Sodium in PDB 9b74: Crystal Structure of Humanized 44H10 Fab Version 14

Protein crystallography data

The structure of Crystal Structure of Humanized 44H10 Fab Version 14, PDB code: 9b74 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) 36.88 / 2.48
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.325, 123.325, 90.714, 90, 90, 120
R / Rfree (%) 17.4 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Humanized 44H10 Fab Version 14 (pdb code 9b74). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 7 binding sites of Sodium where determined in the Crystal Structure of Humanized 44H10 Fab Version 14, PDB code: 9b74:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7;

Sodium binding site 1 out of 7 in 9b74

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Sodium binding site 1 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na305

b:54.9
occ:1.00
 O H:LEU45 2.6 30.9 1.0
O L:HOH457 2.8 30.2 1.0
O L:HOH409 3.3 30.3 1.0
C H:LEU45 3.8 28.6 1.0
O H:HOH493 3.8 38.1 1.0
N H:LEU45 4.3 28.5 1.0
O L:PHE98 4.3 33.6 1.0
N H:GLU46 4.6 28.7 1.0
CA H:GLU46 4.6 28.1 1.0
CA H:LEU45 4.7 28.2 1.0
O L:HOH442 4.7 28.1 1.0
CB L:PHE98 4.8 27.7 1.0
CB H:GLU46 4.9 28.9 1.0
C H:GLY44 4.9 27.9 1.0
N L:PHE98 4.9 35.4 1.0

Sodium binding site 2 out of 7 in 9b74

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Sodium binding site 2 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na306

b:53.3
occ:1.00
 CG H:PRO9 3.0 48.4 1.0
N H:SER19 3.5 39.8 1.0
O H:THR17 3.6 43.1 1.0
CB H:PRO9 3.6 49.1 1.0
CA H:LEU18 4.1 39.0 1.0
CB H:SER19 4.1 37.2 1.0
C H:LEU18 4.2 37.4 1.0
O H:SER19 4.2 44.4 1.0
CA H:SER19 4.3 40.2 1.0
CD H:PRO9 4.3 44.7 1.0
CG2 H:VAL12 4.4 38.4 1.0
C H:THR17 4.6 41.3 1.0
CD1 H:LEU18 4.6 36.4 1.0
C H:SER19 4.7 38.3 1.0
N H:LEU18 4.8 37.2 1.0
CG1 H:VAL12 4.9 38.6 1.0
CA H:PRO9 5.0 46.0 1.0

Sodium binding site 3 out of 7 in 9b74

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Sodium binding site 3 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na307

b:56.4
occ:1.00
 CE H:LYS143 3.4 44.6 1.0
NE2 L:GLN124 3.5 33.8 1.0
CB L:THR129 3.6 38.2 1.0
CE2 H:PHE122 3.8 32.4 1.0
CG L:GLN124 3.8 30.9 1.0
CD H:LYS143 3.9 35.6 1.0
OG1 L:THR129 3.9 37.8 1.0
CG2 L:THR129 3.9 28.8 1.0
OD2 H:ASP144 4.0 43.0 1.0
OG L:SER127 4.0 48.9 1.0
CZ H:PHE122 4.1 31.1 1.0
CD L:GLN124 4.2 33.2 1.0
CG H:LYS143 4.7 40.5 1.0
NZ H:LYS143 4.7 49.9 1.0
CD2 H:PHE122 4.9 31.6 1.0
CA L:THR129 5.0 37.7 1.0

Sodium binding site 4 out of 7 in 9b74

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Sodium binding site 4 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na308

b:50.3
occ:1.00
 N L:GLU165 3.3 33.0 1.0
CB L:THR164 3.8 26.4 1.0
CA L:THR164 3.8 30.5 1.0
O2 H:EDO304 3.9 45.5 1.0
CG L:GLU165 4.0 41.1 1.0
CB L:GLU165 4.0 33.8 1.0
C L:THR164 4.0 30.7 1.0
C1 H:EDO304 4.1 54.1 1.0
CA L:GLU165 4.2 35.5 1.0
CG2 L:THR164 4.3 27.9 1.0
O H:THR165 4.4 31.4 1.0
C2 H:EDO304 4.5 58.7 1.0
CD H:PRO167 4.6 25.6 1.0
O L:GLU165 4.6 31.2 1.0
CG H:PRO167 4.7 23.6 1.0
C L:GLU165 4.9 32.4 1.0
OG1 L:THR164 5.0 31.6 1.0

Sodium binding site 5 out of 7 in 9b74

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Sodium binding site 5 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na309

b:51.0
occ:1.00
 OXT L:ACT306 3.1 56.2 1.0
N L:ARG142 3.3 35.1 1.0
O L:HOH485 3.6 41.0 1.0
CB L:PRO141 3.6 31.5 1.0
C L:ACT306 3.7 62.2 1.0
CE2 L:TYR140 3.7 30.1 1.0
OH L:TYR140 3.7 32.3 1.0
CZ L:TYR140 3.8 29.2 1.0
CA L:PRO141 3.8 27.9 1.0
CB L:ARG142 3.9 37.1 1.0
OH L:TYR173 3.9 45.4 1.0
CE2 L:TYR173 4.0 34.3 1.0
C L:PRO141 4.1 31.2 1.0
CA L:ARG142 4.2 37.0 1.0
O L:ACT306 4.3 58.4 1.0
CZ L:TYR173 4.3 38.9 1.0
CH3 L:ACT306 4.4 65.5 1.0
CD2 L:TYR140 4.5 29.4 1.0
CE1 L:TYR140 4.5 30.2 1.0

Sodium binding site 6 out of 7 in 9b74

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Sodium binding site 6 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na310

b:74.7
occ:1.00
 OG L:SER26 3.1 59.1 1.0
NE2 L:GLN27 3.2 79.0 1.0
O L:ASP1 3.5 62.8 1.0
CB L:SER26 3.6 51.7 1.0
CG L:GLN27 3.9 62.8 1.0
CD L:GLN27 4.0 67.5 1.0
O L:SER26 4.6 57.2 1.0
NE2 L:GLN3 4.6 74.8 1.0
C L:SER26 4.7 58.6 1.0
C L:ASP1 4.7 57.6 1.0
CG L:GLN3 4.7 60.1 1.0
CA L:SER26 4.8 51.8 1.0
CA L:ILE2 4.8 49.1 1.0
N L:GLN3 5.0 47.9 1.0

Sodium binding site 7 out of 7 in 9b74

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Sodium binding site 7 out of 7 in the Crystal Structure of Humanized 44H10 Fab Version 14


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Humanized 44H10 Fab Version 14 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na311

b:49.9
occ:1.00
 O L:LEU201 3.1 40.1 1.0
O L:HIS198 3.2 37.6 1.0
N L:HIS198 3.4 33.2 1.0
CG2 L:THR197 3.5 34.3 1.0
CB L:LEU201 3.7 33.2 1.0
C L:SER203 3.8 40.4 1.0
CA L:THR197 3.8 29.6 1.0
C L:LEU201 3.9 37.2 1.0
N L:PRO204 3.9 42.3 1.0
O L:SER203 4.0 40.6 1.0
C L:HIS198 4.1 32.5 1.0
C L:THR197 4.1 33.2 1.0
CB L:THR197 4.2 32.1 1.0
CA L:SER203 4.2 43.1 1.0
CA L:PRO204 4.2 37.6 1.0
N L:SER203 4.2 39.9 1.0
CA L:LEU201 4.3 33.3 1.0
CD L:PRO204 4.4 36.6 1.0
CA L:HIS198 4.4 28.9 1.0
CG L:PRO204 4.5 35.8 1.0
OG1 L:THR197 4.5 32.0 1.0
C L:SER202 4.5 39.8 1.0
CD1 L:LEU201 4.6 27.7 1.0
CG L:LEU201 4.7 31.3 1.0
N L:LEU201 4.7 33.9 1.0
O L:VAL196 4.7 34.9 1.0
N L:SER202 4.8 36.5 1.0
CB L:PRO204 4.8 36.6 1.0
O L:SER202 4.9 42.5 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: Wed Oct 9 14:27:29 2024

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