Sodium in PDB 6i1o: Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin

The structure of Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin, PDB code: 6i1o was solved by M.Laffranchi, E.L.K.Elliston, E.Miranda, J.Perez, A.Fra, D.A.Lomas, J.A.Irving, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.91 / 1.93
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	99.198, 99.198, 80.073, 90.00, 90.00, 120.00
R / Rfree (%)	19.9 / 23.5

The binding sites of Sodium atom in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin (pdb code 6i1o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin, PDB code: 6i1o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:41.8 occ:1.00 CE H:LYS143 3.1 29.9 1.0 NE2 L:GLN125 3.5 26.6 1.0 CD H:LYS143 3.7 24.8 1.0 OG L:SER128 3.8 41.4 1.0 CG L:GLN125 3.9 29.9 1.0 CA L:GLY130 4.0 30.3 1.0 CD L:GLN125 4.3 23.5 1.0 OH H:TYR122 4.3 29.5 1.0 N L:GLY130 4.4 31.1 1.0 NZ H:LYS143 4.4 46.1 1.0 C L:GLY130 4.7 26.2 1.0 CG H:LYS143 4.8 24.4 1.0 CE2 H:TYR122 4.8 23.8 1.0 O L:HOH472 4.8 43.6 1.0 CZ H:TYR122 4.9 24.8 1.0 CB L:SER128 5.0 37.0 1.0

Sodium binding site 2 out of 4 in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na304 b:46.0 occ:1.00 O H:HOH528 2.5 46.6 1.0 OG1 H:THR195 2.8 34.2 0.5 ND2 H:ASN197 3.1 29.7 1.0 OG H:SER156 3.3 38.3 1.0 O H:HOH478 3.5 47.7 1.0 CA H:ASN155 3.6 32.6 1.0 N H:SER156 3.7 35.7 1.0 O H:HOH540 3.7 45.1 1.0 C H:ASN155 3.8 40.5 1.0 CB H:THR195 4.0 30.1 0.5 CG H:ASN197 4.0 31.8 1.0 OD1 H:ASN197 4.0 34.0 1.0 CG2 H:THR195 4.2 24.5 0.5 CB H:THR195 4.2 30.0 0.5 N H:ASN155 4.3 36.5 1.0 CB H:SER156 4.3 43.9 1.0 O H:HOH415 4.3 37.8 1.0 OD1 H:ASN155 4.4 29.0 1.0 CA H:SER156 4.5 39.0 1.0 O H:HOH407 4.6 41.5 1.0 OG1 H:THR195 4.6 29.4 0.5 CB H:ASN155 4.6 32.7 1.0 O H:ASN155 4.7 41.0 1.0 O H:THR195 4.7 29.2 1.0 CG2 H:THR195 4.9 29.6 0.5 CG H:ASN155 5.0 36.5 1.0

Sodium binding site 3 out of 4 in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:52.1 occ:1.00 NE2 H:GLN171 3.3 28.9 1.0 O H:HOH468 3.4 39.4 1.0 O L:HOH386 3.4 30.0 1.0 O L:HOH473 3.5 26.4 1.0 CG H:GLN171 3.6 34.8 1.0 CD H:GLN171 3.9 35.7 1.0 CG2 L:THR182 4.2 29.4 1.0 CB L:THR182 4.6 26.6 1.0 CB H:GLN171 5.0 30.7 1.0

Sodium binding site 4 out of 4 in the Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Fab Fragment of An Antibody Selective For Wild-Type Alpha-1- Antitrypsin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:52.2 occ:1.00 OG1 H:THR57 3.4 34.7 1.0 OH H:TYR59 3.5 31.8 1.0 O H:HOH502 3.8 34.3 1.0 O H:HOH489 3.9 52.0 1.0 CG2 H:THR68 4.3 31.6 1.0 CE2 H:TYR59 4.4 31.0 1.0 CB H:THR57 4.4 32.9 1.0 CZ H:TYR59 4.4 30.1 1.0 CG2 H:THR57 4.5 31.1 1.0 O H:HOH493 4.5 41.4 1.0 O H:HOH551 4.9 44.4 1.0

M.Laffranchi, E.L.K.Elliston, E.Miranda, J.Perez, N.Heyer-Chauhan, F.Gangemi, A.M.Jagger, A.Fra, J.A.Irving, D.A.Lomas. Characterisation of Polymers Extracted From the Liver Tissue of Individuals with the Mz Alpha-1-Antitrypsin Deficiency Genotype To Be Published.