Calcium in PDB 2y5p: B-Repeat of Listeria Monocytogenes Inlb (Internalin B)

The structure of B-Repeat of Listeria Monocytogenes Inlb (Internalin B), PDB code: 2y5p was solved by M.Ebbes, H.H.Niemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.00 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.610, 58.340, 158.070, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 19.6

The structure of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Calcium atom in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B) (pdb code 2y5p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B), PDB code: 2y5p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1393 b:24.6 occ:0.50 O A:ASN365 2.3 28.5 1.0 OE1 A:GLU363 2.4 38.0 1.0 O A:HOH2052 2.5 33.5 1.0 C A:ASN365 3.4 28.5 1.0 CD A:GLU363 3.6 34.8 1.0 CB A:GLU363 4.0 24.2 1.0 O A:HOH2049 4.1 32.2 1.0 CA A:ASN365 4.2 27.7 1.0 CG A:GLU363 4.2 27.6 1.0 N A:ASN365 4.3 26.7 1.0 CB A:ASN365 4.3 27.6 1.0 N A:GLY366 4.4 29.2 1.0 CA A:GLY366 4.6 29.6 1.0 O A:HOH2050 4.6 36.5 1.0 OE2 A:GLU363 4.6 36.0 1.0 C A:GLY366 4.9 29.4 1.0

Calcium binding site 2 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1394 b:42.8 occ:0.50 OD1 A:ASP330 2.1 27.8 0.5 CG A:ASP330 3.2 21.1 0.5 CA A:ASP330 3.5 18.6 0.5 CA A:ASP330 3.5 18.2 0.5 OD1 A:ASP330 3.5 24.4 0.5 CB A:ASP330 3.7 19.2 0.5 CG A:ASP330 3.8 18.4 0.5 CB A:ASP330 3.8 19.1 0.5 O A:HOH2008 3.9 42.7 1.0 C A:ASP330 3.9 21.1 0.5 C A:ASP330 3.9 21.0 0.5 O A:ASP330 4.1 22.7 0.5 O A:ASP330 4.1 22.7 0.5 CE A:LYS364 4.3 30.1 1.0 O A:HOH2012 4.3 43.8 0.8 OD2 A:ASP330 4.3 28.6 0.5 N A:GLY331 4.5 20.9 1.0 OD2 A:ASP330 4.7 24.3 0.5 N A:ASP330 4.7 17.8 0.5 N A:ASP330 4.7 17.6 0.5 NZ A:LYS364 4.8 31.2 1.0

Calcium binding site 3 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1393 b:17.7 occ:0.70 O B:HOH2048 2.1 19.2 0.5 O B:LYS358 2.3 17.7 1.0 O B:HOH2073 2.3 29.3 0.5 O B:HOH2052 2.4 24.2 1.0 OE2 B:GLU369 2.5 19.8 1.0 OE1 B:GLU369 2.6 21.2 1.0 CD B:GLU369 3.0 17.0 1.0 C B:LYS358 3.5 14.5 1.0 N B:GLY359 4.2 14.0 1.0 CA B:GLY359 4.3 14.9 1.0 OH B:TYR361 4.4 27.1 1.0 CA B:LYS358 4.4 14.5 1.0 O B:HOH2045 4.4 24.4 1.0 O B:HOH2072 4.4 47.0 1.0 CG B:GLU369 4.5 14.6 1.0 O B:HOH2069 4.7 28.4 1.0 CB B:LYS358 4.9 14.7 1.0 CE1 B:TYR361 5.0 16.8 1.0

Calcium binding site 4 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1394 b:11.5 occ:0.80 O B:HOH2078 2.4 15.6 1.0 O B:HOH2079 2.4 16.3 1.0 O C:HOH2109 2.4 14.4 1.0 O B:HOH2067 2.4 18.3 1.0 O B:HOH2074 2.4 23.9 1.0 O B:HOH2081 2.5 14.4 1.0 O C:HOH2093 4.1 15.2 1.0 OD1 C:ASN380 4.2 18.4 1.0 O B:GLU369 4.3 16.5 1.0 OD1 B:ASP375 4.3 13.5 1.0 CB B:ASN371 4.4 12.6 1.0 OG1 B:THR374 4.4 13.2 1.0 ND2 C:ASN380 4.5 13.0 1.0 CE1 B:HIS368 4.6 15.8 1.0 OD2 B:ASP375 4.6 14.3 1.0 CG C:ASN380 4.7 15.1 1.0 O C:HOH2061 4.8 28.6 1.0 O B:HOH2075 4.8 43.0 1.0 O B:HOH2070 4.8 21.8 1.0 O C:HOH2107 4.8 18.8 1.0 CG B:ASP375 4.9 12.6 1.0

Calcium binding site 5 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1393 b:14.9 occ:0.50 O C:HOH2104 2.0 84.0 1.0 O C:HOH2105 2.3 34.2 1.0 O C:HOH2113 2.4 40.9 1.0 O C:HOH2114 2.4 33.8 1.0 O C:ASP381 2.5 15.8 1.0 C C:ASP381 3.6 14.5 1.0 CB C:ASP381 4.3 15.1 1.0 OD1 C:ASN380 4.4 18.4 1.0 CA C:ASP381 4.4 13.8 1.0 O C:HOH2115 4.5 19.8 1.0 N C:PHE382 4.5 13.3 1.0 CA C:PHE382 4.5 12.2 1.0 O C:HOH2112 4.6 43.0 1.0 N C:ASP381 4.6 13.4 1.0 CL C:CL1395 5.0 16.4 1.0

Calcium binding site 6 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1396 b:20.7 occ:0.40 O C:HOH2125 2.1 0.6 1.0 OE2 C:GLU391 2.3 40.0 1.0 O C:HOH2127 2.4 0.6 1.0 O C:HOH2126 2.8 27.3 0.5 CD C:GLU391 3.4 34.6 1.0 OE1 C:GLU391 4.0 41.8 1.0 O C:HOH2042 4.2 32.4 0.5 O C:HOH2047 4.3 81.4 1.0 O C:HOH2085 4.4 33.7 1.0 O C:TYR355 4.5 14.8 1.0 CG2 C:VAL356 4.5 20.5 1.0 CG C:GLU391 4.6 24.5 1.0

Calcium binding site 7 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1397 b:23.7 occ:0.50 O C:HOH2077 2.0 83.3 1.0 O B:HOH2090 2.1 21.4 0.5 O C:HOH2100 2.4 35.2 1.0 O C:HOH2101 2.5 0.2 1.0 O C:HOH2098 2.7 39.1 1.0 O B:HOH2086 4.1 25.5 1.0 OD1 C:ASP375 4.3 18.9 1.0 ND2 B:ASN380 4.4 18.2 0.3 CB C:ASN371 4.4 17.3 1.0 OD2 C:ASP375 4.4 18.4 1.0 O C:GLU369 4.5 18.6 1.0 OD1 B:ASN380 4.5 18.5 0.3 CE1 C:HIS368 4.7 22.6 1.0 OG1 C:THR374 4.7 18.2 1.0 CG B:ASN380 4.8 16.1 0.3 CG C:ASP375 4.8 16.8 1.0

Calcium binding site 8 out of 8 in the B-Repeat of Listeria Monocytogenes Inlb (Internalin B)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of B-Repeat of Listeria Monocytogenes Inlb (Internalin B) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1393 b:0.4 occ:0.20 OD2 D:ASP330 2.3 32.1 0.6 O D:HOH2008 2.4 43.6 1.0 CG D:ASP330 3.3 29.4 0.6 OD1 D:ASP330 3.7 32.1 0.6 O D:HOH2006 4.3 42.6 1.0 OD2 D:ASP330 4.5 35.2 0.4 CG D:ASP330 4.6 28.2 0.4 CB D:ASP330 4.6 26.1 0.4 CB D:ASP330 4.7 26.7 0.6 NZ D:LYS352 5.0 45.5 0.5

M.Ebbes, W.M.Bleymuller, M.Cernescu, R.Nolker, B.Brutschy, H.H.Niemann. Fold and Function of the Inlb B-Repeat. J.Biol.Chem. V. 286 15496 2011.
ISSN: ISSN 0021-9258
PubMed: 21345802
DOI: 10.1074/JBC.M110.189951