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Iodine in PDB 4pgc: Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal

Protein crystallography data

The structure of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal, PDB code: 4pgc was solved by P.Celie, R.P.Joosten, A.Perrakis, J.Neefjes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.11 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 66.179, 90.303, 89.370, 90.00, 111.58, 90.00
R / Rfree (%) 21.2 / 24.3

Iodine Binding Sites:

The binding sites of Iodine atom in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal (pdb code 4pgc). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal, PDB code: 4pgc:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 4pgc

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Iodine binding site 1 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I6

b:62.1
occ:1.00
I1 C:TYI6 0.0 62.1 1.0
CE1 C:TYI6 2.1 59.7 1.0
CZ C:TYI6 3.0 56.6 1.0
CD1 C:TYI6 3.1 57.2 1.0
OH C:TYI6 3.1 42.0 1.0
O C:HOH101 3.3 38.4 1.0
CD C:PRO3 3.3 0.2 1.0
CG C:PRO3 3.6 0.7 1.0
CE2 A:TYR159 3.7 53.1 1.0
CD2 A:TYR159 3.7 48.0 1.0
OG A:SER99 3.8 39.2 1.0
CD1 A:LEU156 3.9 50.2 1.0
OE1 A:GLN114 4.0 42.2 1.0
CE2 C:TYI6 4.3 61.4 1.0
CZ A:TYR159 4.3 54.5 1.0
CG A:TYR159 4.4 49.3 1.0
CG C:TYI6 4.4 55.9 1.0
NE2 A:GLN114 4.6 39.4 1.0
CD A:GLN114 4.6 37.6 1.0
N C:PRO3 4.7 1.0 1.0
CD2 C:TYI6 4.9 53.4 1.0
CE1 A:TYR159 4.9 48.5 1.0
OH A:TYR159 4.9 55.2 1.0
CD1 A:TYR159 4.9 52.6 1.0

Iodine binding site 2 out of 4 in 4pgc

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Iodine binding site 2 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I6

b:59.7
occ:1.00
I2 C:TYI6 0.0 59.7 1.0
CE2 C:TYI6 2.1 61.4 1.0
CZ C:TYI6 3.0 56.6 1.0
CD2 C:TYI6 3.0 53.4 1.0
OH C:TYI6 3.0 42.0 1.0
CG2 A:VAL9 3.7 23.2 1.0
CZ A:PHE74 4.1 30.3 1.0
CE2 A:PHE74 4.1 31.0 1.0
CE1 C:TYI6 4.3 59.7 1.0
CG C:TYI6 4.3 55.9 1.0
CB A:VAL9 4.4 23.5 1.0
O C:PRO3 4.5 0.8 1.0
ND2 A:ASN70 4.5 30.5 1.0
CG A:ASN70 4.6 28.4 1.0
CG1 A:VAL97 4.6 25.6 1.0
OH A:TYR22 4.6 29.1 1.0
CG1 A:VAL9 4.6 24.3 1.0
CB A:VAL97 4.8 23.0 1.0
OD1 A:ASN70 4.8 30.8 1.0
CD1 C:TYI6 4.9 57.2 1.0
OE2 A:GLU24 4.9 28.9 1.0
O C:ALA2 5.0 0.7 1.0

Iodine binding site 3 out of 4 in 4pgc

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Iodine binding site 3 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I6

b:55.4
occ:1.00
I1 F:TYI6 0.0 55.4 1.0
CE1 F:TYI6 2.1 46.6 1.0
CZ F:TYI6 3.1 42.2 1.0
CD1 F:TYI6 3.1 41.1 1.0
OH F:TYI6 3.2 35.5 1.0
CD F:PRO3 3.6 0.1 1.0
CD1 D:LEU156 3.6 60.0 1.0
CG F:PRO3 3.6 0.3 1.0
CD2 D:TYR159 3.7 52.4 1.0
OG D:SER99 3.7 30.7 1.0
CE2 D:TYR159 3.7 56.4 1.0
OE1 D:GLN114 3.8 45.0 1.0
CE2 F:TYI6 4.4 45.9 1.0
CD D:GLN114 4.4 40.2 1.0
NE2 D:GLN114 4.4 44.2 1.0
CG D:TYR159 4.4 45.5 1.0
CG F:TYI6 4.4 44.6 1.0
CZ D:TYR159 4.5 56.3 1.0
CD2 F:TYI6 4.9 41.9 1.0

Iodine binding site 4 out of 4 in 4pgc

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Iodine binding site 4 out of 4 in the Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Mhc Class I in Complex with Modified Sendai Virus Nucleoprotein Peptide Fapgn(3,5-Diiodotyrosine)Pal within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I6

b:50.3
occ:1.00
I2 F:TYI6 0.0 50.3 1.0
CE2 F:TYI6 2.1 45.9 1.0
CZ F:TYI6 3.0 42.2 1.0
OH F:TYI6 3.0 35.5 1.0
CD2 F:TYI6 3.1 41.9 1.0
CG2 D:VAL9 3.7 23.2 1.0
CZ D:PHE74 4.0 35.7 1.0
CE2 D:PHE74 4.1 34.8 1.0
CE1 F:TYI6 4.3 46.6 1.0
CG F:TYI6 4.4 44.6 1.0
CB D:VAL9 4.4 23.6 1.0
CG1 D:VAL97 4.4 24.6 1.0
ND2 D:ASN70 4.5 29.2 1.0
O F:PRO3 4.5 78.3 1.0
CG D:ASN70 4.6 27.5 1.0
CG1 D:VAL9 4.6 25.8 1.0
CB D:VAL97 4.6 23.0 1.0
OH D:TYR22 4.7 29.1 1.0
OD1 D:ASN70 4.8 29.4 1.0
CD1 F:TYI6 4.9 41.1 1.0
CB D:SER99 5.0 27.9 1.0
CG2 D:VAL97 5.0 23.3 1.0
OE2 D:GLU24 5.0 25.5 1.0

Reference:

M.A.Garstka, A.Fish, P.H.Celie, R.P.Joosten, G.M.Janssen, I.Berlin, R.Hoppes, M.Stadnik, L.Janssen, H.Ovaa, P.A.Van Veelen, A.Perrakis, J.Neefjes. The First Step of Peptide Selection in Antigen Presentation By Mhc Class I Molecules. Proc.Natl.Acad.Sci.Usa V. 112 1505 2015.
ISSN: ESSN 1091-6490
PubMed: 25605945
DOI: 10.1073/PNAS.1416543112
Page generated: Sun Aug 11 19:30:09 2024

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