Magnesium in PDB 7qp0: Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Protein crystallography data
The structure of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium, PDB code: 7qp0
was solved by
L.Conchou,
L.Ballut,
S.Violot,
N.Aghajari,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.38 /
1.60
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
95.7,
83.6,
87.8,
90,
106.6,
90
|
R / Rfree (%)
|
17.5 /
20.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
(pdb code 7qp0). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of Metacaspase From Candida Glabrata with Magnesium, PDB code: 7qp0:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 1 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:41.9
occ:1.00
|
O
|
A:HOH540
|
1.9
|
46.8
|
1.0
|
OD1
|
A:ASP188
|
2.1
|
37.5
|
1.0
|
O
|
A:HOH551
|
2.1
|
32.4
|
1.0
|
OD1
|
A:ASP190
|
2.1
|
45.3
|
1.0
|
O
|
A:HOH684
|
2.3
|
39.8
|
1.0
|
O
|
A:HOH510
|
2.3
|
40.5
|
1.0
|
CG
|
A:ASP190
|
3.1
|
54.9
|
1.0
|
CG
|
A:ASP188
|
3.1
|
47.0
|
1.0
|
OD2
|
A:ASP190
|
3.5
|
43.2
|
1.0
|
OD2
|
A:ASP188
|
3.7
|
39.3
|
1.0
|
OD2
|
A:ASP198
|
3.8
|
30.4
|
1.0
|
OD1
|
A:ASP198
|
3.9
|
33.2
|
1.0
|
CB
|
A:ASP188
|
4.2
|
37.2
|
1.0
|
O
|
A:HOH768
|
4.2
|
42.1
|
1.0
|
CG
|
A:ASP198
|
4.3
|
28.4
|
1.0
|
OD2
|
A:ASP215
|
4.3
|
36.9
|
1.0
|
N
|
A:ASP190
|
4.4
|
44.7
|
1.0
|
CA
|
A:ASP188
|
4.4
|
35.8
|
1.0
|
O
|
A:HOH630
|
4.4
|
47.9
|
1.0
|
O
|
A:HOH532
|
4.4
|
41.2
|
1.0
|
C
|
A:ASP190
|
4.4
|
52.2
|
1.0
|
N
|
A:GLY191
|
4.4
|
52.2
|
1.0
|
CB
|
A:ASP190
|
4.4
|
45.4
|
1.0
|
CA
|
A:GLY191
|
4.5
|
66.1
|
1.0
|
C
|
A:ASP188
|
4.6
|
51.3
|
1.0
|
CA
|
A:ASP190
|
4.6
|
46.1
|
1.0
|
CD1
|
A:ILE213
|
4.7
|
24.8
|
1.0
|
O
|
A:ASP190
|
4.8
|
58.2
|
1.0
|
N
|
A:LEU189
|
4.8
|
37.2
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 2 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg403
b:33.7
occ:1.00
|
O
|
A:HOH782
|
2.1
|
36.5
|
1.0
|
O
|
A:HOH756
|
2.2
|
33.4
|
1.0
|
O
|
A:HOH550
|
2.2
|
23.1
|
1.0
|
O
|
A:HOH547
|
2.2
|
27.2
|
1.0
|
O
|
A:HOH515
|
2.3
|
36.8
|
1.0
|
O
|
A:HOH679
|
2.4
|
36.3
|
1.0
|
OD1
|
A:ASP120
|
3.7
|
20.1
|
1.0
|
O
|
A:ILE338
|
4.0
|
29.6
|
1.0
|
OD2
|
A:ASP120
|
4.2
|
17.8
|
1.0
|
O
|
A:HOH736
|
4.2
|
47.4
|
1.0
|
CA
|
A:GLY339
|
4.3
|
18.6
|
1.0
|
CG
|
A:ASP120
|
4.3
|
14.1
|
1.0
|
CA
|
A:GLY116
|
4.3
|
19.7
|
1.0
|
O
|
A:HOH685
|
4.5
|
24.3
|
1.0
|
O
|
A:GLY116
|
4.5
|
20.8
|
1.0
|
O
|
A:GLY339
|
4.5
|
21.4
|
1.0
|
O
|
A:HOH710
|
4.6
|
42.0
|
1.0
|
C
|
A:GLY339
|
4.6
|
20.5
|
1.0
|
C
|
A:GLY116
|
4.6
|
22.9
|
1.0
|
C
|
A:ILE338
|
5.0
|
25.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 3 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:35.3
occ:1.00
|
O
|
A:HOH608
|
1.9
|
34.3
|
1.0
|
O
|
A:HOH527
|
2.1
|
31.1
|
1.0
|
OD2
|
A:ASP214
|
2.1
|
27.2
|
1.0
|
O
|
A:HOH759
|
2.2
|
44.6
|
1.0
|
O
|
A:HOH573
|
2.2
|
41.3
|
1.0
|
O
|
A:HOH541
|
2.2
|
33.4
|
1.0
|
CG
|
A:ASP214
|
3.0
|
23.7
|
1.0
|
OD1
|
A:ASP214
|
3.5
|
24.5
|
1.0
|
OD1
|
A:ASP245
|
3.9
|
50.5
|
1.0
|
CB
|
A:ASP214
|
4.1
|
21.2
|
1.0
|
OD1
|
A:ASP199
|
4.1
|
41.8
|
1.0
|
O
|
A:MET197
|
4.1
|
29.5
|
1.0
|
O
|
A:HOH513
|
4.2
|
48.8
|
1.0
|
N
|
A:ASP199
|
4.3
|
20.6
|
1.0
|
O
|
A:THR242
|
4.3
|
23.2
|
1.0
|
OD1
|
A:ASP215
|
4.5
|
30.2
|
1.0
|
CA
|
A:ASP198
|
4.5
|
26.1
|
1.0
|
OD1
|
A:ASP198
|
4.6
|
33.2
|
1.0
|
CG
|
A:ASP245
|
4.8
|
52.8
|
1.0
|
OD2
|
A:ASP245
|
4.9
|
57.3
|
1.0
|
C
|
A:ASP198
|
4.9
|
25.9
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 4 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:25.6
occ:1.00
|
O
|
B:HOH527
|
2.1
|
21.4
|
1.0
|
O
|
B:HOH790
|
2.1
|
28.8
|
1.0
|
O
|
B:HOH529
|
2.1
|
28.1
|
1.0
|
O
|
B:HOH560
|
2.1
|
19.9
|
1.0
|
O
|
B:HOH799
|
2.2
|
28.8
|
1.0
|
O
|
B:HOH704
|
2.3
|
31.5
|
1.0
|
OD1
|
B:ASP120
|
3.7
|
15.7
|
1.0
|
O
|
B:HOH807
|
3.8
|
46.0
|
1.0
|
O
|
B:HOH804
|
4.0
|
52.6
|
1.0
|
O
|
B:ILE338
|
4.1
|
24.4
|
1.0
|
OD2
|
B:ASP120
|
4.2
|
14.9
|
1.0
|
CA
|
B:GLY339
|
4.3
|
17.0
|
1.0
|
CG
|
B:ASP120
|
4.4
|
17.1
|
1.0
|
O
|
B:GLY339
|
4.4
|
22.0
|
1.0
|
CA
|
B:GLY116
|
4.4
|
16.8
|
1.0
|
O
|
B:GLY116
|
4.4
|
17.1
|
1.0
|
O
|
B:HOH722
|
4.4
|
20.7
|
1.0
|
O
|
B:HOH734
|
4.4
|
45.2
|
1.0
|
C
|
B:GLY339
|
4.6
|
17.4
|
1.0
|
OH
|
B:TYR372
|
4.6
|
34.0
|
1.0
|
O
|
B:HOH795
|
4.7
|
38.1
|
1.0
|
C
|
B:GLY116
|
4.7
|
21.5
|
1.0
|
O
|
B:HOH716
|
4.7
|
32.5
|
1.0
|
O
|
B:HOH580
|
5.0
|
33.9
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 5 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg403
b:28.3
occ:1.00
|
O
|
B:HOH595
|
2.0
|
27.4
|
1.0
|
O
|
B:HOH653
|
2.0
|
30.2
|
1.0
|
O
|
B:HOH524
|
2.1
|
27.5
|
1.0
|
OD2
|
B:ASP214
|
2.1
|
24.3
|
1.0
|
O
|
B:HOH550
|
2.2
|
25.9
|
1.0
|
O
|
B:HOH798
|
2.3
|
35.4
|
1.0
|
CG
|
B:ASP214
|
2.9
|
20.9
|
1.0
|
OD1
|
B:ASP214
|
3.5
|
22.0
|
1.0
|
OD1
|
B:ASP245
|
4.0
|
44.5
|
1.0
|
CB
|
B:ASP214
|
4.0
|
19.9
|
1.0
|
O
|
B:MET197
|
4.1
|
27.2
|
1.0
|
O
|
B:HOH710
|
4.1
|
45.4
|
1.0
|
O
|
B:HOH623
|
4.2
|
39.0
|
1.0
|
OD2
|
B:ASP199
|
4.2
|
35.3
|
1.0
|
O
|
B:HOH685
|
4.3
|
47.6
|
1.0
|
N
|
B:ASP199
|
4.3
|
22.9
|
1.0
|
O
|
B:THR242
|
4.4
|
23.3
|
1.0
|
CA
|
B:ASP198
|
4.4
|
20.8
|
1.0
|
OD1
|
B:ASP215
|
4.4
|
27.8
|
1.0
|
OD1
|
B:ASP198
|
4.5
|
27.9
|
1.0
|
OD2
|
B:ASP245
|
4.6
|
50.9
|
1.0
|
CG
|
B:ASP245
|
4.7
|
43.6
|
1.0
|
C
|
B:ASP198
|
4.9
|
23.0
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7qp0
Go back to
Magnesium Binding Sites List in 7qp0
Magnesium binding site 6 out
of 6 in the Crystal Structure of Metacaspase From Candida Glabrata with Magnesium
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Metacaspase From Candida Glabrata with Magnesium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg404
b:28.8
occ:1.00
|
O
|
B:HOH562
|
2.0
|
26.6
|
1.0
|
O
|
B:HOH593
|
2.1
|
34.7
|
1.0
|
OD1
|
B:ASP188
|
2.1
|
29.4
|
1.0
|
O
|
B:HOH537
|
2.1
|
29.4
|
1.0
|
O
|
B:HOH708
|
2.1
|
37.5
|
1.0
|
OD1
|
B:ASP190
|
2.2
|
33.5
|
1.0
|
CG
|
B:ASP188
|
3.1
|
29.8
|
1.0
|
CG
|
B:ASP190
|
3.2
|
41.6
|
1.0
|
OD2
|
B:ASP190
|
3.5
|
34.8
|
1.0
|
OD2
|
B:ASP188
|
3.6
|
29.0
|
1.0
|
O
|
B:HOH605
|
3.9
|
38.2
|
1.0
|
OD2
|
B:ASP198
|
3.9
|
28.1
|
1.0
|
OD1
|
B:ASP198
|
4.0
|
27.9
|
1.0
|
O
|
B:HOH533
|
4.2
|
37.6
|
1.0
|
O
|
B:HOH652
|
4.2
|
28.7
|
1.0
|
N
|
B:GLY191
|
4.2
|
35.9
|
1.0
|
OD2
|
B:ASP215
|
4.2
|
29.9
|
1.0
|
O
|
B:HOH818
|
4.3
|
40.9
|
1.0
|
CB
|
B:ASP188
|
4.3
|
29.0
|
1.0
|
N
|
B:ASP190
|
4.4
|
33.3
|
1.0
|
CG
|
B:ASP198
|
4.4
|
27.7
|
1.0
|
C
|
B:ASP190
|
4.4
|
39.8
|
1.0
|
CB
|
B:ASP190
|
4.5
|
40.1
|
1.0
|
CA
|
B:ASP188
|
4.5
|
25.7
|
1.0
|
CA
|
B:ASP190
|
4.7
|
38.1
|
1.0
|
CA
|
B:GLY191
|
4.7
|
45.6
|
1.0
|
C
|
B:ASP188
|
4.7
|
28.7
|
1.0
|
CD1
|
B:ILE213
|
4.7
|
25.5
|
1.0
|
O
|
B:HOH585
|
4.8
|
51.9
|
1.0
|
N
|
B:LEU189
|
4.8
|
26.5
|
1.0
|
O
|
B:ASP190
|
5.0
|
50.4
|
1.0
|
|
Reference:
L.Conchou,
B.Doumeche,
F.Galisson,
S.Violot,
C.Dugelay,
E.Diesis,
A.Page,
A.L.Bienvenu,
S.Picot,
N.Aghajari,
L.Ballut.
Structural and Molecular Determinants of Candida Glabrata Metacaspase Maturation and Activation By Calcium. Commun Biol V. 5 1158 2022.
ISSN: ESSN 2399-3642
PubMed: 36316540
DOI: 10.1038/S42003-022-04091-4
Page generated: Thu Oct 3 05:16:39 2024
|