 46.6 0.4

Sodium binding site 2 out of 2 in 6puj

Go back to Sodium Binding Sites List in 6puj
Sodium binding site 2 out of 2 in the Structure of Human Mait A-F7 Tcr in Complex with Human MR1-3`Oh- Propyl-5-Op-U


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 MR1-3`Oh- Propyl-5-Op-U within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na301

b:39.8
occ:1.00
O G:TYR64 2.3 39.2 1.0
O G:HOH629 2.4 43.8 1.0
O G:HOH572 2.4 39.4 1.0
OH G:TYR47 2.5 41.0 1.0
O G:HOH559 2.5 33.6 0.8
O G:PRO61 2.5 34.9 1.0
C G:PRO61 3.5 34.6 1.0
CZ G:TYR47 3.5 37.1 1.0
C G:TYR64 3.5 34.2 1.0
CE1 G:TYR47 3.6 38.3 1.0
N G:TYR64 3.8 35.6 1.0
CA G:ASN62 4.1 38.4 1.0
CB G:PRO61 4.1 33.7 1.0
N G:ASN62 4.2 34.7 1.0
N G:GLY63 4.2 36.8 1.0
CA G:TYR64 4.2 30.5 1.0
ND2 G:ASN65 4.2 43.9 0.6
O G:HOH699 4.3 56.5 1.0
CA G:PRO61 4.3 34.8 1.0
CG G:ASN65 4.5 47.7 0.6
O G:HOH660 4.5 43.1 1.0
O G:HOH547 4.5 57.6 1.0
N G:ASN65 4.5 33.6 1.0
OD1 G:ASN65 4.6 55.0 0.6
C G:ASN62 4.6 38.4 1.0
CA G:ASN65 4.7 39.5 0.4
CE2 G:TYR47 4.8 34.1 1.0
CA G:ASN65 4.8 39.5 0.6
CB G:TYR64 4.8 30.5 1.0
C G:GLY63 4.9 37.5 1.0
OD1 G:ASN62 4.9 47.8 1.0
CB G:ASN65 5.0 44.6 0.4

Reference:

W.Awad, A.N.Keller, J.Rossjohn. The Molecular Basis Underpinning the Potency and Specificity of Mait Cell Antigens To Be Published.
Page generated: Tue Dec 15 12:47:00 2020

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