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Iodine in PDB 7t0k: Crystal Structure of S25-2 Fab Unliganded 4

Protein crystallography data

The structure of Crystal Structure of S25-2 Fab Unliganded 4, PDB code: 7t0k was solved by M.S.G.Legg, R.J.Blackler, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.558, 135.497, 73.977, 90, 94.26, 90
R / Rfree (%) 22.2 / 25.5

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 34;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of S25-2 Fab Unliganded 4 (pdb code 7t0k). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 34 binding sites of Iodine where determined in the Crystal Structure of S25-2 Fab Unliganded 4, PDB code: 7t0k:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 34 in 7t0k

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Iodine binding site 1 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I301

b:41.6
occ:0.91
 NZ L:LYS89 3.3 31.0 1.0
CB H:SER35 3.7 31.9 1.0
OG H:SER35 3.8 32.2 1.0
CD1 H:TRP47 4.0 33.9 1.0
OD2 H:ASP95 4.0 45.5 1.0
CG2 H:VAL37 4.0 33.0 1.0
CD L:LYS89 4.2 31.9 1.0
CE L:LYS89 4.2 30.3 1.0
NE1 H:TRP47 4.4 31.3 1.0
CZ2 H:TRP103 4.5 31.5 1.0
CZ L:PHE98 4.5 31.1 1.0
CB H:ALA93 4.6 30.8 1.0
CG L:ARG96 4.7 36.2 1.0
CG H:ASP95 4.7 43.4 1.0
OH L:TYR36 4.7 34.2 1.0
CE2 L:PHE98 4.9 32.0 1.0
CH2 H:TRP103 5.0 31.8 1.0

Iodine binding site 2 out of 34 in 7t0k

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Iodine binding site 2 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I302

b:40.3
occ:0.69
 O L:HOH422 2.9 38.7 1.0
N L:TRP50 3.4 36.6 1.0
OG L:SER91 3.5 41.3 1.0
N L:LEU33 3.8 35.9 1.0
C L:TYR32 3.9 38.1 1.0
CA L:TYR32 3.9 40.9 1.0
CB L:TYR49 3.9 36.5 1.0
O L:LEU33 4.0 31.2 1.0
C L:LEU33 4.1 36.7 1.0
CD1 L:TRP50 4.1 48.3 1.0
CB L:ALA34 4.1 36.0 1.0
CA L:TYR49 4.2 35.1 1.0
CA L:TRP50 4.2 38.6 1.0
CD1 L:TYR32 4.3 52.9 1.0
C L:TYR49 4.3 36.1 1.0
N L:ALA34 4.4 31.9 1.0
CB L:TYR32 4.4 44.9 1.0
O L:TYR32 4.5 41.5 1.0
CA L:LEU33 4.5 36.8 1.0
CA L:ALA34 4.7 34.4 1.0
O L:ASN31 4.8 38.5 1.0
CB L:SER91 4.8 30.5 1.0
NE1 L:TRP50 4.8 48.3 1.0
CG L:TYR32 4.9 49.0 1.0
CG L:TRP50 4.9 46.2 1.0

Iodine binding site 3 out of 34 in 7t0k

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Iodine binding site 3 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I303

b:46.5
occ:0.52
 N L:LEU94 3.5 33.9 1.0
CZ H:PHE50 4.2 30.6 1.0
NH2 H:ARG52 4.2 36.4 1.0
CA L:LEU94 4.2 35.2 1.0
CA L:ASN93 4.2 37.7 1.0
CD1 L:LEU94 4.3 43.3 1.0
O H:HOH433 4.3 42.5 1.0
C L:ASN93 4.4 34.5 1.0
NH1 L:ARG96 4.5 33.7 1.0
O L:TYR92 4.6 36.3 1.0
ND2 L:ASN93 4.6 49.2 1.0
CE2 H:PHE50 4.7 32.4 1.0
O L:LEU94 5.0 34.6 1.0
N L:ASN93 5.0 36.0 1.0

Iodine binding site 4 out of 34 in 7t0k

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Iodine binding site 4 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I304

b:71.9
occ:0.61
 CD L:PRO40 3.9 61.9 1.0
CE L:LYS103 4.1 50.1 1.0
CG2 L:VAL85 4.1 35.0 1.0
CA L:ALA84 4.2 38.3 1.0
C L:ALA84 4.3 39.4 1.0
CG L:PRO40 4.3 60.4 1.0
N L:VAL85 4.4 35.9 1.0
N L:ALA84 4.5 40.3 1.0
CB L:PRO40 4.5 58.6 1.0
NZ L:LYS103 4.6 55.7 1.0
N L:PRO40 4.6 56.3 1.0
CD1 L:LEU83 4.6 60.0 1.0
O L:ALA84 4.7 38.6 1.0
CG L:LYS103 4.9 48.2 1.0
CD L:LYS103 4.9 50.3 1.0
OD1 L:ASP165 4.9 47.7 1.0
O L:GLN38 4.9 31.9 1.0
CG L:LEU83 4.9 56.2 1.0
CA L:PRO40 5.0 54.5 1.0

Iodine binding site 5 out of 34 in 7t0k

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Iodine binding site 5 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:I305

b:80.3
occ:0.60
 OG L:SER14 3.8 63.6 1.0
C L:ARG108 3.9 49.7 1.0
CA L:ARG108 4.0 52.9 1.0
O L:ARG108 4.1 56.7 1.0
N L:ARG108 4.2 53.7 1.0
N L:ALA109 4.3 53.1 1.0
CB L:SER14 4.4 58.8 1.0
CB L:LYS107 4.5 56.8 1.0
C L:LYS107 4.5 53.0 1.0
O L:LYS107 4.7 60.1 1.0
CA L:ALA109 5.0 52.7 1.0

Iodine binding site 6 out of 34 in 7t0k

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Iodine binding site 6 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I301

b:32.5
occ:0.93
 O H:HOH470 3.4 46.2 1.0
N H:TRP154 3.6 29.4 1.0
CA H:THR153 3.9 33.7 1.0
CA H:SER160 3.9 37.1 1.0
CB H:SER160 4.0 39.8 1.0
CG2 H:VAL163 4.0 33.1 1.0
CB H:THR153 4.1 34.9 1.0
CA H:GLY157 4.2 34.5 1.0
N H:SER160 4.2 35.9 1.0
C H:THR153 4.3 32.6 1.0
CG2 H:THR153 4.4 35.8 1.0
CG1 H:VAL163 4.4 30.5 1.0
O H:GLY157 4.5 37.2 1.0
CB H:VAL163 4.5 32.4 1.0
CB H:TRP154 4.6 29.9 1.0
CD1 H:TRP154 4.6 28.4 1.0
O H:VAL152 4.6 34.5 1.0
O H:TRP154 4.6 33.3 1.0
CA H:TRP154 4.6 30.3 1.0
C H:GLY157 4.7 35.6 1.0
N H:GLY157 4.7 33.9 1.0
C H:LEU159 4.9 32.2 1.0

Iodine binding site 7 out of 34 in 7t0k

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Iodine binding site 7 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I302

b:54.2
occ:0.79
 O B:HOH435 3.5 28.6 1.0
CG H:LYS205 3.6 43.8 1.0
O H:THR204 3.8 34.8 1.0
N H:THR204 3.8 36.0 1.0
CE H:LYS205 3.9 49.0 1.0
CA H:PRO200 3.9 34.1 1.0
C H:THR204 4.0 31.8 1.0
C H:SER203 4.1 34.8 1.0
N H:PRO200 4.1 29.1 1.0
C H:HIS199 4.2 28.5 1.0
CA H:SER203 4.2 34.5 1.0
O H:HIS199 4.3 26.5 1.0
CD H:LYS205 4.3 48.6 1.0
N H:LYS205 4.5 31.7 1.0
N H:HIS199 4.5 27.1 1.0
CA H:THR204 4.5 33.2 1.0
O H:SER203 4.6 32.4 1.0
CB H:PRO200 4.7 35.2 1.0
CB H:ALA198 4.7 33.7 1.0
CD H:PRO200 4.7 32.1 1.0
CG H:PRO200 4.7 33.7 1.0
NZ H:LYS205 4.7 52.2 1.0
CB H:LYS205 4.8 37.4 1.0
C H:PRO200 4.9 31.8 1.0
N H:SER203 4.9 28.0 1.0
O H:PRO200 5.0 33.2 1.0

Iodine binding site 8 out of 34 in 7t0k

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Iodine binding site 8 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I303

b:52.6
occ:0.56
 O H:PHE100C 3.1 79.4 1.0
O H:ASP95 3.5 65.9 1.0
NE H:ARG94 3.6 38.9 1.0
N H:PHE100C 3.9 70.9 1.0
O H:ARG94 4.0 40.3 1.0
C H:PHE100C 4.0 71.8 1.0
C H:ASP95 4.1 54.7 1.0
C H:ARG94 4.1 39.3 1.0
NH1 H:ARG94 4.1 39.8 1.0
CB H:ARG94 4.2 35.6 1.0
N H:ASP95 4.2 45.2 1.0
CG H:ARG94 4.3 35.7 1.0
CE1 H:TYR32 4.3 44.5 1.0
CA H:ARG100B 4.3 67.8 1.0
CZ H:ARG94 4.4 39.8 1.0
CA H:ASP95 4.4 48.4 1.0
CD1 H:TYR32 4.4 39.4 1.0
CD H:ARG94 4.5 37.1 1.0
C H:ARG100B 4.5 68.8 1.0
CA H:PHE100C 4.6 70.0 1.0
CB H:ARG100B 4.7 65.4 1.0
CA H:SER101 4.8 55.2 1.0
N H:SER101 4.8 63.1 1.0
CB H:HIS96 4.8 65.6 1.0
CA H:ARG94 4.8 35.6 1.0
OG H:SER101 4.9 57.7 1.0

Iodine binding site 9 out of 34 in 7t0k

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Iodine binding site 9 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I304

b:43.7
occ:0.47
 O B:HOH436 3.6 44.4 1.0
N H:VAL121 3.9 26.4 1.0
CG1 H:VAL206 4.1 34.4 1.0
NZ H:LYS208 4.2 47.2 1.0
CB H:VAL121 4.3 28.4 1.0
CG2 H:VAL206 4.3 33.9 1.0
O H:VAL121 4.3 31.2 1.0
O H:PRO119 4.5 31.5 1.0
CG2 B:THR204 4.5 34.2 1.0
CA H:VAL121 4.6 28.0 1.0
CG2 H:VAL121 4.6 29.5 1.0
CA H:SER120 4.7 30.5 1.0
C H:SER120 4.8 29.9 1.0
CB H:VAL206 4.9 34.3 1.0
C H:VAL121 5.0 27.6 1.0

Iodine binding site 10 out of 34 in 7t0k

Go back to Iodine Binding Sites List in 7t0k
Iodine binding site 10 out of 34 in the Crystal Structure of S25-2 Fab Unliganded 4


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 S25-2 Fab Unliganded 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:I305

b:53.9
occ:0.45
 N H:SER128 4.0 46.9 1.0
OG H:SER128 4.1 52.6 1.0
O H:ARG213 4.2 61.7 1.0
CA H:GLY127 4.2 41.8 1.0
C H:ARG213 4.3 53.8 1.0
CG L:PRO119 4.4 32.0 1.0
CB H:SER128 4.6 52.3 1.0
C H:GLY127 4.6 42.2 1.0
CB L:PRO119 4.7 29.0 1.0
CA H:SER128 4.9 53.2 1.0

Reference:

R.J.Blackler, S.Muller-Loennies, B.Pokorny-Lehrer, M.S.G.Legg, L.Brade, H.Brade, P.Kosma, S.V.Evans. Antigen Binding By Conformational Selection in Near-Germline Antibodies. J.Biol.Chem. V. 298 01901 2022.
ISSN: ESSN 1083-351X
PubMed: 35395245
DOI: 10.1016/J.JBC.2022.101901
Page generated: Fri Aug 8 23:45:13 2025

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