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

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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

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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

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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

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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

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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

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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

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