Iodine in PDB 7byd: Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104

Protein crystallography data

The structure of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104, PDB code: 7byd was solved by D.Morita, M.Sugita, C.Iwashita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.96 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.937, 95.071, 123.352, 90, 90.89, 90
R / Rfree (%) 18.5 / 25

Other elements in 7byd:

The structure of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 1 atom

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 (pdb code 7byd). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 19 binding sites of Iodine where determined in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104, PDB code: 7byd:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 19 in 7byd

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Iodine binding site 1 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


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 SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I301

b:60.0
occ:1.00
 CB A:SER38 4.1 26.6 1.0
CG A:PRO43 4.1 51.1 1.0
CZ A:PHE36 4.1 21.8 1.0
CB A:ALA71 4.4 18.2 1.0
CG A:LYS68 4.4 34.9 1.0
CE2 A:PHE36 4.6 24.9 1.0
CA A:SER38 4.8 34.0 1.0
CB A:PRO43 4.9 41.7 1.0

Iodine binding site 2 out of 19 in 7byd

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Iodine binding site 2 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


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 SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:107.6
occ:1.00
 OE2 A:GLU53 3.1 99.0 1.0
CD A:GLU53 3.6 85.4 1.0
N A:ALA49 3.7 18.4 1.0
C A:ALA49 3.8 29.0 1.0
N A:PRO50 3.8 29.9 1.0
CG A:GLU53 3.9 60.6 1.0
C A:ARG48 3.9 20.9 1.0
CA A:ALA49 4.0 25.9 1.0
O A:ALA49 4.2 28.7 1.0
CA A:PRO50 4.2 21.4 1.0
CA A:ARG48 4.3 20.9 1.0
O A:PRO47 4.3 30.5 1.0
CD A:PRO50 4.3 24.2 1.0
OE1 A:GLU53 4.4 83.6 1.0
C A:PRO47 4.4 25.3 1.0
N A:ARG48 4.4 22.0 1.0
O A:ARG48 4.5 27.6 1.0
CB A:PRO47 4.6 28.6 1.0
CB A:PRO50 4.9 28.7 1.0

Iodine binding site 3 out of 19 in 7byd

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Iodine binding site 3 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


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 SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:108.8
occ:1.00
 NE A:ARG219 4.1 55.1 1.0
CD A:ARG219 4.1 45.2 1.0
O A:ARG219 4.1 33.8 1.0
CG A:ARG219 4.2 41.3 1.0
OE1 A:GLN224 4.5 55.9 1.0
CB A:ARG219 4.5 40.2 1.0
CB A:GLU222 4.8 50.9 1.0
C A:ARG219 5.0 36.2 1.0

Iodine binding site 4 out of 19 in 7byd

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Iodine binding site 4 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


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 SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:83.0
occ:1.00
 N A:ARG14 3.7 41.8 1.0
O A:ARG14 3.8 73.8 1.0
O A:HOH404 3.8 24.3 1.0
CD A:PRO20 3.9 35.9 1.0
N A:PRO20 3.9 39.2 1.0
C A:GLU19 4.0 51.5 1.0
C A:ARG14 4.0 62.9 1.0
N A:GLU19 4.1 59.0 1.0
C A:GLY18 4.2 68.0 1.0
CA A:GLU19 4.2 57.3 1.0
O A:GLY18 4.2 69.0 1.0
CB A:SER13 4.4 31.6 1.0
O A:GLU19 4.4 44.8 1.0
CA A:ARG14 4.4 47.3 1.0
CA A:PRO20 4.4 34.4 1.0
CA A:SER13 4.4 33.7 1.0
N A:PRO15 4.4 72.9 1.0
CB A:PRO20 4.5 36.5 1.0
C A:SER13 4.5 34.2 1.0
CA A:PRO15 4.7 70.7 1.0
CG A:PRO20 4.7 34.5 1.0
CA A:GLY18 4.7 70.5 1.0

Iodine binding site 5 out of 19 in 7byd

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Iodine binding site 5 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I101

b:73.8
occ:1.00
 NE B:ARG97 3.2 39.0 1.0
CB B:PRO72 3.5 43.0 1.0
CD B:ARG97 3.8 46.1 1.0
OD1 B:ASN17 3.9 79.8 1.0
C B:PRO72 4.0 52.3 1.0
C B:ASN73 4.1 62.4 1.0
N B:ASN73 4.1 60.2 1.0
CZ B:ARG97 4.1 51.9 1.0
O B:ASN73 4.2 58.8 1.0
CG B:PRO72 4.2 31.4 1.0
NH2 B:ARG97 4.2 48.9 1.0
CG B:ASN17 4.3 91.3 1.0
O B:PRO72 4.3 44.5 1.0
CA B:ASN73 4.3 59.3 1.0
CA B:PRO72 4.3 55.6 1.0
N B:GLU74 4.4 59.1 1.0
ND2 B:ASN17 4.6 111.5 1.0
CB B:PRO15 4.7 43.2 1.0
CA B:ASN17 4.7 67.1 1.0
N B:ASN17 4.7 73.1 1.0
CH2 B:TRP95 4.8 33.0 1.0
CG B:ARG97 4.8 53.5 1.0
CA B:GLU74 4.8 68.0 1.0
CZ3 B:TRP95 4.9 25.8 1.0
C B:GLU16 5.0 60.3 1.0

Iodine binding site 6 out of 19 in 7byd

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Iodine binding site 6 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I102

b:62.3
occ:1.00
 N B:GLY43 3.4 21.3 1.0
CE B:LYS94 3.7 62.7 1.0
NZ B:LYS94 3.7 57.2 1.0
CB B:ALA79 3.8 13.5 1.0
O B:GLU77 3.8 29.5 1.0
C B:TYR78 4.0 22.4 1.0
N B:ALA79 4.0 19.6 1.0
N B:ASN42 4.0 23.6 1.0
C B:GLU77 4.1 32.8 1.0
CA B:GLY43 4.1 16.8 1.0
CA B:ASN42 4.2 20.5 1.0
CA B:TYR78 4.2 19.9 1.0
CB B:LEU40 4.2 20.6 1.0
O B:TYR78 4.2 24.2 1.0
CD B:LYS94 4.3 50.0 1.0
CG B:GLU77 4.3 61.0 1.0
C B:ASN42 4.3 29.3 1.0
N B:TYR78 4.3 27.6 1.0
CD B:GLU77 4.4 80.1 1.0
CB B:GLU77 4.5 32.9 1.0
CA B:ALA79 4.6 19.0 1.0
O B:LEU40 4.6 20.9 1.0
OE1 B:GLU77 4.7 66.2 1.0
CD1 B:LEU40 4.7 15.2 1.0
C B:LEU40 4.7 20.1 1.0
OE2 B:GLU77 4.8 71.3 1.0
C B:LYS41 4.8 27.6 1.0
CA B:GLU77 5.0 33.0 1.0

Iodine binding site 7 out of 19 in 7byd

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Iodine binding site 7 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I201

b:85.7
occ:1.00
 ND2 D:ASN56 3.7 52.7 1.0
N D:GLN48 3.8 33.3 1.0
CZ D:PHE45 3.9 28.5 1.0
CG1 D:ILE47 3.9 36.9 1.0
O D:GLN48 4.0 32.2 1.0
CE2 D:PHE45 4.0 22.9 1.0
CA D:ILE47 4.1 29.9 1.0
C D:ILE47 4.5 33.2 1.0
CG2 D:ILE54 4.5 41.7 1.0
CB D:ILE47 4.6 29.6 1.0
CG D:GLN48 4.7 41.1 1.0
CG D:ASN56 4.7 56.3 1.0
CA D:GLN48 4.7 36.5 1.0
O D:ILE46 4.8 34.4 1.0
C D:GLN48 4.8 39.0 1.0
CB D:ASN56 4.9 51.3 1.0

Iodine binding site 8 out of 19 in 7byd

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Iodine binding site 8 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I301

b:120.6
occ:1.00
 NE2 E:GLN215 3.7 48.5 1.0
CA E:GLN235 3.8 48.3 1.0
OE1 E:GLN215 3.9 57.3 1.0
CG2 E:THR234 4.0 51.4 1.0
N E:GLN235 4.0 50.2 1.0
CG E:LYS236 4.0 63.5 1.0
C E:GLN235 4.0 55.0 1.0
N E:LYS236 4.2 53.0 1.0
O E:THR234 4.2 68.3 1.0
CD E:GLN215 4.2 54.3 1.0
C E:THR234 4.2 55.5 1.0
CE E:LYS236 4.4 55.6 1.0
O E:GLN235 4.6 51.6 1.0
CD E:LYS236 4.8 67.2 1.0
CB E:THR234 4.9 46.8 1.0

Iodine binding site 9 out of 19 in 7byd

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Iodine binding site 9 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:I302

b:114.5
occ:1.00
 NZ G:LYS41 3.6 34.4 1.0
CB E:GLN182 3.6 56.3 1.0
OG D:SER148 3.8 98.6 1.0
CA E:GLN182 3.9 49.4 1.0
CB E:ALA184 3.9 38.2 1.0
N E:ALA184 3.9 50.7 1.0
C E:GLN182 4.0 43.1 1.0
CE G:LYS41 4.0 41.0 1.0
N E:PRO183 4.2 46.9 1.0
CD G:LYS41 4.2 46.4 1.0
CG E:GLN182 4.4 55.7 1.0
CD E:PRO183 4.4 49.3 1.0
CB D:SER148 4.5 84.6 1.0
CA E:ALA184 4.5 56.1 1.0
O E:GLN182 4.5 45.9 1.0
CG E:LEU185 4.8 47.5 1.0
CG E:PRO183 5.0 44.1 1.0
C E:PRO183 5.0 47.2 1.0

Iodine binding site 10 out of 19 in 7byd

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Iodine binding site 10 out of 19 in the Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of SN45 Tcr in Complex with Lipopeptide-Bound Mamu- B*05104 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:I301

b:72.1
occ:1.00
 CZ F:PHE36 4.1 33.4 1.0
CB F:SER38 4.2 43.5 1.0
NH2 F:ARG75 4.2 45.0 1.0
CG F:PRO43 4.3 51.5 1.0
CG F:LYS68 4.3 40.8 1.0
CB F:PRO43 4.4 48.4 1.0
CB F:ALA71 4.5 34.9 1.0
CE1 F:PHE36 4.6 32.8 1.0
CA F:SER38 4.6 49.5 1.0
CE F:LYS68 4.8 43.3 1.0
O F:SER38 4.8 53.8 1.0
CB F:LYS68 4.9 27.2 1.0
CA F:LYS68 5.0 28.6 1.0
CD F:LYS68 5.0 44.5 1.0

Reference:

D.Morita, C.Iwashita, T.Mizutani, N.Mori, B.Mikami, M.Sugita. Crystal Structure of the Ternary Complex of Tcr, Mhc Class I and Lipopeptides. Int.Immunol. V. 32 805 2020.
ISSN: ESSN 1460-2377
PubMed: 32720986
DOI: 10.1093/INTIMM/DXAA050
Page generated: Sat Apr 3 16:03:06 2021

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