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Calcium in PDB 5ldt: Crystal Structures of Momp From Campylobacter Jejuni

Protein crystallography data

The structure of Crystal Structures of Momp From Campylobacter Jejuni, PDB code: 5ldt was solved by L.G.M.Ferrara, G.D.Wallat, L.Moynie, J.H.Naismith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.72 / 2.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.360, 99.330, 172.140, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 27.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structures of Momp From Campylobacter Jejuni (pdb code 5ldt). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structures of Momp From Campylobacter Jejuni, PDB code: 5ldt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5ldt

Go back to Calcium Binding Sites List in 5ldt
Calcium binding site 1 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:20.4
occ:1.00
 OE1 A:GLN152 2.3 32.2 1.0
OD2 A:ASP155 2.3 34.3 1.0
OE2 A:GLU288 2.3 35.4 1.0
O A:ASP120 2.3 29.1 1.0
OD2 A:ASP120 2.4 30.9 1.0
CG A:ASP120 2.9 29.0 1.0
CD A:GLN152 3.3 30.5 1.0
CG A:ASP155 3.4 33.1 1.0
CB A:ASP120 3.4 28.9 1.0
C A:ASP120 3.4 28.3 1.0
CD A:GLU288 3.4 34.2 1.0
O A:HOH601 3.5 72.1 1.0
NE2 A:GLN152 3.5 30.4 1.0
OD1 A:ASP120 3.7 29.9 1.0
CB A:ASP155 3.7 31.7 1.0
CA A:ASP120 4.0 28.4 1.0
OE1 A:GLU288 4.2 34.1 1.0
CG A:GLU288 4.3 34.1 1.0
OD2 A:ASP116 4.4 26.8 1.0
OD1 A:ASP155 4.4 34.4 1.0
N A:GLY121 4.6 28.4 1.0
OD2 A:ASP289 4.6 35.1 1.0
CG A:GLN152 4.7 29.9 1.0
CB A:ASP289 4.7 33.0 1.0
CB A:ASP116 4.9 26.6 1.0
CA A:GLY121 4.9 28.4 1.0

Calcium binding site 2 out of 6 in 5ldt

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Calcium binding site 2 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:31.6
occ:1.00
 OD1 A:ASN180 2.3 40.3 1.0
O B:GLY72 2.3 55.3 1.0
OD1 A:ASP145 2.3 39.7 1.0
O A:ASP145 2.3 36.3 1.0
OD1 B:ASN77 2.3 62.3 1.0
CG A:ASP145 3.0 35.6 1.0
C B:GLY72 3.1 50.0 1.0
CG A:ASN180 3.3 36.8 1.0
C A:ASP145 3.3 33.0 1.0
CA B:GLY72 3.4 47.6 1.0
CG B:ASN77 3.4 64.8 1.0
CA A:ASP145 3.6 32.7 1.0
OD2 A:ASP145 3.6 36.0 1.0
ND2 A:ASN180 3.7 38.1 1.0
CB A:ASP145 3.9 34.1 1.0
ND2 B:ASN77 4.1 67.5 1.0
N B:THR73 4.2 50.9 1.0
N A:SER146 4.5 32.0 1.0
CB B:ASN77 4.5 64.3 1.0
CB A:ASN180 4.6 34.7 1.0
N B:GLY72 4.6 45.0 1.0
CA B:THR73 4.6 53.5 1.0
CA B:ASN77 4.7 60.7 1.0
N A:ASN180 4.9 33.4 1.0
CA A:ASN180 4.9 32.6 1.0
O B:GLY71 5.0 43.5 1.0

Calcium binding site 3 out of 6 in 5ldt

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Calcium binding site 3 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:29.9
occ:1.00
 OD1 C:ASP145 2.3 60.5 1.0
OD1 A:ASN77 2.3 67.5 1.0
O C:ASP145 2.4 55.6 1.0
O A:GLY72 2.4 65.7 1.0
OD1 C:ASN180 2.5 56.1 1.0
CG C:ASP145 2.5 57.1 1.0
OD2 C:ASP145 3.1 56.0 1.0
C C:ASP145 3.2 52.2 1.0
C A:GLY72 3.3 62.5 1.0
CG A:ASN77 3.4 68.2 1.0
CG C:ASN180 3.4 53.1 1.0
CA C:ASP145 3.4 53.0 1.0
CB C:ASP145 3.5 54.2 1.0
CA A:GLY72 3.5 60.7 1.0
ND2 C:ASN180 3.7 53.7 1.0
ND2 A:ASN77 4.1 70.1 1.0
CB A:ASN77 4.4 68.7 1.0
N C:SER146 4.4 50.5 1.0
N A:THR73 4.5 62.2 1.0
CA A:ASN77 4.5 66.9 1.0
N A:GLY72 4.6 58.1 1.0
CB C:ASN180 4.8 52.6 1.0
O A:GLY71 4.8 55.6 1.0
N C:ASP145 4.8 51.0 1.0

Calcium binding site 4 out of 6 in 5ldt

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Calcium binding site 4 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:24.7
occ:1.00
 O B:ASP120 2.3 35.9 1.0
OD2 B:ASP120 2.3 41.9 1.0
OE1 B:GLN152 2.3 36.0 1.0
OD2 B:ASP155 2.3 36.0 1.0
OE2 B:GLU288 2.4 39.6 1.0
O B:HOH602 2.4 11.2 1.0
CG B:ASP120 2.5 38.4 1.0
CD B:GLN152 3.2 34.6 1.0
CB B:ASP120 3.2 36.8 1.0
C B:ASP120 3.4 35.1 1.0
CG B:ASP155 3.4 34.2 1.0
NE2 B:GLN152 3.5 34.5 1.0
CD B:GLU288 3.5 37.6 1.0
OD1 B:ASP120 3.5 37.2 1.0
CB B:ASP155 3.8 33.8 1.0
CA B:ASP120 3.9 35.5 1.0
OE1 B:GLU288 4.3 37.6 1.0
CG B:GLU288 4.4 37.5 1.0
OD2 B:ASP116 4.4 37.0 1.0
OD1 B:ASP155 4.5 34.5 1.0
N B:GLY121 4.5 35.0 1.0
CG B:GLN152 4.6 34.7 1.0
OD2 B:ASP289 4.8 37.0 1.0
CB B:ASP289 4.8 36.5 1.0
CB B:ASP116 4.9 36.5 1.0
CA B:GLY121 4.9 34.0 1.0

Calcium binding site 5 out of 6 in 5ldt

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Calcium binding site 5 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:32.2
occ:1.00
 OD1 B:ASN180 2.3 53.9 1.0
O C:GLY72 2.3 60.9 1.0
O B:ASP145 2.3 48.2 1.0
OD1 B:ASP145 2.3 54.0 1.0
OD1 C:ASN77 2.3 67.4 1.0
CG B:ASP145 3.1 48.9 1.0
C C:GLY72 3.1 57.7 1.0
C B:ASP145 3.3 44.8 1.0
CG B:ASN180 3.3 52.2 1.0
CA C:GLY72 3.3 55.2 1.0
CG C:ASN77 3.4 69.7 1.0
CA B:ASP145 3.6 45.0 1.0
OD2 B:ASP145 3.7 49.0 1.0
ND2 B:ASN180 3.7 54.1 1.0
CB B:ASP145 3.9 46.6 1.0
ND2 C:ASN77 4.1 71.4 1.0
N C:THR73 4.2 59.3 1.0
N B:SER146 4.5 44.1 1.0
CB C:ASN77 4.5 69.5 1.0
CB B:ASN180 4.6 51.4 1.0
CA C:THR73 4.6 62.5 1.0
N C:GLY72 4.6 53.3 1.0
CA C:ASN77 4.7 67.9 1.0
CA B:ASN180 4.9 49.4 1.0
N B:ASN180 4.9 50.4 1.0
N B:ASP145 5.0 42.7 1.0

Calcium binding site 6 out of 6 in 5ldt

Go back to Calcium Binding Sites List in 5ldt
Calcium binding site 6 out of 6 in the Crystal Structures of Momp From Campylobacter Jejuni


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structures of Momp From Campylobacter Jejuni within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:24.4
occ:1.00
 OD2 C:ASP120 2.3 48.8 1.0
OE2 C:GLU288 2.3 50.9 1.0
OD2 C:ASP155 2.3 49.1 1.0
OE1 C:GLN152 2.3 48.6 1.0
O C:ASP120 2.3 46.7 1.0
O C:HOH602 2.5 13.3 1.0
CG C:ASP120 2.8 46.0 1.0
CD C:GLN152 3.3 45.5 1.0
CB C:ASP120 3.3 45.2 1.0
CG C:ASP155 3.4 47.0 1.0
CD C:GLU288 3.4 49.0 1.0
C C:ASP120 3.4 44.5 1.0
NE2 C:GLN152 3.5 45.3 1.0
OD1 C:ASP120 3.6 46.5 1.0
CB C:ASP155 3.8 46.4 1.0
CA C:ASP120 4.0 44.3 1.0
OE1 C:GLU288 4.2 49.4 1.0
CG C:GLU288 4.3 49.5 1.0
OD2 C:ASP116 4.4 41.1 1.0
OD1 C:ASP155 4.4 47.8 1.0
N C:GLY121 4.6 44.5 1.0
CG C:GLN152 4.7 45.1 1.0
OD2 C:ASP289 4.7 42.4 1.0
CB C:ASP289 4.7 42.7 1.0
CB C:ASP116 4.9 41.5 1.0
CA C:GLY121 5.0 44.1 1.0

Reference:

L.G.Ferrara, G.D.Wallat, L.Moynie, N.N.Dhanasekar, S.Aliouane, S.Acosta-Gutierrez, J.M.Pages, J.M.Bolla, M.Winterhalter, M.Ceccarelli, J.H.Naismith. Momp From Campylobacter Jejuni Is A Trimer of 18-Stranded Beta-Barrel Monomers with A Ca(2+) Ion Bound at the Constriction Zone. J.Mol.Biol. V. 428 4528 2016.
ISSN: ESSN 1089-8638
PubMed: 27693650
DOI: 10.1016/J.JMB.2016.09.021
Page generated: Wed Jul 9 07:50:50 2025

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