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

Protein crystallography data

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

Other elements in 2y5p:

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

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

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 2y5p

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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 2y5p

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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 2y5p

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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 2y5p

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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 2y5p

Go back to Calcium Binding Sites List in 2y5p
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 2y5p

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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 2y5p

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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 2y5p

Go back to Calcium Binding Sites List in 2y5p
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

Reference:

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
Page generated: Fri Jul 12 19:20:40 2024

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