Magnesium in PDB 6t5m: Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.

Enzymatic activity of Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.

All present enzymatic activity of Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.:
4.1.3.30;

Protein crystallography data

The structure of Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate., PDB code: 6t5m was solved by A.J.Wijaya, P.Brear, S.K.Dolan, M.Welch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.49 / 1.76
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 153.490, 59.400, 147.650, 90.00, 120.30, 90.00
R / Rfree (%) 21.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. (pdb code 6t5m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate., PDB code: 6t5m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6t5m

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Magnesium binding site 1 out of 4 in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.


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-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:26.6
occ:1.00
 OD2 C:ASP87 2.0 22.1 1.0
O C:HOH448 2.1 31.1 1.0
O1 C:PYR302 2.1 21.2 1.0
O C:HOH502 2.1 29.7 1.0
O3 C:PYR302 2.2 25.9 1.0
O C:HOH422 2.2 26.4 1.0
C2 C:PYR302 2.9 29.9 1.0
C1 C:PYR302 3.0 26.4 1.0
CG C:ASP87 3.0 20.5 1.0
OD1 C:ASP87 3.5 20.2 1.0
OD2 C:ASP60 3.9 27.1 1.0
NH1 C:ARG160 4.0 42.0 1.0
N C:GLY49 4.0 20.4 1.0
N C:GLY48 4.1 19.6 1.0
O2 C:PYR302 4.2 22.4 1.0
OD1 C:ASP89 4.2 33.3 1.0
CA C:GLY48 4.3 21.6 1.0
CB C:ASP87 4.3 16.2 1.0
C3 C:PYR302 4.4 23.9 1.0
OD1 C:ASP60 4.5 27.8 1.0
O C:HOH535 4.5 39.0 1.0
C C:GLY48 4.5 20.9 1.0
CE1 C:HIS115 4.6 18.3 1.0
OH C:TYR45 4.6 22.2 1.0
CG C:ASP60 4.6 32.6 1.0
OE1 C:GLU117 4.6 29.8 1.0
CZ C:ARG160 5.0 34.5 1.0

Magnesium binding site 2 out of 4 in 6t5m

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Magnesium binding site 2 out of 4 in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.


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-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:33.2
occ:1.00
 O A:HOH493 2.0 31.9 1.0
OD2 A:ASP87 2.0 23.8 1.0
O1 A:PYR302 2.2 31.9 1.0
O3 A:PYR302 2.3 31.6 1.0
O A:HOH405 2.3 32.5 1.0
O A:HOH414 2.6 29.9 1.0
C1 A:PYR302 2.9 34.3 1.0
C2 A:PYR302 2.9 34.7 1.0
CG A:ASP87 3.1 24.3 1.0
OD1 A:ASP87 3.5 22.2 1.0
NH1 A:ARG160 3.8 37.5 1.0
OD2 A:ASP60 3.9 32.6 1.0
OD1 A:ASP89 4.0 40.8 1.0
N A:GLY49 4.1 25.3 1.0
O2 A:PYR302 4.1 29.1 1.0
N A:GLY48 4.1 17.8 1.0
CA A:GLY48 4.2 21.7 1.0
CB A:ASP87 4.3 21.3 1.0
C3 A:PYR302 4.4 31.3 1.0
OD1 A:ASP60 4.4 30.4 1.0
C A:GLY48 4.6 25.1 1.0
CG A:ASP60 4.6 25.6 1.0
O A:HOH510 4.6 42.6 1.0
CE1 A:HIS115 4.8 23.2 1.0
OE1 A:GLU117 4.8 39.7 1.0
OH A:TYR45 4.8 23.9 1.0

Magnesium binding site 3 out of 4 in 6t5m

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Magnesium binding site 3 out of 4 in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.


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-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:34.0
occ:1.00
 OD2 D:ASP87 1.8 28.8 1.0
O D:HOH413 2.0 36.8 1.0
O2 D:PYR302 2.1 32.3 1.0
O D:HOH472 2.1 30.4 1.0
O3 D:PYR302 2.2 38.0 1.0
O D:HOH437 2.3 31.3 1.0
C1 D:PYR302 2.9 36.6 1.0
CG D:ASP87 2.9 28.9 1.0
C2 D:PYR302 2.9 39.8 1.0
OD1 D:ASP87 3.4 27.0 1.0
N D:GLY49 3.9 29.7 1.0
N D:GLY48 3.9 24.2 1.0
CA D:GLY48 3.9 27.7 1.0
O1 D:PYR302 4.1 31.4 1.0
OD2 D:ASP60 4.1 34.2 1.0
CB D:ASP87 4.1 25.6 1.0
OD1 D:ASP89 4.3 40.2 1.0
C D:GLY48 4.3 25.3 1.0
C3 D:PYR302 4.4 32.1 1.0
NH1 D:ARG160 4.4 41.1 1.0
OH D:TYR45 4.5 24.4 1.0
OD1 D:ASP60 4.7 35.5 1.0
CE1 D:HIS115 4.7 21.9 1.0
CG D:ASP60 4.8 34.1 1.0
CA D:GLY49 4.9 22.7 1.0

Magnesium binding site 4 out of 4 in 6t5m

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Magnesium binding site 4 out of 4 in the Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate.


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-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:44.8
occ:1.00
 O B:HOH451 1.9 44.8 1.0
OD2 B:ASP87 2.1 31.1 1.0
O B:HOH432 2.1 32.1 1.0
O B:HOH412 2.2 41.9 1.0
O2 B:PYR302 2.6 36.9 1.0
O3 B:PYR302 2.6 35.7 1.0
CG B:ASP87 3.1 29.9 1.0
C1 B:PYR302 3.3 37.1 1.0
C2 B:PYR302 3.3 41.2 1.0
OD1 B:ASP87 3.5 32.0 1.0
OD2 B:ASP60 3.7 45.5 1.0
N B:GLY49 4.0 28.6 1.0
OD1 B:ASP89 4.0 40.1 1.0
NH1 B:ARG160 4.1 47.4 1.0
CA B:GLY48 4.2 23.5 1.0
N B:GLY48 4.2 26.5 1.0
CB B:ASP87 4.4 26.9 1.0
C B:GLY48 4.5 26.5 1.0
OD1 B:ASP60 4.5 38.2 1.0
CG B:ASP60 4.5 36.1 1.0
O1 B:PYR302 4.5 32.5 1.0
CE1 B:HIS115 4.7 30.1 1.0
OE1 B:GLU117 4.7 43.7 1.0
C3 B:PYR302 4.8 37.0 1.0
CA B:GLY49 5.0 26.1 1.0

Reference:

A.J.Wijaya, P.Brear, S.K.Dolan, M.Welch. Crystal Structure of 2-Methylisocitrate Lyase (Prpb) From Pseudomonas Aeruginosa in Complex with Mg(II)-Pyruvate. To Be Published.
Page generated: Mon Jan 25 15:12:36 2021

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