Iodine in PDB 5wmp: Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide

Protein crystallography data

The structure of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide, PDB code: 5wmp was solved by S.Gras, J.Rossjohn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.24 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 50.863, 81.720, 110.943, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 19.9

Other elements in 5wmp:

The structure of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 4 atoms
Sodium (Na) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide (pdb code 5wmp). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 4 binding sites of Iodine where determined in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide, PDB code: 5wmp:
Jump to Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 5wmp

Go back to Iodine Binding Sites List in 5wmp
Iodine binding site 1 out of 4 in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:17.0
occ:1.00
O A:HOH523 3.4 17.3 1.0
O A:HOH495 3.5 13.2 1.0
CE A:LYS68 4.0 36.8 1.0
CB A:SER38 4.0 8.0 1.0
CG A:LYS68 4.0 11.5 1.0
CZ A:PHE36 4.1 6.8 1.0
NZ A:LYS68 4.3 46.0 1.0
CA A:SER38 4.4 6.5 1.0
CB A:PRO43 4.4 9.2 1.0
CG A:PRO43 4.5 12.9 1.0
CB A:LYS68 4.6 10.8 1.0
CE1 A:PHE36 4.6 9.3 1.0
CA A:LYS68 4.6 8.9 1.0
CD A:LYS68 4.7 18.0 1.0
O A:SER38 4.8 10.0 1.0
CB A:ALA71 4.9 8.5 1.0

Iodine binding site 2 out of 4 in 5wmp

Go back to Iodine Binding Sites List in 5wmp
Iodine binding site 2 out of 4 in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:39.1
occ:1.00
O A:HOH452 3.1 26.1 1.0
CD A:LYS178 3.5 53.0 1.0
CE A:LYS178 3.9 69.9 1.0
CG2 A:THR31 3.9 11.4 1.0
CD A:PRO50 3.9 17.0 1.0
NE1 A:TRP51 3.9 14.1 1.0
CG A:LYS178 4.2 33.4 1.0
CD1 A:TRP51 4.2 15.1 1.0
NE A:ARG239 4.3 46.8 1.0
CB A:LYS178 4.4 16.4 1.0
CG A:PRO50 4.4 21.8 1.0
O A:HOH659 4.4 38.9 1.0
CB A:ALA49 4.6 13.8 1.0
O A:HOH765 4.6 28.7 1.0
CD A:ARG239 4.9 42.3 1.0
OG1 A:THR31 4.9 11.8 1.0

Iodine binding site 3 out of 4 in 5wmp

Go back to Iodine Binding Sites List in 5wmp
Iodine binding site 3 out of 4 in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:30.6
occ:1.00
O B:HOH330 3.2 24.2 1.0
N B:GLY43 3.3 19.4 1.0
O B:GLU77 3.9 13.6 1.0
CB B:ALA79 3.9 11.4 1.0
N B:ASN42 3.9 15.3 1.0
CA B:GLY43 4.0 20.0 1.0
C B:TYR78 4.0 13.8 1.0
C B:GLU77 4.1 16.7 1.0
N B:ALA79 4.1 10.2 1.0
CA B:ASN42 4.2 16.4 1.0
C B:ASN42 4.2 21.4 1.0
CA B:TYR78 4.2 11.3 1.0
O B:HOH264 4.2 24.1 1.0
N B:TYR78 4.3 12.6 1.0
CB B:GLU77 4.3 18.9 1.0
CB B:LEU40 4.3 11.4 1.0
O B:TYR78 4.3 12.7 1.0
O B:LEU40 4.4 13.1 1.0
C B:LEU40 4.6 13.7 1.0
CA B:ALA79 4.6 10.3 1.0
C B:LYS41 4.7 16.8 1.0
CA B:GLU77 4.9 17.0 1.0
CD1 B:LEU40 4.9 16.2 1.0
NZ B:LYS94 4.9 60.4 1.0
N B:LYS41 5.0 11.9 1.0

Iodine binding site 4 out of 4 in 5wmp

Go back to Iodine Binding Sites List in 5wmp
Iodine binding site 4 out of 4 in the Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of Hla-B7 in Complex with Tpr, A Cmv Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I102

b:33.0
occ:1.00
CE1 B:HIS13 3.4 22.4 1.0
ND1 B:HIS13 3.5 23.3 1.0
O B:HOH209 3.7 36.4 1.0
O B:HOH301 3.7 25.7 1.0
CD1 B:PHE22 3.9 15.7 1.0
O B:HOH280 4.0 25.3 1.0
CA B:ASN21 4.1 15.4 1.0
CE1 B:PHE22 4.2 16.9 1.0
O B:SER20 4.3 20.8 1.0
CD B:ARG12 4.4 16.4 1.0
C B:ASN21 4.4 17.5 1.0
NH1 B:ARG12 4.6 16.0 1.0
NE2 B:HIS13 4.7 22.0 1.0
N B:ASN21 4.7 17.2 1.0
N B:PHE22 4.8 12.7 1.0
C B:SER20 4.8 22.3 1.0
CG B:HIS13 4.8 20.7 1.0
OD1 B:ASN21 4.9 15.8 1.0
O B:ASN21 4.9 15.5 1.0

Reference:

L.C.Rowntree, T.H.O.Nguyen, H.Halim, A.W.Purcell, J.Rossjohn, S.Gras, T.C.Kotsimbos, N.A.Mifsud. Inability to Detect Cross-Reactive Memory T Cells Challenges the Frequency of Heterologous Immunity Among Common Viruses. J. Immunol. V. 200 3993 2018.
ISSN: ESSN 1550-6606
PubMed: 29735483
DOI: 10.4049/JIMMUNOL.1800010
Page generated: Sun Dec 13 19:41:57 2020

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