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Sodium in PDB 6iwh: Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide

Protein crystallography data

The structure of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide, PDB code: 6iwh was solved by Y.Yamamoto, D.Morita, M.Sugita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.40 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.103, 80.791, 106.421, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide (pdb code 6iwh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide, PDB code: 6iwh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6iwh

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Sodium binding site 1 out of 5 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:38.4
occ:1.00
 O A:HOH458 2.3 42.8 1.0
O A:HOH539 2.3 42.5 1.0
O A:LEU266 2.4 29.8 1.0
OE1 A:GLN262 2.4 37.6 1.0
O A:HOH540 2.6 44.0 1.0
O A:HIS263 2.8 23.1 1.0
CD A:GLN262 3.0 42.1 1.0
NE2 A:GLN262 3.3 42.4 1.0
C A:LEU266 3.6 33.4 1.0
C A:HIS263 3.7 24.9 1.0
N A:HIS263 4.1 24.0 1.0
CG A:GLN262 4.2 37.3 1.0
O A:HOH535 4.2 34.2 1.0
O A:PRO267 4.2 43.0 1.0
N A:LEU266 4.3 28.4 1.0
CA A:LEU266 4.3 26.9 1.0
CA A:GLU264 4.4 19.9 1.0
C A:PRO267 4.4 40.7 1.0
N A:GLU264 4.4 22.6 1.0
CB A:LEU266 4.4 25.3 1.0
O A:HOH432 4.5 34.6 1.0
O A:GLU264 4.5 27.9 1.0
C A:GLU264 4.5 26.4 1.0
CA A:HIS263 4.5 21.0 1.0
N A:PRO267 4.6 32.4 1.0
CA A:PRO267 4.7 33.2 1.0
O A:GLU268 4.9 28.5 1.0
C A:GLU268 4.9 33.8 1.0
N A:GLU268 4.9 35.8 1.0

Sodium binding site 2 out of 5 in 6iwh

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Sodium binding site 2 out of 5 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:54.2
occ:1.00
 OE2 A:GLU264 1.8 48.0 1.0
O2 A:EDO305 2.6 37.0 1.0
CD A:GLU264 2.7 43.8 1.0
OE1 A:GLU264 2.9 57.2 1.0
O1 A:EDO305 3.0 33.7 1.0
C2 A:EDO305 3.7 34.4 1.0
C1 A:EDO305 3.8 30.4 1.0
CA A:GLY1 3.9 61.8 1.0
CG A:GLU264 4.1 26.8 1.0
N A:GLY1 4.4 53.9 1.0
CE1 A:HIS3 4.5 23.2 1.0
NE2 A:HIS3 4.9 23.2 1.0

Sodium binding site 3 out of 5 in 6iwh

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Sodium binding site 3 out of 5 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:32.9
occ:1.00
 O A:HOH490 2.4 38.4 1.0
OD1 A:ASP183 2.4 46.2 1.0
O A:THR178 2.5 20.1 1.0
O A:HIS181 2.6 29.2 1.0
O2 A:EDO307 2.6 40.9 1.0
CG A:ASP183 3.4 43.8 1.0
C A:THR178 3.6 27.5 1.0
C A:HIS181 3.6 29.9 1.0
CD1 A:TYR209 3.6 19.7 1.0
O1 A:EDO307 3.8 48.8 1.0
C2 A:EDO307 3.8 40.6 1.0
CB A:HIS181 3.8 32.1 1.0
OD2 A:ASP183 3.8 47.7 1.0
CA A:THR178 4.0 29.4 1.0
C1 A:EDO307 4.0 46.1 1.0
CD2 A:HIS181 4.1 36.4 1.0
CA A:HIS181 4.1 28.1 1.0
CG A:TYR209 4.2 16.1 1.0
CE1 A:TYR209 4.3 16.4 1.0
N A:HIS181 4.3 25.2 1.0
CB A:TYR209 4.3 17.4 1.0
CG A:HIS181 4.3 40.2 1.0
N A:ASP183 4.5 22.8 1.0
O A:HOH416 4.5 23.1 1.0
CB A:THR178 4.5 27.1 1.0
CB A:ASP183 4.7 27.0 1.0
N A:ALA182 4.7 28.9 1.0
N A:LEU179 4.7 19.1 1.0

Sodium binding site 4 out of 5 in 6iwh

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Sodium binding site 4 out of 5 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na101

b:24.4
occ:1.00
 O B:LEU87 2.3 20.0 1.0
O B:HOH275 2.3 25.9 1.0
O B:HIS84 2.3 16.7 1.0
O B:HOH203 2.4 19.4 1.0
O B:HOH260 2.5 25.9 1.0
O B:HOH277 2.6 27.9 1.0
C B:HIS84 3.4 18.3 1.0
C B:LEU87 3.4 25.7 1.0
N B:HIS84 3.9 18.5 1.0
N B:LEU87 4.0 23.2 1.0
CA B:LEU87 4.1 19.4 1.0
CA B:VAL85 4.1 17.0 1.0
N B:VAL85 4.1 17.4 1.0
CB B:LEU87 4.1 18.4 1.0
N B:GLY89 4.2 29.2 1.0
O B:VAL85 4.2 19.9 1.0
C B:VAL85 4.2 19.7 1.0
CA B:HIS84 4.3 20.4 1.0
N B:SER88 4.5 26.6 1.0
ND2 B:ASN83 4.5 37.7 1.0
O B:GLY89 4.6 23.0 1.0
CA B:SER88 4.7 30.9 1.0
C B:ASN83 4.8 17.9 1.0
CA B:GLY89 4.9 21.4 1.0
N B:THR86 4.9 16.1 1.0
C B:SER88 4.9 31.4 1.0
C B:GLY89 4.9 23.1 1.0
CB B:ASN83 5.0 24.1 1.0
CA B:ASN83 5.0 18.9 1.0

Sodium binding site 5 out of 5 in 6iwh

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Sodium binding site 5 out of 5 in the Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Rhesus Macaque Mhc Class I Molecule Mamu-B*05104 Complexed with C14-Gggi Lipopeptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na102

b:70.1
occ:1.00
 O B:HOH276 2.3 47.1 1.0
O B:HOH265 2.3 36.5 1.0
O B:HOH222 2.3 32.8 1.0
O B:HOH272 2.6 38.9 1.0
O B:ILE35 2.6 21.9 1.0
OH B:TYR66 3.7 27.0 1.0
C B:ILE35 3.9 24.9 1.0
O B:HOH253 4.3 27.7 1.0
N B:ILE35 4.4 15.4 1.0
O B:HOH209 4.5 27.8 1.0
CG2 B:ILE35 4.7 15.9 1.0
N B:GLU36 4.8 17.9 1.0
CA B:ILE35 4.8 19.8 1.0
CA B:GLU36 4.8 20.0 1.0
CZ B:TYR66 4.9 21.8 1.0

Reference:

Y.Yamamoto, D.Morita, Y.Shima, A.Midorikawa, T.Mizutani, J.Suzuki, N.Mori, T.Shiina, H.Inoko, Y.Tanaka, B.Mikami, M.Sugita. Identification and Structure of An Mhc Class I-Encoded Protein with the Potential to Presentn-Myristoylated 4-Mer Peptides to T Cells. J Immunol. V. 202 3349 2019.
ISSN: ESSN 1550-6606
PubMed: 31043477
DOI: 10.4049/JIMMUNOL.1900087
Page generated: Tue Oct 8 09:40:09 2024

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