Sodium in PDB 8h63: Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound

The structure of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound, PDB code: 8h63 was solved by J.M.M.Caaveiro, S.Nagatoish, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.55 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.581, 52.42, 103.06, 90, 128.65, 90
R / Rfree (%)	16.1 / 19

The binding sites of Sodium atom in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound (pdb code 8h63). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound, PDB code: 8h63:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound


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 Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:34.3 occ:1.00 O A:HOH892 2.2 26.4 1.0 O A:HOH670 2.2 17.7 1.0 O A:GLU468 2.3 13.8 1.0 O A:HOH782 2.3 20.2 1.0 OG1 A:THR466 2.4 18.0 1.0 CG2 A:THR466 3.4 16.4 1.0 CB A:THR466 3.4 15.8 1.0 C A:GLU468 3.5 13.8 1.0 O A:HOH1216 3.8 27.0 0.6 OE1 A:GLU468 3.8 16.0 0.8 OD2 A:ASP449 4.0 14.2 1.0 CD A:GLU468 4.1 15.0 0.8 N A:GLU468 4.2 13.4 1.0 OD1 A:ASP449 4.3 17.4 1.0 O A:HOH814 4.4 30.1 1.0 CA A:GLU468 4.4 13.9 1.0 O A:HOH770 4.5 17.7 1.0 N A:VAL469 4.5 11.3 1.0 CG A:ASP449 4.5 14.5 1.0 CA A:THR466 4.6 14.9 1.0 CA A:VAL469 4.6 10.9 1.0 CG1 A:VAL469 4.6 12.2 1.0 CG A:GLU468 4.6 15.7 1.0 OE2 A:GLU468 4.7 14.1 0.8 C A:THR466 4.7 15.2 1.0 N A:ASN467 4.7 14.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound


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 Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:42.3 occ:1.00 O A:HOH1024 2.2 30.4 1.0 O A:HOH1197 2.6 30.5 0.6 OG A:SER358 2.7 16.8 1.0 O A:HOH968 2.8 27.0 1.0 O A:SER355 2.8 11.8 1.0 C A:SER355 3.6 11.0 1.0 CB A:SER358 3.8 14.2 1.0 CA A:PRO356 4.1 10.7 1.0 N A:PRO356 4.1 10.0 1.0 CB A:SER355 4.2 11.7 1.0 OG A:SER355 4.2 12.1 1.0 O A:HOH986 4.4 39.5 1.0 CA A:SER355 4.4 10.9 1.0 N A:SER358 4.6 12.4 1.0 C A:PRO356 4.6 11.0 1.0 OG A:SER359 4.7 17.7 0.4 CA A:SER358 4.7 13.2 1.0 O A:PRO356 4.8 12.6 1.0 O A:HOH1098 4.8 26.4 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound


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 Internalin A From Listeria Monocytogenes with Nanobody VHH10 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:33.6 occ:1.00 O A:HOH763 2.2 25.4 1.0 OE2 A:GLU455 2.7 19.2 1.0 O A:HOH1035 2.8 23.9 1.0 O A:HOH711 3.1 28.9 1.0 CD A:GLU455 3.6 21.6 1.0 OE1 A:GLU455 3.9 23.9 1.0 O A:HOH854 4.1 20.9 1.0 O A:HOH631 4.3 21.2 1.0 O A:HOH1159 4.5 28.4 1.0 O A:LEU441 4.7 14.1 1.0 CB A:LEU441 5.0 13.6 1.0

T.Yamazaki, S.Nagatoishi, T.Yamawaki, T.Nozawa, R.Matsunaga, M.Nakakido, J.M.M.Caaveiro, I.Nakagawa, K.Tsumoto. Anti-Inla Single-Domain Antibodies That Inhibit the Cell Invasion of Listeria Monocytogenes. J.Biol.Chem. 05254 2023.
ISSN: ESSN 1083-351X
PubMed: 37716701
DOI: 10.1016/J.JBC.2023.105254