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Magnesium in PDB 9hhy: Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid

Enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid

All present enzymatic activity of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid, PDB code: 9hhy was solved by W.Stuart, M.Isupov, N.J.Harmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.24 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.785, 115.55, 195.241, 90, 92.34, 90
R / Rfree (%) 21.4 / 26.5

Other elements in 9hhy:

The structure of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid (pdb code 9hhy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid, PDB code: 9hhy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 9hhy

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Magnesium binding site 1 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:78.5
occ:1.00
 OD2 A:ASP81 2.0 61.4 1.0
O2 A:ICT301 2.1 84.3 1.0
O A:HOH419 2.4 59.4 1.0
O A:HOH428 2.4 49.6 1.0
O A:HOH445 2.5 68.1 1.0
O7 A:ICT301 2.8 85.1 1.0
C1 A:ICT301 3.1 100.0 1.0
CG A:ASP81 3.1 46.6 1.0
NZ A:LYS116 3.5 75.0 1.0
C2 A:ICT301 3.5 119.6 1.0
N A:GLY44 3.7 39.4 1.0
OD1 A:ASP81 3.7 54.9 1.0
N A:GLY43 3.9 37.1 1.0
OD1 A:ASP83 3.9 69.7 1.0
CA A:GLY43 3.9 25.1 1.0
OD2 A:ASP54 4.1 38.0 1.0
C A:GLY43 4.2 31.5 1.0
C3 A:ICT301 4.2 110.2 1.0
O1 A:ICT301 4.3 51.7 1.0
O6 A:ICT301 4.3 45.3 1.0
CB A:ASP81 4.4 43.3 1.0
NH2 A:ARG152 4.5 85.7 1.0
OH A:TYR40 4.5 34.7 1.0
CA A:GLY44 4.6 44.3 1.0
C6 A:ICT301 4.6 79.2 1.0
OD1 A:ASP54 4.6 37.6 1.0
CG A:ASP54 4.8 42.1 1.0
CE1 A:HIS108 4.8 35.1 1.0
CE A:LYS116 4.9 73.8 1.0

Magnesium binding site 2 out of 12 in 9hhy

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Magnesium binding site 2 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:85.5
occ:1.00
 OD2 B:ASP81 2.0 56.0 1.0
O2 B:ICT301 2.1 84.1 1.0
O B:HOH441 2.4 57.9 1.0
O B:HOH422 2.5 55.8 1.0
O B:HOH410 2.5 63.5 1.0
O7 B:ICT301 3.0 97.8 1.0
CG B:ASP81 3.1 37.4 1.0
C1 B:ICT301 3.1 88.5 1.0
NZ B:LYS116 3.4 66.9 1.0
C2 B:ICT301 3.5 94.4 1.0
OD1 B:ASP81 3.6 38.0 1.0
O6 B:ICT301 3.8 73.4 1.0
OD1 B:ASP83 3.9 75.0 1.0
N B:GLY44 4.0 44.2 1.0
C3 B:ICT301 4.1 87.8 1.0
N B:GLY43 4.1 29.3 1.0
CA B:GLY43 4.2 32.6 1.0
O1 B:ICT301 4.3 62.2 1.0
NH2 B:ARG152 4.3 39.5 1.0
OD2 B:ASP54 4.3 52.4 1.0
CB B:ASP81 4.3 34.9 1.0
C6 B:ICT301 4.4 76.5 1.0
OH B:TYR40 4.4 42.6 1.0
C B:GLY43 4.6 42.8 1.0
CE1 B:HIS108 4.6 38.3 1.0
CE B:LYS116 4.8 123.4 1.0
OD1 B:ASP54 4.8 46.5 1.0
CA B:GLY44 5.0 41.9 1.0
CG B:ASP54 5.0 43.6 1.0
OE1 B:GLU110 5.0 61.6 1.0

Magnesium binding site 3 out of 12 in 9hhy

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Magnesium binding site 3 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:69.6
occ:1.00
 OD2 C:ASP81 2.0 55.8 1.0
O2 C:ICT301 2.1 67.0 1.0
O C:HOH433 2.4 54.1 1.0
O C:HOH420 2.4 55.6 1.0
O C:HOH412 2.4 67.0 1.0
O7 C:ICT301 2.8 54.7 1.0
C1 C:ICT301 3.1 64.2 1.0
CG C:ASP81 3.1 43.2 1.0
C2 C:ICT301 3.4 81.9 1.0
NZ C:LYS116 3.6 90.4 1.0
OD1 C:ASP81 3.6 55.4 1.0
N C:GLY44 3.8 41.6 1.0
O6 C:ICT301 3.9 54.8 1.0
OD1 C:ASP83 4.0 100.7 1.0
N C:GLY43 4.0 37.7 1.0
C3 C:ICT301 4.1 72.1 1.0
CA C:GLY43 4.1 49.1 1.0
OD2 C:ASP54 4.2 50.6 1.0
O1 C:ICT301 4.3 84.3 1.0
NH2 C:ARG152 4.3 53.9 1.0
CB C:ASP81 4.3 44.8 1.0
C6 C:ICT301 4.4 71.9 1.0
C C:GLY43 4.4 52.6 1.0
OH C:TYR40 4.4 47.2 1.0
CE1 C:HIS108 4.7 47.6 1.0
OD1 C:ASP54 4.7 55.1 1.0
CA C:GLY44 4.8 46.4 1.0
CG C:ASP54 4.9 62.0 1.0
CE C:LYS116 4.9 66.2 1.0

Magnesium binding site 4 out of 12 in 9hhy

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Magnesium binding site 4 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg309

b:54.9
occ:1.00
 OD2 D:ASP81 2.0 42.9 1.0
O2 D:ICT302 2.1 71.3 1.0
O D:HOH422 2.4 54.0 1.0
O D:HOH419 2.4 48.0 1.0
O D:HOH402 2.4 51.4 1.0
O7 D:ICT302 2.8 86.0 1.0
CG D:ASP81 3.1 37.2 1.0
C1 D:ICT302 3.1 81.0 1.0
C2 D:ICT302 3.4 78.0 1.0
NZ D:LYS116 3.5 85.6 1.0
OD1 D:ASP81 3.6 37.2 1.0
N D:GLY44 3.9 31.5 1.0
OD1 D:ASP83 3.9 68.1 1.0
O6 D:ICT302 3.9 74.4 1.0
N D:GLY43 4.0 28.5 1.0
C3 D:ICT302 4.1 66.2 1.0
CA D:GLY43 4.1 26.8 1.0
OD2 D:ASP54 4.2 44.8 1.0
NH2 D:ARG152 4.3 34.2 1.0
O1 D:ICT302 4.3 53.2 1.0
CB D:ASP81 4.3 41.5 1.0
C6 D:ICT302 4.4 65.0 1.0
C D:GLY43 4.4 41.7 1.0
OH D:TYR40 4.4 35.3 1.0
CE1 D:HIS108 4.6 32.8 1.0
OD1 D:ASP54 4.7 47.5 1.0
CE D:LYS116 4.8 55.0 1.0
CA D:GLY44 4.8 33.8 1.0
CG D:ASP54 4.9 43.0 1.0
OE1 D:GLU110 5.0 41.8 1.0

Magnesium binding site 5 out of 12 in 9hhy

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Magnesium binding site 5 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg303

b:77.1
occ:1.00
 OD2 E:ASP81 2.0 70.6 1.0
O2 E:ICT301 2.1 87.3 1.0
O E:HOH404 2.4 48.6 1.0
O E:HOH409 2.4 53.3 1.0
O E:HOH407 2.4 78.0 1.0
CG E:ASP81 3.1 61.2 1.0
O7 E:ICT301 3.2 74.0 1.0
C1 E:ICT301 3.2 85.7 1.0
NZ E:LYS116 3.4 72.3 1.0
OD1 E:ASP81 3.6 64.9 1.0
C2 E:ICT301 3.7 98.5 1.0
N E:GLY44 3.9 69.6 1.0
OD1 E:ASP83 3.9 86.6 1.0
N E:GLY43 4.0 59.0 1.0
CA E:GLY43 4.1 72.0 1.0
OD2 E:ASP54 4.2 83.4 1.0
NH2 E:ARG152 4.3 78.4 1.0
C3 E:ICT301 4.3 112.7 1.0
O1 E:ICT301 4.3 91.7 1.0
CB E:ASP81 4.3 77.3 1.0
C E:GLY43 4.4 81.4 1.0
OH E:TYR40 4.5 62.7 1.0
O6 E:ICT301 4.6 66.0 1.0
CE1 E:HIS108 4.7 52.1 1.0
OD1 E:ASP54 4.7 109.3 1.0
CA E:GLY44 4.8 57.9 1.0
CE E:LYS116 4.8 66.2 1.0
C6 E:ICT301 4.8 97.2 1.0
CG E:ASP54 4.8 78.7 1.0
OE1 E:GLU110 4.9 87.8 1.0

Magnesium binding site 6 out of 12 in 9hhy

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Magnesium binding site 6 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg305

b:97.9
occ:1.00
 OD2 F:ASP81 1.9 66.0 1.0
O2 F:ICT301 2.1 111.0 1.0
O F:HOH404 2.4 67.6 1.0
O F:HOH402 2.4 69.8 1.0
O F:HOH414 2.4 52.9 1.0
O7 F:ICT301 3.0 87.6 1.0
CG F:ASP81 3.1 52.2 1.0
C1 F:ICT301 3.2 109.5 1.0
NZ F:LYS116 3.4 78.2 1.0
C2 F:ICT301 3.6 105.4 1.0
OD1 F:ASP81 3.6 48.9 1.0
N F:GLY44 3.8 58.4 1.0
OD1 F:ASP83 3.9 107.1 1.0
N F:GLY43 4.0 41.4 1.0
O6 F:ICT301 4.0 65.6 1.0
CA F:GLY43 4.1 43.4 1.0
OD2 F:ASP54 4.2 60.2 1.0
C3 F:ICT301 4.3 99.6 1.0
O1 F:ICT301 4.3 83.0 1.0
CB F:ASP81 4.3 65.7 1.0
NH2 F:ARG152 4.3 65.0 1.0
C F:GLY43 4.4 51.6 1.0
OH F:TYR40 4.4 51.1 1.0
C6 F:ICT301 4.6 77.9 1.0
CE1 F:HIS108 4.6 55.5 1.0
OD1 F:ASP54 4.7 68.2 1.0
CA F:GLY44 4.8 48.3 1.0
CE F:LYS116 4.8 89.3 1.0
CG F:ASP54 4.9 64.2 1.0

Magnesium binding site 7 out of 12 in 9hhy

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Magnesium binding site 7 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg307

b:80.2
occ:1.00
 OD2 G:ASP81 2.0 52.6 1.0
O2 G:ICT301 2.1 116.8 1.0
O G:HOH424 2.4 45.8 1.0
O G:HOH404 2.4 74.4 1.0
O G:HOH412 2.4 76.1 1.0
CG G:ASP81 3.0 47.5 1.0
C1 G:ICT301 3.2 93.8 1.0
O7 G:ICT301 3.2 74.0 1.0
NZ G:LYS116 3.2 74.0 1.0
OD1 G:ASP81 3.5 69.1 1.0
C2 G:ICT301 3.7 111.7 1.0
OD1 G:ASP83 3.7 66.1 1.0
O6 G:ICT301 4.0 68.2 1.0
N G:GLY44 4.0 49.0 1.0
N G:GLY43 4.2 48.1 1.0
NH2 G:ARG152 4.2 59.4 1.0
CA G:GLY43 4.2 56.1 1.0
OD2 G:ASP54 4.2 50.5 1.0
O1 G:ICT301 4.3 58.5 1.0
CB G:ASP81 4.3 42.0 1.0
C3 G:ICT301 4.3 101.4 1.0
CE1 G:HIS108 4.5 61.9 1.0
OH G:TYR40 4.5 44.5 1.0
C G:GLY43 4.5 47.4 1.0
C6 G:ICT301 4.6 78.3 1.0
CE G:LYS116 4.7 65.6 1.0
OD1 G:ASP54 4.7 64.8 1.0
OE1 G:GLU110 4.7 69.9 1.0
CG G:ASP54 4.9 50.0 1.0
CZ G:ARG152 4.9 68.3 1.0
CG G:ASP83 5.0 63.7 1.0
CA G:GLY44 5.0 44.4 1.0

Magnesium binding site 8 out of 12 in 9hhy

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Magnesium binding site 8 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


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 the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg307

b:94.7
occ:1.00
 OD2 H:ASP81 2.0 72.8 1.0
O2 H:ICT301 2.1 124.9 1.0
O H:HOH428 2.4 61.1 1.0
O H:HOH409 2.4 66.9 1.0
O H:HOH408 2.5 56.4 1.0
CG H:ASP81 3.1 61.5 1.0
C1 H:ICT301 3.2 114.0 1.0
NZ H:LYS116 3.3 100.5 1.0
O7 H:ICT301 3.3 74.1 1.0
OD1 H:ASP81 3.6 61.8 1.0
C2 H:ICT301 3.8 102.1 1.0
N H:GLY44 3.9 42.1 1.0
OD2 H:ASP83 3.9 105.8 1.0
N H:GLY43 4.0 45.1 1.0
CA H:GLY43 4.1 48.2 1.0
OD2 H:ASP54 4.2 48.5 1.0
O6 H:ICT301 4.3 64.3 1.0
O1 H:ICT301 4.3 95.1 1.0
CB H:ASP81 4.3 54.4 1.0
C3 H:ICT301 4.4 118.5 1.0
C H:GLY43 4.4 50.1 1.0
NH2 H:ARG152 4.5 53.2 1.0
OH H:TYR40 4.5 50.8 1.0
OD1 H:ASP54 4.6 68.0 1.0
CE1 H:HIS108 4.7 42.0 1.0
CE H:LYS116 4.7 76.8 1.0
C6 H:ICT301 4.8 81.9 1.0
CG H:ASP54 4.8 68.9 1.0
CA H:GLY44 4.8 34.8 1.0
OE1 H:GLU110 5.0 73.2 1.0
CG H:ASP83 5.0 79.3 1.0

Magnesium binding site 9 out of 12 in 9hhy

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Magnesium binding site 9 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg303

b:76.1
occ:1.00
 OD2 I:ASP81 2.0 45.8 1.0
O2 I:ICT301 2.1 115.3 1.0
O I:HOH417 2.4 58.7 1.0
O I:HOH402 2.4 66.4 1.0
O I:HOH403 2.4 72.6 1.0
O7 I:ICT301 2.8 77.2 1.0
C1 I:ICT301 3.1 107.4 1.0
CG I:ASP81 3.1 36.9 1.0
NZ I:LYS116 3.4 65.5 1.0
C2 I:ICT301 3.4 94.1 1.0
OD1 I:ASP81 3.6 42.7 1.0
N I:GLY44 3.7 37.0 1.0
OD1 I:ASP83 3.9 80.8 1.0
N I:GLY43 3.9 42.7 1.0
CA I:GLY43 4.0 37.1 1.0
C3 I:ICT301 4.1 83.1 1.0
OD2 I:ASP54 4.1 61.6 1.0
O6 I:ICT301 4.1 76.5 1.0
C I:GLY43 4.2 38.0 1.0
O1 I:ICT301 4.3 85.2 1.0
CB I:ASP81 4.3 32.1 1.0
NH2 I:ARG152 4.4 51.5 1.0
OH I:TYR40 4.5 39.9 1.0
C6 I:ICT301 4.5 83.5 1.0
OD1 I:ASP54 4.6 68.5 1.0
CA I:GLY44 4.6 40.6 1.0
CG I:ASP54 4.8 47.2 1.0
CE1 I:HIS108 4.8 38.0 1.0
CE I:LYS116 4.9 55.0 1.0

Magnesium binding site 10 out of 12 in 9hhy

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Magnesium binding site 10 out of 12 in the Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Coxiella Burnetii 2-Methylisocitrate Lyase Bound to Inhibitor Isocitric Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg304

b:111.6
occ:1.00
 OD2 J:ASP81 2.0 68.3 1.0
O2 J:ICT301 2.1 107.5 1.0
O J:HOH432 2.4 54.0 1.0
O J:HOH405 2.4 57.8 1.0
O J:HOH401 2.4 66.9 1.0
O7 J:ICT301 3.0 81.5 1.0
C1 J:ICT301 3.1 119.0 1.0
CG J:ASP81 3.1 51.0 1.0
NZ J:LYS116 3.4 71.2 1.0
C2 J:ICT301 3.5 118.5 1.0
OD1 J:ASP81 3.6 49.4 1.0
N J:GLY44 3.8 39.8 1.0
OD1 J:ASP83 3.8 99.1 1.0
CA J:GLY43 3.9 38.6 1.0
N J:GLY43 3.9 49.1 1.0
O6 J:ICT301 4.0 69.5 1.0
C3 J:ICT301 4.0 119.6 1.0
OD2 J:ASP54 4.2 69.1 1.0
O1 J:ICT301 4.2 94.7 1.0
C J:GLY43 4.3 57.7 1.0
CB J:ASP81 4.3 47.7 1.0
C6 J:ICT301 4.4 108.5 1.0
NH2 J:ARG152 4.5 44.8 1.0
OD1 J:ASP54 4.6 64.1 1.0
OH J:TYR40 4.6 47.5 1.0
CE J:LYS116 4.6 107.5 1.0
CA J:GLY44 4.7 36.9 1.0
CE1 J:HIS108 4.8 28.5 1.0
CG J:ASP54 4.8 56.1 1.0
CG J:ASP83 5.0 80.3 1.0

Reference:

W.S.Stuart, C.H.Jenkins, P.M.Ireland, M.N.Isupov, I.H.Norville, N.J.Harmer. Structure and Catalytic Mechanism of Methylisocitrate Lyase, A Potential Drug Target Against Coxiella Burnetii. J.Biol.Chem. V. 301 08517 2025.
ISSN: ESSN 1083-351X
PubMed: 40250561
DOI: 10.1016/J.JBC.2025.108517
Page generated: Sat Aug 23 06:02:48 2025

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