Atomistry » Iodine » PDB 7ben-7fgj » 7byd
Atomistry »
  Iodine »
    PDB 7ben-7fgj »
      7byd »

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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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

Go back to Iodine Binding Sites List in 7byd
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: Mon Aug 12 00:52:45 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy