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Sodium in PDB 6ghg: Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges

Protein crystallography data

The structure of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges, PDB code: 6ghg was solved by J.Regula, S.Imhof-Jung, M.Molhoj, J.Benz, A.Ehler, A.Bujotzek, W.Schaefer, C.Klein, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.95 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.560, 59.800, 79.090, 99.49, 89.56, 92.61
R / Rfree (%) 19.5 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges (pdb code 6ghg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges, PDB code: 6ghg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ghg

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Sodium binding site 1 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:30.7
occ:1.00
 O A:HOH432 2.4 24.8 1.0
O A:HOH451 2.8 25.3 1.0
CG2 A:THR69 4.1 27.1 1.0
O A:HOH405 4.1 24.3 1.0
CG2 A:THR58 4.2 21.9 1.0
O A:ILE70 4.3 23.3 1.0
OG1 A:THR58 4.6 27.9 1.0
OH A:TYR60 4.7 24.4 1.0
CB A:THR58 5.0 23.1 1.0

Sodium binding site 2 out of 6 in 6ghg

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Sodium binding site 2 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:39.6
occ:1.00
 OE1 A:GLU46 2.5 28.2 1.0
O A:HOH406 2.8 20.3 1.0
O A:HOH419 2.8 35.9 1.0
NE A:ARG38 3.4 23.9 1.0
CD A:GLU46 3.6 38.9 1.0
CG A:ARG38 3.7 19.3 1.0
CB A:GLU46 3.8 18.8 1.0
CD A:ARG38 3.9 17.9 1.0
CB A:ALA40 4.1 23.4 1.0
N A:ALA40 4.1 22.0 1.0
CZ A:ARG38 4.2 34.0 1.0
CG A:GLU46 4.2 24.2 1.0
NH2 A:ARG38 4.4 23.6 1.0
OE2 A:GLU46 4.6 33.3 1.0
CA A:ALA40 4.6 22.3 1.0
O A:HOH548 4.7 39.2 1.0
O A:ARG38 4.7 18.3 1.0
O A:GLU89 4.8 26.9 1.0
C A:ARG38 4.9 20.2 1.0
CB A:ALA92 4.9 18.8 1.0
C A:GLN39 4.9 22.9 1.0
CB A:ARG38 5.0 17.3 1.0
CA A:GLN39 5.0 16.7 1.0

Sodium binding site 3 out of 6 in 6ghg

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Sodium binding site 3 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:38.9
occ:1.00
 O A:HOH405 2.6 24.3 1.0
O A:HOH497 2.9 26.6 1.0
N A:ARG72 3.1 22.3 1.0
O A:ARG72 3.2 27.7 1.0
CA A:SER71 3.7 21.6 1.0
CD1 A:ILE51 3.7 25.6 1.0
CB A:SER71 3.8 23.7 1.0
CG A:ARG72 3.8 26.8 1.0
C A:SER71 3.9 24.2 1.0
CA A:ARG72 4.0 23.6 1.0
C A:ARG72 4.0 28.4 1.0
O A:HOH432 4.1 24.8 1.0
CA A:GLY55 4.2 25.8 1.0
O A:GLY55 4.3 27.5 1.0
CB A:ARG72 4.4 23.4 1.0
C A:GLY55 4.7 27.6 1.0
CD A:ARG72 4.9 23.2 1.0
OG A:SER71 5.0 31.3 1.0

Sodium binding site 4 out of 6 in 6ghg

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Sodium binding site 4 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:45.4
occ:1.00
 OG1 A:THR69 2.6 29.9 1.0
O A:ARG67 3.1 24.4 1.0
ND2 A:ASN84 3.1 34.2 1.0
N A:THR69 3.3 24.9 1.0
CB A:THR69 3.3 28.9 1.0
O A:GLN82 3.4 25.2 1.0
C A:PHE68 3.5 26.9 1.0
C A:ARG67 3.8 25.0 1.0
CG A:ASN84 3.8 38.0 1.0
CG A:GLN82 3.9 30.7 1.0
CA A:PHE68 3.9 22.1 1.0
CA A:THR69 3.9 23.9 1.0
CB A:GLN82 4.0 21.4 1.0
O A:PHE68 4.1 27.1 1.0
C A:GLN82 4.1 25.2 1.0
N A:PHE68 4.2 22.1 1.0
CB A:ASN84 4.4 25.9 1.0
OD1 A:ASN84 4.5 32.0 1.0
N A:ASN84 4.7 25.9 1.0
CG2 A:THR69 4.7 27.1 1.0
CA A:GLN82 4.7 19.3 1.0
CA A:ARG67 5.0 24.0 1.0

Sodium binding site 5 out of 6 in 6ghg

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Sodium binding site 5 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:48.8
occ:1.00
 OD1 B:ASP71 2.2 56.6 1.0
O B:HOH416 2.9 47.4 1.0
CB B:SER22 3.0 26.4 1.0
O B:PHE72 3.1 24.7 1.0
OG B:SER22 3.2 37.7 1.0
O B:HOH513 3.4 62.9 1.0
CG B:ASP71 3.4 52.1 1.0
NH2 B:ARG24 3.6 51.4 1.0
CA B:SER22 3.7 19.7 1.0
CZ B:ARG24 3.7 66.8 1.0
NE B:ARG24 3.7 53.8 1.0
OG1 B:THR73 3.8 27.1 1.0
N B:CYS23 3.9 23.2 1.0
C B:PHE72 3.9 23.6 1.0
N B:PHE72 4.0 20.6 1.0
OD2 B:ASP71 4.0 60.6 1.0
CG B:ARG24 4.1 36.4 1.0
O B:CYS23 4.2 27.9 1.0
C B:SER22 4.3 24.6 1.0
NH1 B:ARG24 4.4 55.3 1.0
C B:ASP71 4.5 25.1 1.0
CB B:ASP71 4.5 25.3 1.0
CD B:ARG24 4.5 48.9 1.0
C B:CYS23 4.5 28.1 1.0
CA B:PHE72 4.6 20.1 1.0
CA B:ASP71 4.6 22.6 1.0
N B:THR73 4.8 19.4 1.0
CA B:CYS23 4.9 24.4 1.0
CB B:THR73 4.9 22.8 1.0
CA B:THR73 4.9 18.9 1.0
N B:SER22 5.0 20.1 1.0

Sodium binding site 6 out of 6 in 6ghg

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Sodium binding site 6 out of 6 in the Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Variable Heavy - Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na301

b:43.8
occ:1.00
 O L:HOH553 2.5 31.8 1.0
OG1 L:THR181 2.6 27.0 1.0
O L:THR179 2.6 22.4 1.0
CB L:THR181 3.3 29.2 1.0
N L:GLN161 3.5 25.0 1.0
C L:THR179 3.6 23.3 1.0
N L:THR181 3.7 22.6 1.0
CA L:SER160 3.9 23.9 1.0
CG L:GLN161 3.9 43.3 1.0
CB L:GLN161 3.9 27.9 1.0
C L:SER160 3.9 29.3 1.0
O L:ASN159 4.0 26.8 1.0
CB L:THR179 4.0 27.1 1.0
CG2 L:THR179 4.1 24.9 1.0
CA L:THR181 4.1 22.8 1.0
C L:LEU180 4.2 24.7 1.0
CD L:GLN161 4.3 63.0 1.0
CA L:GLN161 4.3 26.1 1.0
N L:LEU180 4.4 19.8 1.0
CA L:THR179 4.4 21.6 1.0
CA L:LEU180 4.5 20.0 1.0
N L:SER160 4.5 23.7 1.0
C L:ASN159 4.5 27.5 1.0
CG2 L:THR181 4.5 26.1 1.0
O L:HOH426 4.6 44.8 1.0
NE2 L:GLN161 4.7 56.8 1.0
OE1 L:GLN161 4.7 58.8 1.0
O L:SER160 4.8 29.6 1.0
O L:LEU180 4.9 24.1 1.0
O L:GLN161 5.0 26.7 1.0

Reference:

J.T.Regula, S.Imhof-Jung, M.Molhoj, J.Benz, A.Ehler, A.Bujotzek, W.Schaefer, C.Klein. Variable Heavy-Variable Light Domain and Fab-Arm Crossmabs with Charged Residue Exchanges to Enforce Correct Light Chain Assembly. Protein Eng. Des. Sel. V. 31 289 2018.
ISSN: ESSN 1741-0134
PubMed: 30169707
DOI: 10.1093/PROTEIN/GZY021
Page generated: Tue Dec 15 12:17:26 2020

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