Chlorine in PDB 8h64: Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound

The structure of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound, PDB code: 8h64 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)	62.06 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	129.73, 141.12, 198.61, 90, 90, 90
R / Rfree (%)	18.8 / 22.7

The binding sites of Chlorine atom in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound (pdb code 8h64). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound, PDB code: 8h64:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl501 b:65.8 occ:1.00 OD1 A:ASN98 3.7 47.4 1.0 CD1 A:TYR96 3.7 73.4 1.0 O A:GLU95 4.0 43.7 1.0 CE1 A:TYR96 4.1 64.4 1.0 O A:HOH605 4.3 44.0 1.0 CA A:TYR96 4.5 54.9 1.0 CG A:ASN98 4.6 54.2 1.0 C A:GLU95 4.6 46.7 1.0 ND2 A:ASN98 4.6 52.9 1.0 CG A:TYR96 4.7 60.6 1.0 O A:HOH692 4.9 38.2 1.0 N A:TYR96 4.9 42.5 1.0 OE1 A:GLN72 4.9 73.9 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl502 b:63.5 occ:1.00 O B:SER104 3.5 23.1 1.0 NE1 A:TRP387 4.0 34.2 1.0 OG A:SER389 4.1 28.3 1.0 O A:LEU410 4.2 29.7 1.0 C A:LEU410 4.3 26.2 1.0 CB B:SER105 4.3 24.8 1.0 N A:GLY411 4.4 25.4 1.0 C B:SER104 4.4 22.9 1.0 CA A:GLY411 4.4 26.2 1.0 CB B:SER104 4.5 23.9 1.0 CB A:SER389 4.5 23.0 1.0 OG B:SER104 4.6 29.3 1.0 N A:LEU410 4.8 31.6 1.0 CD1 A:TRP387 4.9 34.8 1.0 O A:HOH705 4.9 16.2 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl501 b:55.0 occ:1.00 O F:SER104 3.6 25.6 1.0 NE1 E:TRP387 3.7 32.0 1.0 O E:LEU410 4.2 27.2 1.0 OG E:SER389 4.2 29.4 1.0 C E:LEU410 4.2 29.1 1.0 CB F:SER104 4.3 30.6 1.0 N E:GLY411 4.3 25.6 1.0 C F:SER104 4.4 25.1 1.0 OG F:SER104 4.5 35.8 1.0 CB E:SER389 4.5 27.2 1.0 N E:LEU410 4.5 28.4 1.0 CA E:GLY411 4.6 25.7 1.0 CD1 E:TRP387 4.6 31.5 1.0 CB F:SER105 4.6 22.3 1.0 CE2 E:TRP387 4.7 33.7 1.0 CA E:LEU410 4.9 30.7 1.0 CA F:SER104 5.0 27.2 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Internalin A From Listeria Monocytogenes with Nanobody VHH24 Bound within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl501 b:52.4 occ:1.00 O H:SER104 3.8 26.6 1.0 NE1 G:TRP387 3.9 23.8 1.0 O G:LEU410 4.1 32.5 1.0 OG G:SER389 4.2 25.8 1.0 C G:LEU410 4.3 34.3 1.0 N G:GLY411 4.4 34.4 1.0 CB H:SER104 4.5 27.6 1.0 CA G:GLY411 4.5 30.4 1.0 C H:SER104 4.6 26.7 1.0 CB G:SER389 4.6 24.8 1.0 N G:LEU410 4.7 32.1 1.0 CD1 G:TRP387 4.8 24.7 1.0 O A:HOH602 4.8 32.1 1.0 CB H:SER105 4.8 29.8 1.0 CE2 G:TRP387 4.8 24.8 1.0 OG H:SER104 4.9 29.5 1.0 NE2 G:GLN409 5.0 31.5 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