Atomistry » Sodium » PDB 6p9k-6puk » 6puc
Atomistry »
  Sodium »
    PDB 6p9k-6puk »
      6puc »

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 Oct 8 12:45:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy