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Magnesium in PDB 3fa4: Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form

Enzymatic activity of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form

All present enzymatic activity of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form:
4.1.3.32;

Protein crystallography data

The structure of Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form, PDB code: 3fa4 was solved by B.C.Narayanan, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.83 / 2.18
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.090, 115.470, 115.750, 119.66, 90.71, 96.28
R / Rfree (%) 20 / 26.5

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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form (pdb code 3fa4). 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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form, PDB code: 3fa4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3fa4

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Magnesium binding site 1 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:51.1
occ:1.00
 O A:HOH765 1.9 34.4 1.0
O A:HOH480 2.2 30.1 1.0
OD2 A:ASP87 2.2 42.9 1.0
OD2 A:ASP89 2.2 40.3 1.0
CG A:ASP87 3.2 38.8 1.0
CG A:ASP89 3.4 38.8 1.0
OD1 A:ASP87 3.5 36.8 1.0
OD1 A:ASP59 3.8 40.4 1.0
OD2 A:ASP59 4.1 41.7 1.0
OD1 A:ASP89 4.1 41.5 1.0
O A:HOH825 4.1 29.7 1.0
CG A:ASP59 4.3 40.6 1.0
O A:HOH1044 4.4 39.6 1.0
CB A:ASP87 4.5 37.1 1.0
CB A:ASP89 4.5 35.8 1.0
CA A:GLY47 4.6 33.5 1.0
CA A:ASP89 4.7 37.5 1.0
OE1 A:GLU116 4.7 35.7 1.0
O A:HOH1124 4.8 36.7 1.0
N A:ASP89 4.9 37.2 1.0
C A:GLY47 4.9 34.0 1.0

Magnesium binding site 2 out of 12 in 3fa4

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Magnesium binding site 2 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:35.8
occ:1.00
 O B:HOH370 2.0 28.2 1.0
O B:HOH902 2.0 28.3 1.0
OD1 B:ASP89 2.0 41.1 1.0
O B:HOH903 2.3 37.2 1.0
OD2 B:ASP87 2.3 40.9 1.0
CG B:ASP87 3.1 39.8 1.0
OD1 B:ASP87 3.2 42.0 1.0
CG B:ASP89 3.3 38.9 1.0
OD1 B:ASP59 4.0 38.2 1.0
OD2 B:ASP89 4.1 43.6 1.0
OD2 B:ASP59 4.2 43.1 1.0
CB B:ASP89 4.3 35.7 1.0
OE1 B:GLU116 4.3 37.2 1.0
CA B:ASP89 4.3 35.9 1.0
O B:HOH896 4.4 27.1 1.0
CB B:ASP87 4.5 35.4 1.0
N B:ASP89 4.5 36.8 1.0
O B:HOH420 4.5 36.1 1.0
CG B:ASP59 4.5 40.0 1.0
CA B:GLY47 4.6 35.2 1.0

Magnesium binding site 3 out of 12 in 3fa4

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Magnesium binding site 3 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg401

b:46.6
occ:1.00
 OD2 C:ASP87 2.2 45.0 1.0
OD1 C:ASP89 2.5 39.9 1.0
CG C:ASP87 3.2 39.4 1.0
OD1 C:ASP87 3.6 40.1 1.0
CG C:ASP89 3.6 36.6 1.0
OD1 C:ASP59 3.8 39.2 1.0
OD2 C:ASP59 4.0 40.2 1.0
O C:HOH511 4.2 34.7 1.0
OD2 C:ASP89 4.3 36.8 1.0
CG C:ASP59 4.3 38.9 1.0
CA C:GLY47 4.4 34.4 1.0
CB C:ASP87 4.5 37.8 1.0
O C:HOH455 4.6 36.5 1.0
CA C:ASP89 4.7 35.9 1.0
OE1 C:GLU116 4.7 37.9 1.0
CB C:ASP89 4.7 36.5 1.0
C C:GLY47 4.7 34.5 1.0
N C:ALA48 4.7 35.9 1.0
N C:GLY47 4.9 35.3 1.0

Magnesium binding site 4 out of 12 in 3fa4

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Magnesium binding site 4 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:40.2
occ:1.00
 O D:HOH868 1.8 35.7 1.0
OD1 D:ASP89 2.2 40.3 1.0
O D:HOH905 2.4 32.3 1.0
OD2 D:ASP87 2.5 35.2 1.0
O D:HOH495 2.5 26.1 1.0
CG D:ASP89 3.4 40.4 1.0
CG D:ASP87 3.6 40.8 1.0
OD2 D:ASP59 3.8 40.0 1.0
OD1 D:ASP59 3.9 38.8 1.0
OD1 D:ASP87 3.9 40.8 1.0
O D:HOH796 4.0 34.1 1.0
OD2 D:ASP89 4.1 41.4 1.0
CG D:ASP59 4.3 40.6 1.0
CB D:ASP89 4.3 39.0 1.0
CA D:ASP89 4.4 39.0 1.0
OE2 D:GLU116 4.4 36.0 1.0
CA D:GLY47 4.5 35.0 1.0
O D:HOH906 4.6 32.8 1.0
N D:ASP89 4.8 39.4 1.0
O D:HOH312 4.8 31.4 1.0
CB D:ASP87 4.9 36.5 1.0
C D:GLY47 4.9 35.1 1.0
O D:HOH306 5.0 39.4 1.0

Magnesium binding site 5 out of 12 in 3fa4

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Magnesium binding site 5 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg401

b:40.1
occ:1.00
 O E:HOH760 1.9 38.2 1.0
O E:HOH869 2.0 27.2 1.0
OD1 E:ASP89 2.2 38.8 1.0
OD2 E:ASP87 2.3 41.5 1.0
CG E:ASP87 3.3 37.2 1.0
CG E:ASP89 3.4 38.8 1.0
OD1 E:ASP87 3.6 42.0 1.0
OD2 E:ASP59 3.8 42.5 1.0
OD2 E:ASP89 4.0 36.1 1.0
OD1 E:ASP59 4.1 43.4 1.0
CA E:GLY47 4.1 37.1 1.0
O E:HOH387 4.4 37.1 1.0
CG E:ASP59 4.4 41.7 1.0
C E:GLY47 4.5 37.1 1.0
CB E:ASP89 4.5 35.2 1.0
CB E:ASP87 4.5 33.6 1.0
CA E:ASP89 4.6 37.1 1.0
N E:ALA48 4.8 38.7 1.0
N E:GLY47 4.8 37.1 1.0
N E:ASP89 4.9 37.3 1.0
OE1 E:GLU116 5.0 38.7 1.0
O E:GLY47 5.0 36.8 1.0

Magnesium binding site 6 out of 12 in 3fa4

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Magnesium binding site 6 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg401

b:44.1
occ:1.00
 OD1 F:ASP89 2.1 41.9 1.0
OD2 F:ASP87 2.3 33.9 1.0
O F:HOH840 2.8 36.0 1.0
CG F:ASP87 3.3 36.9 1.0
CG F:ASP89 3.4 38.0 1.0
OD2 F:ASP59 3.6 42.4 1.0
O F:HOH1033 3.6 34.1 1.0
OD1 F:ASP87 3.8 42.1 1.0
CA F:GLY47 3.9 33.8 1.0
OD2 F:ASP89 4.0 38.8 1.0
C F:GLY47 4.2 33.8 1.0
OD1 F:ASP59 4.2 40.6 1.0
CG F:ASP59 4.3 39.5 1.0
N F:ALA48 4.4 34.8 1.0
CB F:ASP87 4.5 37.7 1.0
CB F:ASP89 4.5 35.9 1.0
N F:GLY47 4.5 34.4 1.0
CA F:ASP89 4.8 36.1 1.0
O F:GLY47 4.8 35.1 1.0
CE F:MET68 4.8 30.4 1.0
O F:HOH398 4.9 35.5 1.0

Magnesium binding site 7 out of 12 in 3fa4

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Magnesium binding site 7 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg401

b:37.1
occ:1.00
 O G:HOH598 2.0 38.7 1.0
O G:HOH918 2.1 36.7 1.0
O G:HOH762 2.2 32.3 1.0
OD1 G:ASP89 2.3 38.0 1.0
O G:HOH1071 2.3 32.8 1.0
OD2 G:ASP87 2.3 41.9 1.0
CG G:ASP87 3.3 38.7 1.0
OD1 G:ASP87 3.5 41.0 1.0
CG G:ASP89 3.5 37.6 1.0
OD2 G:ASP59 3.9 38.6 1.0
OD1 G:ASP59 3.9 43.0 1.0
O G:HOH948 4.1 30.0 1.0
OD2 G:ASP89 4.2 37.2 1.0
CA G:GLY47 4.3 33.3 1.0
CG G:ASP59 4.3 39.6 1.0
CA G:ASP89 4.5 36.2 1.0
O G:HOH324 4.5 29.2 1.0
C G:GLY47 4.6 34.1 1.0
CB G:ASP89 4.6 35.4 1.0
CB G:ASP87 4.6 33.7 1.0
OE1 G:GLU116 4.7 37.8 1.0
N G:ALA48 4.8 34.4 1.0
O G:HOH1235 4.8 39.1 1.0
O G:HOH679 4.8 32.5 1.0
N G:ASP89 4.8 36.9 1.0
N G:GLY47 4.9 37.5 1.0

Magnesium binding site 8 out of 12 in 3fa4

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Magnesium binding site 8 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg401

b:43.3
occ:1.00
 OD1 H:ASP89 2.0 39.0 1.0
O H:HOH884 2.2 40.7 1.0
OD2 H:ASP87 2.5 44.7 1.0
O H:HOH873 2.5 38.7 1.0
CG H:ASP89 3.2 36.9 1.0
CG H:ASP87 3.4 41.7 1.0
OD1 H:ASP59 3.6 44.8 1.0
OD1 H:ASP87 3.7 45.9 1.0
OD2 H:ASP89 3.8 40.0 1.0
OD2 H:ASP59 4.0 43.0 1.0
CG H:ASP59 4.3 44.9 1.0
CB H:ASP89 4.3 38.3 1.0
CA H:GLY47 4.3 35.1 1.0
C H:GLY47 4.6 36.4 1.0
CA H:ASP89 4.6 37.5 1.0
CB H:ASP87 4.7 37.0 1.0
N H:ALA48 4.8 36.1 1.0
N H:GLY47 5.0 34.6 1.0
OE2 H:GLU116 5.0 45.0 1.0
N H:ASP89 5.0 36.6 1.0

Magnesium binding site 9 out of 12 in 3fa4

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Magnesium binding site 9 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:42.3
occ:1.00
 OD1 I:ASP87 2.2 38.2 1.0
OD1 I:ASP89 2.2 39.4 1.0
CG I:ASP87 2.8 38.5 1.0
OD2 I:ASP87 2.8 38.9 1.0
CG I:ASP89 3.4 39.0 1.0
CA I:ASP89 4.1 37.2 1.0
CB I:ASP87 4.2 37.5 1.0
CB I:ASP89 4.2 37.9 1.0
N I:ASP89 4.2 36.8 1.0
OE1 I:GLU116 4.3 41.2 1.0
O I:HOH483 4.3 45.4 1.0
OD2 I:ASP89 4.3 39.1 1.0
CA I:GLY47 4.5 36.2 1.0
OD1 I:ASP59 4.7 36.1 1.0
OD2 I:ASP59 4.8 37.2 1.0
C I:GLY47 5.0 36.5 1.0
O I:HOH763 5.0 32.4 1.0

Magnesium binding site 10 out of 12 in 3fa4

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Magnesium binding site 10 out of 12 in the Crystal Structure of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form


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 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member, Triclinic Crystal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg401

b:47.8
occ:1.00
 OD1 J:ASP89 2.3 45.4 1.0
OD2 J:ASP87 2.7 42.0 1.0
OD1 J:ASP87 3.0 39.6 1.0
CG J:ASP87 3.2 38.0 1.0
CG J:ASP89 3.5 42.9 1.0
OE1 J:GLU116 3.8 40.9 1.0
CA J:ASP89 4.0 39.8 1.0
CB J:ASP89 4.3 40.2 1.0
N J:ASP89 4.4 38.9 1.0
O J:HOH969 4.4 40.6 1.0
OD2 J:ASP89 4.5 44.0 1.0
CD J:GLU116 4.5 38.9 1.0
OE2 J:GLU116 4.7 38.5 1.0
OD1 J:ASP59 4.7 45.8 1.0
O J:HOH815 4.7 37.6 1.0
CB J:ASP87 4.7 36.5 1.0
OD2 J:ASP59 4.8 45.2 1.0

Reference:

B.Narayanan, W.Niu, H.J.Joosten, Z.Li, R.K.Kuipers, P.J.Schaap, D.Dunaway-Mariano, O.Herzberg. Structure and Function of 2,3-Dimethylmalate Lyase, A Pep Mutase/Isocitrate Lyase Superfamily Member. J.Mol.Biol. V. 386 486 2009.
ISSN: ISSN 0022-2836
PubMed: 19133276
DOI: 10.1016/J.JMB.2008.12.037
Page generated: Wed Aug 14 13:36:37 2024

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