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Potassium in PDB 9b76: Crystal Structure of Humanized 44H10 Fab Version 21

Protein crystallography data

The structure of Crystal Structure of Humanized 44H10 Fab Version 21, PDB code: 9b76 was solved by A.Kassardjian, J.P.Julien, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.87 / 1.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 36.701, 86.068, 67.447, 90, 105.73, 90
R / Rfree (%) 17.5 / 21.2

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Humanized 44H10 Fab Version 21 (pdb code 9b76). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Crystal Structure of Humanized 44H10 Fab Version 21, PDB code: 9b76:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 9b76

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Potassium binding site 1 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K301

b:26.6
occ:1.00
 O H:HOH441 2.8 40.5 1.0
O H:THR73 2.8 45.2 1.0
N H:LEU29 3.4 21.9 1.0
C H:THR73 3.7 40.6 1.0
OG H:SER76 3.8 38.0 1.0
CA H:THR73 3.8 32.6 1.0
CB H:LEU29 3.9 22.9 1.0
CA H:SER76 3.9 23.5 1.0
CG H:LEU29 4.0 19.8 1.0
CA H:SER28 4.1 20.4 1.0
CB H:THR73 4.2 40.5 1.0
CD1 H:LEU29 4.2 22.1 1.0
C H:SER28 4.2 24.4 1.0
CA H:LEU29 4.2 20.4 1.0
OG H:SER28 4.3 28.0 1.0
CB H:SER76 4.3 25.2 1.0
N H:SER76 4.4 24.9 1.0
O H:PHE27 4.6 24.2 1.0
CB H:SER28 4.6 24.7 1.0
CG2 H:THR73 4.8 30.5 1.0
N H:SER74 5.0 39.6 1.0

Potassium binding site 2 out of 10 in 9b76

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Potassium binding site 2 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:K302

b:83.6
occ:1.00
 O H:GLY8 2.9 38.4 1.0
OG1 H:THR107 2.9 34.4 1.0
CG1 H:VAL10 3.3 44.4 1.0
N H:GLY8 3.6 41.8 1.0
C H:GLY8 3.9 55.8 1.0
CA H:SER7 4.0 22.6 1.0
CB H:THR107 4.0 28.4 1.0
C H:SER7 4.1 29.7 1.0
CA H:GLY8 4.4 43.4 1.0
CG2 H:THR107 4.6 24.4 1.0
O H:GLU6 4.7 24.7 1.0
CB H:VAL10 4.8 40.0 1.0
CB H:SER7 4.8 36.3 1.0
O H:HOH470 4.9 50.5 1.0
N H:SER7 4.9 21.9 1.0

Potassium binding site 3 out of 10 in 9b76

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Potassium binding site 3 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K302

b:37.7
occ:1.00
 ND2 L:ASN137 3.6 44.3 1.0
OG L:SER114 3.7 46.6 1.0
CB L:SER114 3.8 33.5 1.0
CG2 H:THR183 4.1 39.1 1.0
CE1 L:PHE116 4.2 41.5 1.0
CZ L:PHE116 4.2 41.3 1.0
CB L:ASN137 4.2 33.1 1.0
ND2 L:ASN138 4.3 42.2 1.0
OG1 H:THR135 4.3 59.1 1.0
CG L:ASN137 4.5 38.8 1.0
CG2 H:THR135 4.7 66.8 1.0
CB H:THR183 4.8 44.0 1.0
OG1 H:THR183 4.9 40.7 1.0

Potassium binding site 4 out of 10 in 9b76

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Potassium binding site 4 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K303

b:42.0
occ:1.00
 OE1 L:GLN160 2.7 61.9 1.0
O H:HOH504 2.8 59.5 1.0
O L:HOH541 3.0 50.3 1.0
O L:HOH419 3.6 34.2 1.0
CD L:GLN160 3.7 60.0 1.0
CB L:GLN160 3.8 29.6 1.0
CG L:GLN160 4.1 35.0 1.0
CB L:THR178 4.3 34.8 1.0
CG2 L:THR178 4.5 35.5 1.0
CG1 H:VAL169 4.5 48.8 1.0
OE1 H:GLN171 4.5 65.5 1.0
CG H:GLN171 4.5 56.2 1.0
CB H:VAL169 4.6 47.4 1.0
CB H:SER177 4.6 34.6 1.0
OG H:SER177 4.7 59.0 1.0
NE2 L:GLN160 4.7 53.8 1.0
OG1 L:THR178 4.8 30.9 1.0
OG1 L:THR180 4.9 44.9 1.0
CD H:GLN171 4.9 63.6 1.0
O L:HOH492 5.0 25.8 1.0
O L:THR178 5.0 30.8 1.0

Potassium binding site 5 out of 10 in 9b76

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Potassium binding site 5 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K304

b:38.4
occ:1.00
 N L:VAL110 3.6 27.8 1.0
O L:HOH416 3.8 35.8 1.0
CG2 L:VAL110 4.1 23.5 1.0
CB L:VAL110 4.1 26.2 1.0
CA L:THR109 4.2 29.2 1.0
CB L:THR109 4.2 26.7 1.0
C L:THR109 4.4 29.1 1.0
CA L:VAL110 4.5 30.9 1.0
CG2 L:THR109 4.5 29.9 1.0

Potassium binding site 6 out of 10 in 9b76

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Potassium binding site 6 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K305

b:45.1
occ:1.00
 CA L:GLN199 3.7 34.0 1.0
N L:GLN199 3.9 28.2 1.0
CB L:GLN199 4.1 24.5 1.0
C L:HIS198 4.1 34.4 1.0
O L:HIS198 4.3 32.6 1.0
CG2 L:THR197 4.4 35.2 1.0
CA L:HIS198 4.9 27.9 1.0
O L:HOH489 4.9 25.2 1.0
C L:GLN199 5.0 32.5 1.0
N L:HIS198 5.0 28.4 1.0

Potassium binding site 7 out of 10 in 9b76

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Potassium binding site 7 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K306

b:45.7
occ:1.00
 N L:ILE117 3.6 34.0 1.0
CA L:PHE116 3.9 29.1 1.0
O L:ILE117 4.0 31.8 1.0
CD2 L:PHE116 4.0 42.2 1.0
CB L:PHE116 4.2 30.2 1.0
NZ L:LYS207 4.3 68.0 1.0
C L:PHE116 4.3 29.7 1.0
CG2 L:ILE117 4.5 36.1 1.0
CG L:PHE116 4.6 43.5 1.0
CA L:ILE117 4.7 31.0 1.0
O L:VAL115 4.7 34.8 1.0
C L:ILE117 4.8 34.3 1.0

Potassium binding site 8 out of 10 in 9b76

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Potassium binding site 8 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K307

b:62.7
occ:1.00
 N L:VAL115 3.5 32.1 1.0
CA L:SER114 4.0 34.0 1.0
CE L:LYS207 4.2 62.1 1.0
C L:SER114 4.3 33.9 1.0
CG1 L:VAL205 4.3 52.9 1.0
O L:PRO113 4.3 33.2 1.0
O L:VAL115 4.4 34.8 1.0
CB L:VAL115 4.4 32.1 1.0
CA L:VAL115 4.4 29.2 1.0
NZ L:LYS207 4.5 68.0 1.0
CG2 L:VAL115 4.6 32.0 1.0
CB L:SER114 4.8 33.5 1.0
C L:VAL115 4.9 33.6 1.0

Potassium binding site 9 out of 10 in 9b76

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Potassium binding site 9 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K308

b:74.2
occ:1.00
 CB L:ASN93 3.9 36.7 1.0
O L:HOH457 4.1 43.3 1.0
ND2 L:ASN93 4.3 35.4 1.0
CG L:ASN93 4.5 32.4 1.0
O L:THR92 5.0 24.7 1.0

Potassium binding site 10 out of 10 in 9b76

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Potassium binding site 10 out of 10 in the Crystal Structure of Humanized 44H10 Fab Version 21


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Crystal Structure of Humanized 44H10 Fab Version 21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:K309

b:69.7
occ:1.00
 O L:GLY68 3.2 56.1 1.0
N L:ILE29 3.2 28.3 1.0
OE1 L:GLU28 3.3 70.8 1.0
CD L:GLU28 3.6 60.1 1.0
CG2 L:THR69 3.7 60.6 1.0
CA L:GLU28 3.7 36.9 1.0
OE2 L:GLU28 3.8 61.2 1.0
CG1 L:ILE29 3.8 21.5 1.0
CA L:THR69 3.8 56.6 1.0
O L:SER30 3.8 38.8 1.0
C L:GLU28 4.0 26.6 1.0
CE1 L:PHE71 4.0 33.4 1.0
C L:GLY68 4.0 54.2 1.0
N L:SER30 4.1 29.9 1.0
CZ L:PHE71 4.1 28.0 1.0
O L:GLN27 4.2 33.8 1.0
CA L:ILE29 4.2 26.3 1.0
N L:THR69 4.3 59.7 1.0
CB L:THR69 4.3 47.6 1.0
CG L:GLU28 4.4 41.9 1.0
C L:ILE29 4.4 30.8 1.0
CB L:GLU28 4.6 44.5 1.0
CB L:ILE29 4.6 21.8 1.0
N L:GLU28 4.6 37.2 1.0
NH1 L:ARG66 4.7 71.9 1.0
C L:SER30 4.7 45.6 1.0
CA L:SER30 4.8 33.5 1.0
C L:GLN27 4.8 42.4 1.0
C L:THR69 4.8 35.6 1.0
CB L:ALA25 4.9 27.0 1.0
CD1 L:ILE29 5.0 19.8 1.0

Reference:

A.Kassardjian, D.Ivanochko, B.Barber, A.Jetha, J.P.Julien. Humanization of Pan-Hla-Dr Mab 44H10 Hinges on Critical Residues in the Antibody Framework. Antibodies V. 13 2024.
ISSN: ISSN 2073-4468
PubMed: 39051333
DOI: 10.3390/ANTIB13030057
Page generated: Tue Aug 13 01:21:31 2024

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