Calcium in PDB 8h62: Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12

The structure of Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12, PDB code: 8h62 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)	34.80 / 1.91
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	55.35, 69.58, 72.49, 101.48, 97.77, 105.99
R / Rfree (%)	17.6 / 21

The binding sites of Calcium atom in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12 (pdb code 8h62). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12, PDB code: 8h62:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:47.2 occ:1.00 O A:LEU410 2.2 19.4 1.0 O A:HOH760 2.4 26.1 1.0 O A:THR483 2.5 21.6 1.0 OD1 B:ASP1 2.6 36.9 1.0 O A:HOH941 2.7 41.2 1.0 O A:HOH640 2.7 24.2 1.0 C A:LEU410 3.4 20.6 1.0 C A:THR483 3.6 24.1 1.0 CG B:ASP1 3.6 34.2 1.0 N A:LEU410 3.9 21.4 1.0 CB A:THR484 4.0 23.3 1.0 OD2 B:ASP1 4.0 37.6 1.0 CA A:THR484 4.1 23.4 1.0 OG1 A:THR484 4.1 22.9 1.0 O B:HOH515 4.1 30.0 1.0 CA A:LEU410 4.3 21.0 1.0 O A:HOH998 4.3 59.0 1.0 N A:THR484 4.3 23.4 1.0 NE2 A:GLN409 4.4 35.6 1.0 N A:GLY411 4.4 21.2 1.0 CA A:GLY411 4.6 21.3 1.0 O A:HOH669 4.6 24.9 0.5 O B:HOH590 4.6 46.2 1.0 N A:THR483 4.6 22.4 1.0 O A:HOH888 4.7 34.3 1.0 CA A:THR483 4.7 23.6 1.0 CB A:LEU410 4.8 21.6 1.0 CB B:ASP1 4.9 31.5 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:20.6 occ:1.00 O B:ASN104 2.2 21.0 1.0 O B:ASN143 2.3 21.6 1.0 OD1 B:ASN102 2.3 23.5 1.0 OD2 B:ASP136 2.4 19.1 1.0 OD2 B:ASP195 2.4 21.0 1.0 OD1 B:ASP134 2.6 23.7 1.0 OD2 B:ASP134 2.6 22.7 1.0 CG B:ASP134 2.9 24.0 1.0 CG B:ASP195 3.3 22.0 1.0 CG B:ASP136 3.4 21.6 1.0 C B:ASN104 3.5 21.9 1.0 CG B:ASN102 3.5 23.7 1.0 C B:ASN143 3.5 22.5 1.0 CB B:ASP195 3.8 22.0 1.0 CB B:ASP136 3.8 21.1 1.0 ND2 B:ASN102 4.1 24.3 1.0 N B:ASN104 4.2 20.8 1.0 CA B:ASN104 4.2 20.9 1.0 OD1 B:ASP195 4.3 21.2 1.0 CA B:ASN143 4.4 24.4 1.0 CB B:ASP134 4.4 23.6 1.0 CB B:ASN143 4.4 24.6 1.0 CB B:ASN104 4.5 20.3 1.0 N B:LYS105 4.5 24.3 1.0 N B:ALA144 4.5 23.1 1.0 OD1 B:ASP136 4.5 19.5 1.0 CD1 B:LEU201 4.6 27.2 1.0 CA B:ALA144 4.7 24.5 1.0 CA B:LYS105 4.7 26.7 1.0 CB B:ASN102 4.7 22.2 1.0 CA B:ASN102 4.8 22.7 1.0 C B:LYS105 4.8 24.8 1.0 CD B:PRO106 4.8 23.1 1.0 N B:ASP103 4.9 19.0 1.0 N B:ASP136 4.9 20.4 1.0 N B:PRO106 4.9 23.3 1.0 C B:ASN102 4.9 20.8 1.0 CA B:ASP136 5.0 21.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:21.7 occ:1.00 OD1 B:ASP100 2.3 19.7 1.0 OE2 B:GLU69 2.4 22.7 1.0 OE2 B:GLU11 2.4 18.8 1.0 OD2 B:ASP103 2.4 22.7 1.0 OD1 B:ASP136 2.4 19.5 1.0 O B:GLN101 2.5 20.0 1.0 OE1 B:GLU69 2.7 21.8 1.0 CD B:GLU69 2.8 22.5 1.0 CG B:ASP100 3.4 21.2 1.0 CG B:ASP136 3.4 21.6 1.0 CD B:GLU11 3.4 19.6 1.0 CG B:ASP103 3.4 23.1 1.0 C B:GLN101 3.7 21.9 1.0 OE1 B:GLU11 3.8 19.1 1.0 ND2 B:ASN104 3.9 19.4 1.0 OD2 B:ASP100 3.9 21.1 1.0 N B:GLN101 3.9 22.6 1.0 CA B:CA303 4.0 21.8 1.0 OD1 B:ASP103 4.0 22.4 1.0 CB B:ASP136 4.0 21.1 1.0 N B:ASP103 4.0 19.0 1.0 CA B:ASP136 4.3 21.1 1.0 CG B:GLU69 4.3 21.7 1.0 OD2 B:ASP136 4.3 19.1 1.0 CA B:GLN101 4.4 24.3 1.0 NE B:ARG68 4.5 25.4 1.0 CB B:ASP100 4.5 21.4 1.0 CB B:ASP103 4.5 22.6 1.0 CA B:ASP100 4.6 21.7 1.0 CG B:GLU11 4.7 19.0 1.0 N B:ASN102 4.7 22.4 1.0 NH2 B:ARG68 4.7 23.8 1.0 CA B:ASP103 4.8 21.3 1.0 C B:ASP100 4.8 22.9 1.0 CA B:ASN102 4.9 22.7 1.0 C B:ASN102 4.9 20.8 1.0 N B:ASN104 5.0 20.8 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Internalin A From Listeria Monocytogenes with Human E-Cadherin EC12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:21.8 occ:1.00 OE1 B:GLU69 2.3 21.8 1.0 OD1 B:ASP103 2.3 22.4 1.0 OD1 B:ASP67 2.3 19.4 1.0 O B:HOH542 2.3 22.2 1.0 OE1 B:GLU11 2.4 19.1 1.0 O B:HOH450 2.4 23.9 1.0 CG B:ASP103 3.1 23.1 1.0 CG B:ASP67 3.2 21.3 1.0 OD2 B:ASP103 3.2 22.7 1.0 CD B:GLU11 3.3 19.6 1.0 CD B:GLU69 3.5 22.5 1.0 OE2 B:GLU11 3.7 18.8 1.0 OD2 B:ASP67 3.9 20.6 1.0 CA B:CA302 4.0 21.7 1.0 CB B:ASP67 4.0 21.6 1.0 CA B:ASP67 4.1 21.1 1.0 ND2 B:ASN104 4.2 19.4 1.0 O B:HOH429 4.2 29.2 1.0 N B:ARG68 4.2 21.2 1.0 N B:GLU69 4.3 21.2 1.0 ND2 B:ASN12 4.3 21.8 1.0 CB B:GLU69 4.4 21.9 1.0 OD1 B:ASN12 4.4 24.3 1.0 OE2 B:GLU69 4.4 22.7 1.0 CG B:GLU69 4.4 21.7 1.0 C B:ASP67 4.4 19.8 1.0 O B:HOH477 4.4 32.1 1.0 CB B:ASP103 4.5 22.6 1.0 O B:HOH555 4.6 45.1 1.0 CG B:GLU11 4.6 19.0 1.0 O B:HOH576 4.8 50.4 1.0 CG B:ASN12 4.8 22.7 1.0 CB B:GLU11 5.0 19.6 1.0 CA B:GLU69 5.0 22.5 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