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Sodium in PDB 7lfm: Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution

Enzymatic activity of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution

All present enzymatic activity of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution:
7.1.1.2;

Protein crystallography data

The structure of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution, PDB code: 7lfm was solved by D.R.Tomchick, J.Deisenhofer, S.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.09 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.743, 65.019, 54.584, 98.55, 98.22, 112.36
R / Rfree (%) 18.4 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution (pdb code 7lfm). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution, PDB code: 7lfm:

Sodium binding site 1 out of 1 in 7lfm

Go back to Sodium Binding Sites List in 7lfm
Sodium binding site 1 out of 1 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Val Mutant, Triclinic Cell, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2002

b:39.2
occ:1.00
 OD1 A:ASP183 2.0 33.5 1.0
HA A:ASP183 3.0 31.7 1.0
O A:ALA182 3.2 29.5 1.0
CG A:ASP183 3.2 32.9 1.0
HB2 A:ARG181 3.4 37.1 1.0
CA A:ASP183 3.7 26.4 1.0
C A:ALA182 3.7 24.3 1.0
HD2 A:ARG181 3.9 40.2 1.0
N A:ASP183 3.9 22.9 1.0
CB A:ASP183 4.0 26.9 1.0
HE A:ARG181 4.1 42.3 1.0
H A:ALA182 4.1 29.1 1.0
HG3 A:ARG181 4.1 35.2 1.0
OD2 A:ASP183 4.2 38.1 1.0
CB A:ARG181 4.3 30.9 1.0
HB3 A:ASP183 4.3 32.3 1.0
HD2 A:PRO184 4.3 30.7 1.0
CD A:ARG181 4.5 33.5 1.0
H A:ASP183 4.5 27.5 1.0
CG A:ARG181 4.5 29.4 1.0
N A:ALA182 4.5 24.2 1.0
NE A:ARG181 4.6 35.3 1.0
HD3 A:PRO184 4.6 30.7 1.0
HB2 A:ASP183 4.8 32.3 1.0
CA A:ALA182 4.8 23.9 1.0
HB3 A:ARG181 4.8 37.1 1.0
CD A:PRO184 4.9 25.6 1.0

Reference:

A.Strand, S.T.Shen, D.R.Tomchick, J.Wang, C.R.Wang, J.Deisenhofer. Structure and Dynamics of Major Histocompatibility Class Ib Molecule H2-M3 Complexed with Mitochondrial-Derived Peptides. J.Biomol.Struct.Dyn. 1 2021.
ISSN: ESSN 1538-0254
PubMed: 34176438
DOI: 10.1080/07391102.2021.1942214
Page generated: Tue Oct 8 17:36:34 2024

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