Iodine in PDB 8c3l: PAAR2 N-Terminal Domain in Complex with Nanobody 33

Protein crystallography data

The structure of PAAR2 N-Terminal Domain in Complex with Nanobody 33, PDB code: 8c3l was solved by R.Loris, M.Prolic-Kalinsek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.17 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.599, 56.563, 128.292, 90, 90, 90
R / Rfree (%) 21.9 / 25.4

Other elements in 8c3l:

The structure of PAAR2 N-Terminal Domain in Complex with Nanobody 33 also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Iodine atom in the PAAR2 N-Terminal Domain in Complex with Nanobody 33 (pdb code 8c3l). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 13 binding sites of Iodine where determined in the PAAR2 N-Terminal Domain in Complex with Nanobody 33, PDB code: 8c3l:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 13 in 8c3l

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Iodine binding site 1 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I101

b:36.8
occ:0.38
 CD A:GLN2 3.7 56.6 1.0
NE2 A:GLN2 3.7 55.2 1.0
CG A:LYS4 3.9 75.1 1.0
CG A:GLN2 4.0 53.7 1.0
N A:LYS4 4.0 70.5 1.0
N A:LYS3 4.1 51.2 1.0
OE1 A:GLN2 4.2 54.1 1.0
CE A:LYS4 4.2 61.9 1.0
CB A:GLN2 4.2 39.2 1.0
CB A:LYS3 4.4 64.8 1.0
CD A:LYS4 4.4 71.3 1.0
CB A:LYS4 4.5 75.9 1.0
CA A:LYS3 4.7 59.2 1.0
C A:LYS3 4.8 60.6 1.0
C A:GLN2 4.9 43.3 1.0
CA A:LYS4 4.9 68.2 1.0
CA A:GLN2 4.9 35.5 1.0

Iodine binding site 2 out of 13 in 8c3l

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Iodine binding site 2 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I102

b:58.3
occ:0.90
 CG A:LYS23 3.2 57.5 1.0
CB A:LYS23 3.5 44.0 1.0
N A:LYS23 3.6 35.3 1.0
CD A:LYS23 3.8 62.2 1.0
O B:THR57 3.8 24.8 1.0
N B:THR57 3.9 23.4 1.0
O B:HOH331 4.0 31.2 1.0
CB B:THR56 4.0 28.3 1.0
CD A:PRO22 4.0 26.9 1.0
CG2 B:THR56 4.2 32.1 1.0
CA A:LYS23 4.2 35.4 1.0
N A:PRO22 4.2 29.4 1.0
CA B:THR56 4.3 22.5 1.0
CB A:PRO22 4.4 23.0 1.0
CE A:LYS23 4.4 69.4 1.0
CB A:PRO21 4.5 26.7 1.0
CG A:PRO22 4.6 27.4 1.0
C A:PRO22 4.6 29.5 1.0
OG1 B:THR57 4.6 32.8 1.0
C A:PRO21 4.6 30.3 1.0
C B:THR56 4.7 22.8 1.0
CA A:PRO22 4.7 34.9 1.0
C B:THR57 4.7 28.5 1.0
CA A:PRO21 4.8 29.9 1.0
CA B:THR57 4.9 25.5 1.0

Iodine binding site 3 out of 13 in 8c3l

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Iodine binding site 3 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I103

b:69.4
occ:0.69
 CG A:GLU13 3.7 34.3 0.4
CE A:LYS12 3.8 42.3 1.0
CG A:LYS12 3.8 46.5 1.0
CD A:LYS12 3.8 46.7 1.0
OE1 A:GLU13 3.8 43.5 0.6
CA A:GLU13 4.2 34.6 0.4
CA A:GLU13 4.2 34.9 0.6
O A:LYS12 4.3 33.6 1.0
N A:GLU13 4.4 32.8 1.0
C A:LYS12 4.4 30.2 1.0
CB A:LYS16 4.4 40.8 1.0
CG A:LYS16 4.4 39.8 1.0
CB A:GLU13 4.6 34.1 0.4
CB A:GLU13 4.6 34.0 0.6
CB A:LYS12 4.6 35.5 1.0
CD1 A:LEU9 4.7 58.0 1.0
CD A:GLU13 4.8 39.9 0.6
CD A:GLU13 4.9 38.0 0.4
OE2 A:GLU13 4.9 34.2 0.4

Iodine binding site 4 out of 13 in 8c3l

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Iodine binding site 4 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I104

b:34.9
occ:0.73
 CG2 A:THR49 3.5 18.8 0.6
CG1 A:ILE46 3.7 40.1 1.0
CE1 B:HIS54 4.0 45.0 1.0
CB A:THR49 4.0 23.4 0.5
CB A:THR49 4.1 24.2 0.6
CG2 A:THR49 4.1 15.9 0.5
CE2 A:TYR27 4.2 38.5 1.0
CD A:ARG45 4.3 36.8 0.5
CG A:ARG45 4.3 42.0 0.5
CA A:ILE46 4.3 31.9 1.0
CD1 A:ILE46 4.6 42.3 1.0
NE2 B:HIS54 4.6 43.3 1.0
CB A:ILE46 4.6 38.5 1.0
N A:ILE46 4.7 29.7 1.0
CG A:ARG45 4.7 41.7 0.5
CD2 A:TYR27 4.7 38.5 1.0
CE1 A:TYR50 4.7 27.0 1.0
O A:ARG45 4.8 32.1 1.0
C A:ARG45 4.9 39.0 1.0
CD A:ARG45 5.0 38.9 0.5

Iodine binding site 5 out of 13 in 8c3l

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Iodine binding site 5 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I201

b:34.8
occ:0.72
 O B:HOH313 3.6 26.1 1.0
NE1 B:TRP101 3.8 27.6 1.0
CA B:GLY99 4.0 33.1 1.0
CZ3 A:TRP14 4.3 31.8 1.0
CH2 A:TRP14 4.4 25.8 1.0
CZ2 B:TRP101 4.4 22.6 1.0
CE2 B:TRP101 4.5 27.8 1.0
N B:GLY99 4.5 26.4 1.0
CG A:PRO53 4.5 28.6 1.0
OG1 B:THR96 4.6 28.9 1.0
C B:GLY99 4.7 32.6 1.0
O B:GLY99 4.8 25.5 1.0
CD A:PRO53 4.8 30.8 1.0
CD1 B:TRP101 4.9 28.8 1.0

Iodine binding site 6 out of 13 in 8c3l

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Iodine binding site 6 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I202

b:46.6
occ:0.65
 O B:HOH350 3.1 49.9 1.0
N B:TYR59 3.6 22.2 1.0
CA B:SER58 3.8 22.9 1.0
CD A:PRO22 4.0 26.9 1.0
O B:HOH331 4.0 31.2 1.0
CB B:SER58 4.1 20.4 1.0
CD2 B:TYR59 4.1 24.6 1.0
CG A:PRO22 4.2 27.4 1.0
C B:SER58 4.2 26.5 1.0
O B:TYR59 4.4 27.2 1.0
CG B:GLU64 4.4 43.8 1.0
CG2 A:THR19 4.4 44.5 1.0
O B:HOH319 4.4 47.1 1.0
CA B:TYR59 4.6 21.2 1.0
O B:THR57 4.6 24.8 1.0
CB B:TYR59 4.6 22.8 1.0
CG B:TYR59 4.9 25.2 1.0
N B:SER58 4.9 22.4 1.0
C B:TYR59 5.0 29.7 1.0
CE2 B:TYR59 5.0 24.7 1.0

Iodine binding site 7 out of 13 in 8c3l

Go back to Iodine Binding Sites List in 8c3l
Iodine binding site 7 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I203

b:30.4
occ:0.42
 O D:HOH321 3.5 27.7 1.0
O D:HOH310 3.5 32.3 1.0
O B:HOH306 3.8 37.6 1.0
CG2 D:THR68 3.8 32.4 1.0
CG B:GLN81 3.9 23.2 1.0
O B:HOH351 3.9 54.0 1.0
CB D:THR68 4.1 30.6 1.0
CB D:GLN81 4.2 21.5 1.0
OG1 B:THR68 4.2 30.8 1.0
CB B:THR68 4.4 25.6 1.0
CB B:GLN81 4.5 23.1 1.0
CG D:GLN81 4.5 25.4 1.0
O B:HOH326 4.5 27.7 1.0
CG2 B:THR68 4.7 35.8 1.0
CD B:GLN81 4.7 23.1 1.0
OE1 B:GLN81 4.7 23.2 1.0
OG1 D:THR68 4.8 34.4 1.0
OG D:SER70 5.0 28.6 1.0

Iodine binding site 8 out of 13 in 8c3l

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Iodine binding site 8 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I101

b:41.7
occ:0.67
 O C:HOH207 3.6 42.2 1.0
CA C:SER26 4.1 27.4 1.0
OG C:SER29 4.1 48.2 1.0
CB C:SER29 4.1 32.7 1.0
O C:LYS25 4.5 28.0 1.0
CB C:SER26 4.5 44.1 1.0
N C:SER26 4.6 30.8 1.0
C C:LYS25 4.7 34.5 1.0
CG C:LYS25 4.7 42.9 1.0

Iodine binding site 9 out of 13 in 8c3l

Go back to Iodine Binding Sites List in 8c3l
Iodine binding site 9 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I102

b:30.9
occ:0.76
 OG C:SER29 3.6 48.2 1.0
CA C:SER29 4.0 30.9 1.0
CE C:MET32 4.1 33.5 1.0
CB C:SER29 4.1 32.7 1.0
CB C:MET32 4.5 32.1 1.0
O C:SER29 4.6 32.7 1.0
CD2 C:LEU20 4.7 34.1 1.0
C C:SER29 4.8 28.1 1.0

Iodine binding site 10 out of 13 in 8c3l

Go back to Iodine Binding Sites List in 8c3l
Iodine binding site 10 out of 13 in the PAAR2 N-Terminal Domain in Complex with Nanobody 33


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of PAAR2 N-Terminal Domain in Complex with Nanobody 33 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I103

b:33.5
occ:0.67
 CG C:LYS23 3.7 48.7 1.0
N C:LYS23 3.7 26.4 1.0
CB C:LYS23 3.7 43.7 1.0
N D:THR57 3.7 26.4 1.0
CB D:THR56 3.8 30.1 1.0
O D:THR57 3.9 23.8 1.0
CG2 D:THR56 4.0 36.8 1.0
O D:HOH331 4.0 30.8 1.0
CA D:THR56 4.0 25.1 1.0
CD C:PRO22 4.1 36.9 1.0
CD C:LYS23 4.1 48.1 1.0
N C:PRO22 4.3 29.9 1.0
CA C:LYS23 4.3 40.8 1.0
OG1 D:THR57 4.3 25.6 1.0
NZ C:LYS23 4.4 43.5 0.5
C D:THR56 4.4 22.7 1.0
CB C:PRO22 4.5 36.9 1.0
CG C:PRO22 4.6 35.1 1.0
CB C:PRO21 4.6 27.2 1.0
C C:PRO22 4.7 31.6 1.0
CA C:PRO22 4.7 34.5 1.0
CA D:THR57 4.7 23.2 1.0
C D:THR57 4.7 23.3 1.0
C C:PRO21 4.8 27.4 1.0
CE C:LYS23 4.8 46.9 0.6
CE C:LYS23 4.9 46.7 0.5
CA C:PRO21 5.0 29.3 1.0

Reference:

M.Prolik-Kalinsek, A.Volkov, R.Loris. PAAR2, the Ci Equivalent in Escherichia Coli O157:H7 Cryptic Prophage Cp-933P To Be Published.
Page generated: Wed Apr 5 09:27:02 2023

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