Calcium in PDB 8bad: TPP80AA1
Protein crystallography data
The structure of TPP80AA1, PDB code: 8bad
was solved by
H.L.Best,
L.J.Williamson,
P.J.Rizkallah,
C.Berry,
E.Lloyd-Evans,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
57.72 /
1.81
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
133.827,
63.853,
107.292,
90,
120.4,
90
|
R / Rfree (%)
|
17.9 /
21
|
Calcium Binding Sites:
The binding sites of Calcium atom in the TPP80AA1
(pdb code 8bad). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
TPP80AA1, PDB code: 8bad:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 8bad
Go back to
Calcium Binding Sites List in 8bad
Calcium binding site 1 out
of 2 in the TPP80AA1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of TPP80AA1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:62.5
occ:1.00
|
OD1
|
A:ASN132
|
2.3
|
44.5
|
1.0
|
OD1
|
A:ASN36
|
2.4
|
42.8
|
1.0
|
O
|
A:ILE85
|
2.4
|
37.9
|
1.0
|
OD1
|
A:ASN84
|
2.5
|
40.5
|
1.0
|
O
|
A:VAL37
|
2.5
|
39.2
|
1.0
|
O
|
A:VAL133
|
2.6
|
39.7
|
1.0
|
CG
|
A:ASN132
|
3.2
|
47.2
|
1.0
|
CG
|
A:ASN36
|
3.3
|
44.3
|
1.0
|
CG
|
A:ASN84
|
3.3
|
41.3
|
1.0
|
C
|
A:ILE85
|
3.5
|
38.8
|
1.0
|
C
|
A:VAL37
|
3.6
|
38.9
|
1.0
|
ND2
|
A:ASN36
|
3.6
|
44.4
|
1.0
|
N
|
A:VAL133
|
3.6
|
40.9
|
1.0
|
N
|
A:ILE85
|
3.6
|
39.5
|
1.0
|
C
|
A:VAL133
|
3.6
|
39.8
|
1.0
|
N
|
A:VAL37
|
3.6
|
40.4
|
1.0
|
ND2
|
A:ASN132
|
3.6
|
48.4
|
1.0
|
ND2
|
A:ASN84
|
3.7
|
40.9
|
1.0
|
CA
|
A:ILE85
|
4.0
|
37.9
|
1.0
|
CA
|
A:VAL37
|
4.0
|
38.0
|
1.0
|
CA
|
A:VAL133
|
4.0
|
39.5
|
1.0
|
O
|
A:HOH662
|
4.1
|
42.0
|
1.0
|
CB
|
A:ILE85
|
4.3
|
37.4
|
1.0
|
CB
|
A:VAL37
|
4.3
|
36.8
|
1.0
|
CB
|
A:VAL133
|
4.3
|
38.3
|
1.0
|
C
|
A:ASN132
|
4.5
|
42.7
|
1.0
|
CB
|
A:ASN132
|
4.5
|
46.9
|
1.0
|
C
|
A:ASN36
|
4.6
|
41.4
|
1.0
|
CB
|
A:ASN36
|
4.6
|
44.7
|
1.0
|
C
|
A:ASN84
|
4.6
|
40.2
|
1.0
|
CA
|
A:ASN132
|
4.6
|
44.6
|
1.0
|
CB
|
A:ASN84
|
4.6
|
42.3
|
1.0
|
CA
|
A:ASN36
|
4.7
|
43.1
|
1.0
|
N
|
A:GLN86
|
4.7
|
37.3
|
1.0
|
CA
|
A:ASN84
|
4.7
|
41.1
|
1.0
|
N
|
A:GLN38
|
4.7
|
38.9
|
1.0
|
N
|
A:GLN134
|
4.8
|
39.9
|
1.0
|
|
Calcium binding site 2 out
of 2 in 8bad
Go back to
Calcium Binding Sites List in 8bad
Calcium binding site 2 out
of 2 in the TPP80AA1
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of TPP80AA1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:52.7
occ:1.00
|
OD1
|
B:ASN36
|
2.4
|
25.2
|
1.0
|
OD1
|
B:ASN132
|
2.4
|
29.1
|
1.0
|
O
|
B:ILE85
|
2.4
|
26.2
|
1.0
|
OD1
|
B:ASN84
|
2.5
|
27.4
|
1.0
|
O
|
B:VAL37
|
2.5
|
24.8
|
1.0
|
O
|
B:VAL133
|
2.6
|
27.4
|
1.0
|
CG
|
B:ASN36
|
3.3
|
25.4
|
1.0
|
CG
|
B:ASN132
|
3.3
|
29.0
|
1.0
|
CG
|
B:ASN84
|
3.3
|
28.6
|
1.0
|
C
|
B:ILE85
|
3.5
|
26.2
|
1.0
|
C
|
B:VAL37
|
3.5
|
25.2
|
1.0
|
ND2
|
B:ASN36
|
3.6
|
27.1
|
1.0
|
ND2
|
B:ASN84
|
3.6
|
27.1
|
1.0
|
N
|
B:ILE85
|
3.6
|
26.7
|
1.0
|
C
|
B:VAL133
|
3.6
|
28.0
|
1.0
|
N
|
B:VAL133
|
3.6
|
26.6
|
1.0
|
ND2
|
B:ASN132
|
3.6
|
30.1
|
1.0
|
N
|
B:VAL37
|
3.6
|
24.0
|
1.0
|
CA
|
B:ILE85
|
4.0
|
26.9
|
1.0
|
CA
|
B:VAL37
|
4.0
|
24.3
|
1.0
|
CA
|
B:VAL133
|
4.0
|
27.3
|
1.0
|
CB
|
B:VAL133
|
4.3
|
26.4
|
1.0
|
CB
|
B:VAL37
|
4.3
|
23.7
|
1.0
|
CB
|
B:ILE85
|
4.3
|
26.5
|
1.0
|
C
|
B:ASN132
|
4.5
|
27.1
|
1.0
|
C
|
B:ASN36
|
4.5
|
24.4
|
1.0
|
CB
|
B:ASN36
|
4.5
|
25.7
|
1.0
|
C
|
B:ASN84
|
4.5
|
28.1
|
1.0
|
CB
|
B:ASN132
|
4.6
|
28.7
|
1.0
|
CB
|
B:ASN84
|
4.6
|
29.0
|
1.0
|
CA
|
B:ASN36
|
4.6
|
24.2
|
1.0
|
CA
|
B:ASN132
|
4.6
|
27.9
|
1.0
|
CA
|
B:ASN84
|
4.6
|
28.0
|
1.0
|
N
|
B:GLN86
|
4.7
|
24.2
|
1.0
|
N
|
B:GLN38
|
4.7
|
26.2
|
1.0
|
N
|
B:GLN134
|
4.8
|
29.1
|
1.0
|
|
Reference:
H.L.Best,
L.J.Williamson,
M.Lipka-Lloyd,
H.Waller-Evans,
E.Lloyd-Evans,
P.J.Rizkallah,
C.Berry.
The Crystal Structure of Bacillus Thuringiensis TPP80AA1 and Its Interaction with Galactose-Containing Glycolipids. Toxins V. 14 2022.
ISSN: ESSN 2072-6651
PubMed: 36548760
DOI: 10.3390/TOXINS14120863
Page generated: Tue Apr 4 19:27:52 2023
|