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

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

All present enzymatic activity of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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, Thr Mutant, Refined at 1.60 Angstroms Resolution, PDB code: 7lfk 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) 31.62 / 1.60
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 63.43, 69.1, 54.8, 102.54, 93.86, 114.1
R / Rfree (%) 20.8 / 24.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution (pdb code 7lfk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution, PDB code: 7lfk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7lfk

Go back to Sodium Binding Sites List in 7lfk
Sodium binding site 1 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2002

b:41.8
occ:1.00
 OE1 A:GLU229 2.3 36.7 1.0
HH11 A:ARG202 2.3 34.0 1.0
HB3 A:ALA246 2.4 26.2 1.0
NH1 A:ARG202 3.0 28.3 1.0
HZ3 A:TRP244 3.0 21.9 1.0
HB3 A:GLU229 3.1 31.0 1.0
HH12 A:ARG202 3.2 34.0 1.0
CB A:ALA246 3.2 21.8 1.0
HH2 A:TRP244 3.3 24.2 1.0
HB1 A:ALA246 3.3 26.2 1.0
CD A:GLU229 3.4 32.2 1.0
CZ3 A:TRP244 3.5 18.2 1.0
O A:HOH2189 3.5 29.8 1.0
HB2 A:ALA246 3.6 26.2 1.0
CH2 A:TRP244 3.7 20.2 1.0
HG21 A:THR200 3.7 33.6 1.0
HE A:ARG202 3.8 24.9 1.0
O A:HOH2216 3.8 36.6 1.0
CB A:GLU229 3.8 25.8 1.0
HB2 A:GLU229 4.0 31.0 1.0
CZ A:ARG202 4.0 25.9 1.0
HG23 A:THR200 4.1 33.6 1.0
CG A:GLU229 4.1 34.9 1.0
NE A:ARG202 4.3 20.7 1.0
OE2 A:GLU229 4.3 42.6 1.0
CG2 A:THR200 4.3 28.0 1.0
HG2 A:GLU229 4.4 41.9 1.0
CE3 A:TRP244 4.5 16.9 1.0
CA A:ALA246 4.5 19.5 1.0
HG22 A:THR200 4.7 33.6 1.0
HE3 A:TRP244 4.8 20.3 1.0
H A:ALA246 4.8 25.6 1.0
C A:ALA246 4.8 24.6 1.0
CZ2 A:TRP244 4.8 16.0 1.0
O A:ALA246 4.9 23.9 1.0
N A:ALA246 5.0 21.3 1.0
HE2 B:MET99 5.0 54.5 1.0
H A:GLU229 5.0 30.6 1.0
HG3 A:GLU229 5.0 41.9 1.0

Sodium binding site 2 out of 6 in 7lfk

Go back to Sodium Binding Sites List in 7lfk
Sodium binding site 2 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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 2 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2003

b:48.8
occ:1.00
 H A:TRP274 2.3 49.3 1.0
O A:TYR257 2.4 39.9 1.0
O A:GLU254 2.8 42.4 1.0
HA A:LYS273 2.9 49.5 1.0
HB3 A:LYS273 3.0 55.1 1.0
N A:TRP274 3.1 41.0 1.0
HB2 A:TYR257 3.2 40.8 1.0
HZ3 A:TRP217 3.2 40.4 1.0
HD13 A:LEU201 3.2 37.1 1.0
HB3 A:TRP274 3.3 53.5 1.0
C A:TYR257 3.4 36.3 1.0
CA A:LYS273 3.5 41.2 1.0
H A:TYR257 3.6 51.2 1.0
CB A:LYS273 3.6 45.9 1.0
HH2 A:TRP217 3.7 38.9 1.0
HG2 A:LYS273 3.7 59.5 1.0
HA A:GLN255 3.7 53.1 1.0
C A:LYS273 3.8 37.7 1.0
HB2 A:TRP274 3.9 53.5 1.0
CB A:TRP274 3.9 44.5 1.0
CB A:TYR257 3.9 34.2 1.0
C A:GLU254 3.9 40.2 1.0
CZ3 A:TRP217 4.0 33.6 1.0
HD11 A:LEU201 4.0 37.1 1.0
CD1 A:LEU201 4.0 30.8 1.0
CA A:TYR257 4.0 37.8 1.0
HA A:THR258 4.1 42.7 1.0
CA A:TRP274 4.1 40.6 1.0
HG11 A:VAL189 4.2 36.2 1.0
N A:TYR257 4.2 42.6 1.0
CG A:LYS273 4.2 49.5 1.0
HB3 A:TYR257 4.2 40.8 1.0
CH2 A:TRP217 4.2 32.4 1.0
HB3 A:GLU254 4.3 46.1 1.0
HD12 A:LEU201 4.3 37.1 1.0
N A:THR258 4.5 36.3 1.0
HB2 A:LYS273 4.5 55.1 1.0
CA A:GLN255 4.5 44.4 1.0
HD3 A:LYS273 4.5 59.8 1.0
HG21 A:VAL189 4.6 36.4 1.0
N A:GLN255 4.7 43.2 1.0
HA A:TRP274 4.7 48.8 1.0
CA A:THR258 4.8 35.5 1.0
O A:LEU272 4.8 41.6 1.0
HA A:GLU254 4.8 53.5 1.0
C A:GLN255 4.8 44.6 1.0
N A:LYS273 4.9 41.9 1.0
CA A:GLU254 4.9 44.5 1.0
HD22 A:LEU201 4.9 34.4 1.0
CD A:LYS273 4.9 49.8 1.0
HA A:TYR257 4.9 45.4 1.0
HD1 A:TYR257 5.0 46.3 1.0
HG3 A:LYS273 5.0 59.5 1.0
OE1 A:GLN255 5.0 55.3 1.0
HE22 A:GLN255 5.0 59.6 1.0

Sodium binding site 3 out of 6 in 7lfk

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Sodium binding site 3 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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 3 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na2004

b:47.0
occ:1.00
 OE1 A:GLU264 2.3 36.3 1.0
HG2 A:PRO210 2.5 29.9 1.0
HB2 A:GLU264 2.7 37.5 1.0
O A:HOH2161 2.9 26.6 1.0
HG3 A:PRO210 3.2 29.9 1.0
HB3 A:GLU264 3.3 37.5 1.0
CG A:PRO210 3.3 24.8 1.0
CB A:GLU264 3.4 31.2 1.0
CD A:GLU264 3.4 34.4 1.0
HB3 A:ASP212 3.5 29.9 1.0
HD2 A:PRO210 3.7 25.4 1.0
CG A:GLU264 3.9 37.9 1.0
CD A:PRO210 4.0 21.1 1.0
H A:GLU264 4.2 33.2 1.0
HG3 A:GLU264 4.3 45.5 1.0
HB2 A:PRO210 4.3 25.8 1.0
CB A:ASP212 4.4 24.9 1.0
CB A:PRO210 4.4 21.5 1.0
OE2 A:GLU264 4.5 45.3 1.0
HD3 A:PRO210 4.6 25.4 1.0
HB2 A:ASP212 4.6 29.9 1.0
OD2 A:ASP212 4.6 37.9 1.0
CA A:GLU264 4.7 29.2 1.0
HG2 A:GLU264 4.7 45.5 1.0
H A:ASP212 4.8 24.7 1.0
N A:GLU264 4.8 27.9 1.0
O A:ASP212 5.0 26.3 1.0
O A:HOH2156 5.0 23.8 1.0

Sodium binding site 4 out of 6 in 7lfk

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Sodium binding site 4 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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 4 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:50.9
occ:1.00
 OD2 D:ASP122 2.4 26.7 1.0
CG D:ASP122 3.2 32.6 1.0
OD1 D:ASP122 3.2 29.4 1.0
HE1 E:TRP60 4.5 27.7 1.0
CB D:ASP122 4.6 22.1 1.0
HB2 D:ASP122 4.8 26.6 1.0
HB3 D:ASP122 4.9 26.6 1.0

Sodium binding site 5 out of 6 in 7lfk

Go back to Sodium Binding Sites List in 7lfk
Sodium binding site 5 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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 5 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na302

b:36.4
occ:1.00
 O D:ALA182 2.2 25.2 1.0
O D:HOH444 2.8 29.9 1.0
O D:HOH513 2.9 27.7 1.0
O A:HOH2121 3.2 30.3 1.0
HB3 D:ALA182 3.3 30.4 1.0
H D:ALA182 3.4 31.9 1.0
O D:HOH536 3.4 36.1 1.0
C D:ALA182 3.4 21.4 1.0
HD3 D:PRO184 3.6 30.6 1.0
HA2 D:GLY265 3.8 24.0 1.0
N D:ALA182 4.0 26.5 1.0
CB D:ALA182 4.1 25.3 1.0
CA D:ALA182 4.1 22.3 1.0
HA D:ASP183 4.1 25.8 1.0
O D:HOH556 4.4 35.8 1.0
HA3 D:GLY265 4.4 24.0 1.0
CD D:PRO184 4.5 25.5 1.0
N D:ASP183 4.5 22.2 1.0
HB1 D:ALA182 4.5 30.4 1.0
OD2 A:ASP122 4.5 22.4 1.0
CA D:GLY265 4.5 20.0 1.0
O D:GLY265 4.6 22.1 1.0
HD2 D:PRO184 4.6 30.6 1.0
CA D:ASP183 4.7 21.4 1.0
HB2 D:ALA182 4.8 30.4 1.0
OD1 D:ASP183 4.9 37.2 1.0
HA D:ALA182 5.0 26.8 1.0

Sodium binding site 6 out of 6 in 7lfk

Go back to Sodium Binding Sites List in 7lfk
Sodium binding site 6 out of 6 in the Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, 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 6 of Model of Mhc Class Ib H2-M3 with Mouse ND1 N-Terminal Heptapeptide, Thr Mutant, Refined at 1.60 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na101

b:52.5
occ:1.00
 O E:MET87 2.3 39.9 1.0
O E:HOH227 2.7 39.2 1.0
O E:HIS84 3.0 37.5 1.0
HA E:ASP85 3.4 47.2 1.0
HG3 E:LYS83 3.5 46.8 1.0
C E:MET87 3.6 43.5 1.0
HE2 E:LYS83 3.7 71.9 1.0
H E:HIS84 3.8 40.3 1.0
C E:HIS84 3.8 36.5 1.0
H E:MET87 3.8 45.5 1.0
HG2 E:LYS83 4.0 46.8 1.0
O E:ALA88 4.1 52.6 1.0
HB2 E:MET87 4.1 42.7 1.0
CA E:ASP85 4.2 39.3 1.0
CG E:LYS83 4.2 39.0 1.0
C E:ALA88 4.2 44.1 1.0
HA E:ALA88 4.2 52.6 1.0
N E:HIS84 4.3 33.8 1.0
N E:ASP85 4.3 37.7 1.0
N E:MET87 4.4 37.8 1.0
CA E:MET87 4.5 37.6 1.0
N E:ALA88 4.5 45.5 1.0
C E:ASP85 4.5 41.5 1.0
CA E:ALA88 4.5 44.0 1.0
CE E:LYS83 4.6 59.9 1.0
N E:GLU89 4.6 44.3 1.0
O E:ASP85 4.6 43.7 1.0
HZ3 E:LYS83 4.7 80.0 1.0
HA E:GLU89 4.7 52.0 1.0
CA E:HIS84 4.7 33.6 1.0
CB E:MET87 4.8 35.7 1.0
HA E:LYS83 4.8 45.4 1.0
OD1 E:ASP85 4.9 56.9 1.0
CD E:LYS83 4.9 56.4 1.0
H E:GLU89 5.0 53.2 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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