Magnesium in PDB 7ebe: Crystal Structure of Isocitrate Lyase-1 From Candida Albicans

Enzymatic activity of Crystal Structure of Isocitrate Lyase-1 From Candida Albicans

All present enzymatic activity of Crystal Structure of Isocitrate Lyase-1 From Candida Albicans:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Lyase-1 From Candida Albicans, PDB code: 7ebe was solved by K.Hiragi, K.Nishio, S.Moriyama, T.Hamaguchi, A.Mizoguchi, K.Yonekura, K.Tani, T.Mizushima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.11 / 2.69
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.971, 139.91, 200.301, 90, 92.55, 90
R / Rfree (%) 21.5 / 24.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans (pdb code 7ebe). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans, PDB code: 7ebe:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 7ebe

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Magnesium binding site 1 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:46.5
occ:1.00
 O A:HOH707 2.1 48.4 1.0
O A:HOH702 2.2 44.1 1.0
O A:HOH709 2.6 42.3 1.0
OD2 A:ASP172 2.7 47.1 1.0
O A:HOH705 2.8 42.1 1.0
N A:TRP103 2.9 65.9 1.0
N A:GLY102 3.3 56.4 1.0
OG A:SER101 3.5 59.0 1.0
OD2 A:ASP118 3.5 69.0 1.0
CB A:TRP103 3.5 65.2 1.0
O A:HOH701 3.6 46.2 1.0
CA A:GLY102 3.7 55.1 1.0
C A:GLY102 3.7 59.0 1.0
CA A:TRP103 3.8 63.5 1.0
C A:FMT602 3.8 72.3 1.0
O1 A:FMT602 3.8 76.8 1.0
CG A:ASP172 3.9 48.6 1.0
OH A:TYR99 4.0 51.4 1.0
CG A:ASP118 4.2 72.9 1.0
C A:SER101 4.2 52.5 1.0
OD1 A:ASP118 4.3 72.4 1.0
CA A:SER101 4.5 52.4 1.0
CB A:SER101 4.5 57.0 1.0
CB A:ASP172 4.6 45.4 1.0
O2 A:FMT602 4.8 70.1 1.0
CG A:TRP103 4.8 64.8 1.0
OD1 A:ASP172 4.9 45.2 1.0
O A:GLY102 4.9 61.4 1.0

Magnesium binding site 2 out of 8 in 7ebe

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Magnesium binding site 2 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:63.1
occ:1.00
 O B:HOH706 1.9 60.1 1.0
OD2 B:ASP172 2.0 55.5 1.0
O B:HOH701 2.3 52.0 1.0
O B:HOH715 2.9 38.5 1.0
CG B:ASP172 3.2 53.3 1.0
O1 B:FMT602 3.3 84.5 1.0
N B:TRP103 3.4 58.9 1.0
OD2 B:ASP118 3.4 92.6 1.0
N B:GLY102 3.6 56.6 1.0
CA B:GLY102 3.7 61.6 1.0
OD1 B:ASP118 3.9 79.6 1.0
C B:GLY102 3.9 59.0 1.0
OD1 B:ASP172 3.9 55.1 1.0
CG B:ASP118 4.0 77.2 1.0
NZ B:LYS208 4.1 75.8 1.0
C B:FMT602 4.1 83.6 1.0
OD1 B:ASP174 4.1 59.1 1.0
CB B:ASP172 4.2 52.1 1.0
O2 B:FMT602 4.3 78.1 1.0
CA B:TRP103 4.4 59.9 1.0
CB B:TRP103 4.4 60.1 1.0
OH B:TYR99 4.4 55.3 1.0
OG B:SER101 4.6 59.3 1.0
OE1 B:GLU201 4.8 66.5 1.0
C B:SER101 4.8 55.6 1.0
CE B:LYS208 4.8 76.4 1.0
CE1 B:HIS199 4.9 49.5 1.0
O B:GLY102 5.0 57.7 1.0

Magnesium binding site 3 out of 8 in 7ebe

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Magnesium binding site 3 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:52.8
occ:1.00
 O C:HOH707 1.9 44.3 1.0
OD2 C:ASP172 2.3 48.9 1.0
O C:HOH718 2.3 46.3 1.0
O C:HOH704 2.5 43.7 1.0
O C:HOH702 2.8 44.0 1.0
O C:HOH701 2.9 46.9 1.0
N C:TRP103 3.2 60.5 1.0
N C:GLY102 3.4 59.2 1.0
CG C:ASP172 3.5 51.1 1.0
OD2 C:ASP118 3.6 61.6 1.0
CA C:GLY102 3.7 56.9 1.0
O2 C:FMT602 3.8 70.0 1.0
C C:GLY102 3.9 59.2 1.0
OG C:SER101 4.0 60.2 1.0
OH C:TYR99 4.0 53.3 1.0
CB C:TRP103 4.0 64.7 1.0
C C:FMT602 4.1 68.0 1.0
CA C:TRP103 4.1 59.1 1.0
OD1 C:ASP118 4.2 59.4 1.0
CG C:ASP118 4.3 61.7 1.0
CB C:ASP172 4.3 48.6 1.0
OD1 C:ASP172 4.4 54.2 1.0
C C:SER101 4.4 54.5 1.0
CA C:SER101 4.7 51.6 1.0
NZ C:LYS208 4.8 73.4 1.0
OD1 C:ASP174 4.9 56.0 1.0
CB C:SER101 4.9 55.6 1.0

Magnesium binding site 4 out of 8 in 7ebe

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Magnesium binding site 4 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:66.4
occ:1.00
 O D:HOH703 1.9 65.1 1.0
O D:HOH705 2.4 48.8 1.0
OD2 D:ASP172 2.5 60.2 1.0
O D:HOH709 2.5 45.9 1.0
O1 D:FMT602 3.0 72.5 1.0
OD2 D:ASP118 3.3 70.7 1.0
N D:TRP103 3.3 64.9 1.0
CG D:ASP172 3.7 50.9 1.0
N D:GLY102 3.7 52.7 1.0
CA D:GLY102 3.9 54.3 1.0
CB D:TRP103 4.0 66.3 1.0
C D:GLY102 4.0 57.2 1.0
CG D:ASP118 4.0 67.5 1.0
OD1 D:ASP118 4.0 73.4 1.0
C D:FMT602 4.1 63.1 1.0
CA D:TRP103 4.1 61.0 1.0
OG D:SER101 4.2 51.6 1.0
OH D:TYR99 4.3 50.5 1.0
NZ D:LYS208 4.5 82.6 1.0
OD1 D:ASP172 4.5 53.8 1.0
O2 D:FMT602 4.5 63.5 1.0
CB D:ASP172 4.6 51.3 1.0
C D:SER101 4.7 48.8 1.0
OD1 D:ASP174 4.8 52.8 1.0
NH1 D:ARG247 5.0 55.5 1.0

Magnesium binding site 5 out of 8 in 7ebe

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Magnesium binding site 5 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:69.9
occ:1.00
 O E:HOH702 1.7 74.5 1.0
OD2 E:ASP172 2.2 67.4 1.0
O E:HOH714 2.6 54.8 1.0
OD2 E:ASP118 3.2 95.2 1.0
CG E:ASP172 3.4 67.0 1.0
N E:TRP103 3.6 73.6 1.0
OD1 E:ASP118 3.9 81.9 1.0
N E:GLY102 3.9 76.1 1.0
CG E:ASP118 4.0 84.2 1.0
NZ E:LYS208 4.0 88.6 1.0
CA E:GLY102 4.0 77.0 1.0
OD1 E:ASP172 4.1 66.7 1.0
C E:GLY102 4.2 72.9 1.0
OD1 E:ASP174 4.3 60.6 1.0
CB E:ASP172 4.5 61.5 1.0
OH E:TYR99 4.5 78.8 1.0
CA E:TRP103 4.5 78.1 1.0
OE2 E:GLU201 4.6 82.0 1.0
CB E:TRP103 4.6 79.9 1.0
NH1 E:ARG247 4.7 77.4 1.0
OG E:SER101 4.8 72.9 1.0
CE E:LYS208 4.8 86.4 1.0
CE1 E:HIS199 4.9 61.1 1.0

Magnesium binding site 6 out of 8 in 7ebe

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Magnesium binding site 6 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


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 Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:71.1
occ:1.00
 O F:HOH706 2.0 81.2 1.0
OD2 F:ASP172 2.1 70.3 1.0
O F:HOH711 2.1 50.0 1.0
CG F:ASP172 3.3 67.3 1.0
OD2 F:ASP118 3.6 79.2 1.0
N F:TRP103 3.8 76.8 1.0
N F:GLY102 3.9 71.2 1.0
OD1 F:ASP172 4.0 68.7 1.0
OH F:TYR99 4.1 63.7 1.0
CA F:GLY102 4.1 71.9 1.0
NZ F:LYS208 4.3 91.6 1.0
OD1 F:ASP118 4.3 95.6 1.0
CG F:ASP118 4.3 86.0 1.0
CB F:ASP172 4.3 64.5 1.0
C F:GLY102 4.4 70.7 1.0
OE2 F:GLU201 4.5 92.9 1.0
CB F:TRP103 4.6 76.5 1.0
NH1 F:ARG247 4.6 70.6 1.0
OD1 F:ASP174 4.6 65.6 1.0
OG F:SER101 4.6 66.7 1.0
CE1 F:HIS199 4.7 56.9 1.0
CA F:TRP103 4.7 71.0 1.0
NE2 F:HIS199 4.9 52.9 1.0

Magnesium binding site 7 out of 8 in 7ebe

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Magnesium binding site 7 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:62.5
occ:1.00
 O G:HOH716 1.6 56.2 1.0
OD2 G:ASP172 2.2 70.4 1.0
O G:HOH701 2.2 52.0 1.0
O G:HOH727 2.4 54.5 1.0
OD2 G:ASP118 3.3 72.0 1.0
O2 G:FMT602 3.3 76.2 1.0
CG G:ASP172 3.4 63.3 1.0
C G:FMT602 3.6 80.0 1.0
N G:TRP103 3.6 68.6 1.0
OD1 G:ASP118 3.9 75.0 1.0
N G:GLY102 3.9 66.3 1.0
CG G:ASP118 4.0 74.1 1.0
CA G:GLY102 4.0 71.9 1.0
OD1 G:ASP172 4.1 62.3 1.0
NZ G:LYS208 4.2 72.8 1.0
C G:GLY102 4.2 70.0 1.0
OD1 G:ASP174 4.4 55.7 1.0
CB G:TRP103 4.4 75.1 1.0
OH G:TYR99 4.4 58.5 1.0
O1 G:FMT602 4.4 69.0 1.0
CB G:ASP172 4.5 60.6 1.0
CA G:TRP103 4.5 71.4 1.0
OE1 G:GLU201 4.6 81.5 1.0
NH1 G:ARG247 4.7 68.8 1.0
OG G:SER101 4.7 77.0 1.0
CE1 G:HIS199 4.9 63.5 1.0

Magnesium binding site 8 out of 8 in 7ebe

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Magnesium binding site 8 out of 8 in the Crystal Structure of Isocitrate Lyase-1 From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Isocitrate Lyase-1 From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:70.4
occ:1.00
 O H:HOH716 2.1 63.5 1.0
OD2 H:ASP172 2.1 69.9 1.0
O H:HOH725 2.7 42.0 1.0
O1 H:FMT602 3.1 68.6 1.0
OH H:TYR99 3.2 65.2 1.0
O H:HOH705 3.2 61.4 1.0
CG H:ASP172 3.3 63.7 1.0
O2 H:FMT602 3.4 71.7 1.0
CE1 H:HIS199 3.6 62.1 1.0
C H:FMT602 3.7 76.2 1.0
NH1 H:ARG247 3.8 70.3 1.0
NE2 H:HIS199 3.9 61.1 1.0
OD1 H:ASP172 3.9 69.3 1.0
OE2 H:GLU201 4.1 82.9 1.0
CB H:ASP172 4.3 60.9 1.0
CH2 H:TRP400 4.5 63.3 1.0
N H:GLY102 4.5 59.0 1.0
CZ H:TYR99 4.5 68.1 1.0
OD2 H:ASP118 4.7 74.5 1.0
OG1 H:THR464 4.7 81.2 1.0
NZ H:LYS208 4.8 94.1 1.0
ND1 H:HIS199 4.9 61.9 1.0
N H:TRP103 4.9 67.8 1.0
CZ H:ARG247 5.0 72.5 1.0

Reference:

K.Hiragi, K.Nishio, S.Moriyama, T.Hamaguchi, A.Mizoguchi, K.Yonekura, K.Tani, T.Mizushima. Structural Insights Into the Targeting Specificity of Ubiquitin Ligase For S. Cerevisiae Isocitrate Lyase But Not C. Albicans Isocitrate Lyase. J.Struct.Biol. V. 213 07748 2021.
ISSN: ESSN 1095-8657
PubMed: 34033899
DOI: 10.1016/J.JSB.2021.107748
Page generated: Sun Jul 11 16:32:26 2021

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