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Magnesium in PDB 3b8i: Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.

Enzymatic activity of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.

All present enzymatic activity of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.:
4.1.1.3;

Protein crystallography data

The structure of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+., PDB code: 3b8i 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) 47.60 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 260.065, 83.835, 104.874, 90.00, 112.14, 90.00
R / Rfree (%) 19.1 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. (pdb code 3b8i). 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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+., PDB code: 3b8i:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3b8i

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Magnesium binding site 1 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg289

b:27.5
occ:1.00
 O A:HOH292 2.0 19.4 1.0
O A:HOH293 2.1 20.8 1.0
OD2 A:ASP88 2.1 20.4 1.0
O A:HOH294 2.2 25.8 1.0
O1 A:OXL288 2.2 31.8 1.0
O4 A:OXL288 2.3 36.4 1.0
C1 A:OXL288 3.0 32.8 1.0
C2 A:OXL288 3.1 35.4 1.0
CG A:ASP88 3.1 20.2 1.0
OD1 A:ASP88 3.4 22.6 1.0
OD1 A:ASP90 3.6 28.1 1.0
OD2 A:ASP61 3.7 23.9 1.0
O A:HOH333 3.9 35.7 1.0
O A:HOH437 4.0 26.1 1.0
OD1 A:ASP61 4.2 24.3 1.0
N A:GLY49 4.2 21.3 1.0
O3 A:OXL288 4.2 29.8 1.0
O2 A:OXL288 4.3 38.3 1.0
N A:SER50 4.3 21.7 1.0
CG A:ASP61 4.4 23.2 1.0
OE1 A:GLU117 4.4 36.4 1.0
NH1 A:ARG159 4.4 17.6 1.0
CA A:GLY49 4.5 20.8 1.0
CB A:ASP88 4.5 21.1 1.0
CG A:ASP90 4.6 28.2 1.0
NH2 A:ARG159 4.6 29.2 1.0
CZ A:ARG159 4.8 26.5 1.0
C A:GLY49 4.8 21.1 1.0

Magnesium binding site 2 out of 6 in 3b8i

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Magnesium binding site 2 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg289

b:37.7
occ:1.00
 O B:HOH292 1.9 29.8 1.0
O B:HOH294 2.1 45.7 1.0
OD2 B:ASP88 2.1 30.4 1.0
O B:HOH293 2.2 33.5 1.0
O3 B:OXL288 2.4 47.5 1.0
O2 B:OXL288 2.6 51.5 1.0
CG B:ASP88 3.1 30.5 1.0
C1 B:OXL288 3.2 48.8 1.0
C2 B:OXL288 3.3 52.2 1.0
OD1 B:ASP90 3.4 41.8 1.0
OD1 B:ASP88 3.5 28.0 1.0
OD2 B:ASP61 3.8 32.1 1.0
N B:GLY49 4.1 26.0 1.0
OD1 B:ASP61 4.2 30.1 1.0
N B:SER50 4.3 25.3 1.0
CA B:GLY49 4.3 26.6 1.0
CG B:ASP90 4.3 39.1 1.0
CG B:ASP61 4.4 31.9 1.0
CB B:ASP88 4.4 30.7 1.0
O1 B:OXL288 4.4 48.5 1.0
O4 B:OXL288 4.5 52.2 1.0
NH2 B:ARG159 4.5 43.4 1.0
NH1 B:ARG159 4.6 40.2 1.0
C B:GLY49 4.7 26.5 1.0
OD2 B:ASP90 4.7 43.6 1.0
OE1 B:GLU117 4.7 47.8 1.0
CZ B:ARG159 4.9 41.5 1.0

Magnesium binding site 3 out of 6 in 3b8i

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Magnesium binding site 3 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg289

b:39.3
occ:1.00
 O C:HOH291 1.9 37.7 1.0
O C:HOH290 2.0 32.3 1.0
O C:HOH477 2.0 26.8 1.0
OD2 C:ASP88 2.0 29.2 1.0
O2 C:OXL288 2.3 39.5 1.0
O3 C:OXL288 2.7 48.5 1.0
CG C:ASP88 3.0 27.3 1.0
C2 C:OXL288 3.1 43.6 1.0
C1 C:OXL288 3.2 48.5 1.0
OD1 C:ASP88 3.4 31.2 1.0
OD1 C:ASP90 3.7 37.6 1.0
OD2 C:ASP61 3.9 29.6 1.0
N C:GLY49 4.1 26.2 1.0
CA C:GLY49 4.3 25.7 1.0
O4 C:OXL288 4.3 45.2 1.0
CB C:ASP88 4.3 28.4 1.0
NH2 C:ARG159 4.4 31.1 1.0
O1 C:OXL288 4.4 51.9 1.0
N C:SER50 4.4 26.7 1.0
OD1 C:ASP61 4.4 30.2 1.0
CG C:ASP90 4.5 33.6 1.0
NH1 C:ARG159 4.5 31.3 1.0
CG C:ASP61 4.6 30.9 1.0
OE1 C:GLU117 4.6 38.8 1.0
CZ C:ARG159 4.7 28.8 1.0
C C:GLY49 4.8 25.6 1.0
OD2 C:ASP90 4.9 40.2 1.0

Magnesium binding site 4 out of 6 in 3b8i

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Magnesium binding site 4 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg289

b:49.8
occ:1.00
 O D:HOH293 1.7 40.8 1.0
O D:HOH291 1.9 52.8 1.0
O D:HOH292 2.0 41.1 1.0
OD1 D:ASP88 2.1 36.7 1.0
O1 D:OXL288 2.5 48.1 1.0
O4 D:OXL288 2.7 51.8 1.0
CG D:ASP88 3.0 34.2 1.0
C1 D:OXL288 3.3 51.6 1.0
OD2 D:ASP88 3.3 33.7 1.0
C2 D:OXL288 3.3 52.0 1.0
OD2 D:ASP90 3.6 39.3 1.0
OD2 D:ASP61 3.8 40.7 1.0
N D:GLY49 4.1 33.5 1.0
CA D:GLY49 4.3 32.6 1.0
O D:HOH457 4.3 42.3 1.0
CB D:ASP88 4.4 32.7 1.0
NH2 D:ARG159 4.4 43.2 1.0
N D:SER50 4.4 32.5 1.0
OE1 D:GLU117 4.4 42.3 1.0
O3 D:OXL288 4.5 49.5 1.0
OD1 D:ASP61 4.5 42.0 1.0
O2 D:OXL288 4.5 53.1 1.0
CG D:ASP90 4.5 35.4 1.0
CG D:ASP61 4.6 40.5 1.0
CZ D:ARG159 4.8 41.9 1.0
C D:GLY49 4.8 33.0 1.0
NH1 D:ARG159 4.8 42.1 1.0
OD1 D:ASP90 4.9 38.7 1.0

Magnesium binding site 5 out of 6 in 3b8i

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Magnesium binding site 5 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg289

b:29.4
occ:1.00
 O E:HOH631 2.0 21.0 1.0
O E:HOH632 2.0 14.1 1.0
O E:HOH633 2.1 23.2 1.0
OD2 E:ASP88 2.2 21.7 1.0
O3 E:OXL288 2.3 27.0 1.0
O2 E:OXL288 2.6 35.8 1.0
C1 E:OXL288 3.1 33.1 1.0
CG E:ASP88 3.2 18.9 1.0
C2 E:OXL288 3.2 37.2 1.0
OD1 E:ASP88 3.4 21.6 1.0
OD2 E:ASP61 3.7 22.5 1.0
O E:HOH757 3.8 42.5 1.0
O E:HOH677 3.9 28.5 1.0
OD1 E:ASP90 4.1 36.6 1.0
N E:GLY49 4.3 18.0 1.0
OD1 E:ASP61 4.3 23.9 1.0
OD2 E:ASP90 4.3 26.1 1.0
O1 E:OXL288 4.3 34.8 1.0
NH1 E:ARG159 4.4 21.2 1.0
NH2 E:ARG159 4.4 18.8 1.0
N E:SER50 4.4 18.4 1.0
O4 E:OXL288 4.4 40.1 1.0
CA E:GLY49 4.4 18.6 1.0
CG E:ASP61 4.5 22.5 1.0
CG E:ASP90 4.5 25.8 1.0
OE1 E:GLU117 4.5 26.3 1.0
CB E:ASP88 4.5 19.2 1.0
CZ E:ARG159 4.6 15.6 1.0
C E:GLY49 4.8 17.8 1.0

Magnesium binding site 6 out of 6 in 3b8i

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Magnesium binding site 6 out of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.


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 Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg289

b:49.1
occ:1.00
 O F:HOH292 1.9 39.0 1.0
OD2 F:ASP88 2.1 26.1 1.0
O F:HOH291 2.1 26.3 1.0
O F:HOH293 2.2 48.6 1.0
O4 F:OXL288 2.2 42.5 1.0
O1 F:OXL288 2.6 44.7 1.0
CG F:ASP88 3.1 27.7 1.0
C2 F:OXL288 3.1 44.7 1.0
C1 F:OXL288 3.2 46.8 1.0
OD1 F:ASP88 3.4 31.1 1.0
OD1 F:ASP90 3.7 38.6 1.0
OD2 F:ASP61 4.0 36.4 1.0
N F:GLY49 4.2 27.8 1.0
O2 F:OXL288 4.3 44.6 1.0
OE1 F:GLU117 4.3 47.5 1.0
OD1 F:ASP61 4.3 38.9 1.0
CA F:GLY49 4.4 27.4 1.0
O3 F:OXL288 4.4 46.7 1.0
CB F:ASP88 4.4 26.7 1.0
CG F:ASP90 4.4 36.0 1.0
N F:SER50 4.5 27.0 1.0
NH1 F:ARG159 4.5 45.3 1.0
CG F:ASP61 4.6 36.0 1.0
NH2 F:ARG159 4.7 44.1 1.0
OD2 F:ASP90 4.7 44.9 1.0
CZ F:ARG159 4.8 45.0 1.0
C F:GLY49 4.9 27.8 1.0

Reference:

B.C.Narayanan, W.Niu, Y.Han, J.Zou, P.S.Mariano, D.Dunaway-Mariano, O.Herzberg. Structure and Function of PA4872 From Pseudomonas Aeruginosa, A Novel Class of Oxaloacetate Decarboxylase From the Pep Mutase/Isocitrate Lyase Superfamily. Biochemistry V. 47 167 2008.
ISSN: ISSN 0006-2960
PubMed: 18081320
DOI: 10.1021/BI701954P
Page generated: Mon Dec 14 07:54:57 2020

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