Magnesium in PDB 3p0x: Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate

Enzymatic activity of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate

All present enzymatic activity of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate:
4.1.3.1;

Protein crystallography data

The structure of Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate, PDB code: 3p0x was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.60 / 2.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.910, 135.930, 181.790, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate (pdb code 3p0x). 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 Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate, PDB code: 3p0x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3p0x

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Magnesium binding site 1 out of 4 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate


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 From Brucella Melitensis, Bound to Magnesium Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg430

b:15.8
occ:1.00
 OD2 A:ASP147 2.0 12.1 1.0
O7 A:ICT450 2.0 18.5 1.0
O A:HOH584 2.1 10.3 1.0
O2 A:ICT450 2.1 19.8 1.0
O A:HOH586 2.2 10.5 1.0
O A:HOH585 2.2 5.8 1.0
C1 A:ICT450 2.9 19.6 1.0
C2 A:ICT450 2.9 20.5 1.0
CG A:ASP147 3.0 10.1 1.0
OD1 A:ASP147 3.5 10.6 1.0
C3 A:ICT450 3.8 21.7 1.0
O5 A:ICT450 4.1 21.9 1.0
O1 A:ICT450 4.1 15.4 1.0
N A:GLY85 4.1 10.9 1.0
NZ A:LYS183 4.1 17.9 1.0
NH1 A:ARG222 4.1 15.2 1.0
OD2 A:ASP101 4.1 10.4 1.0
N A:TRP86 4.2 11.5 1.0
CB A:ASP147 4.3 10.6 1.0
C6 A:ICT450 4.3 21.0 1.0
OD1 A:ASP101 4.3 13.2 1.0
CE1 A:HIS174 4.3 12.8 1.0
CA A:GLY85 4.3 11.2 1.0
CE A:LYS183 4.5 19.9 1.0
OE1 A:GLU176 4.5 14.6 1.0
CG A:GLU149 4.6 13.1 1.0
CG A:ASP101 4.7 13.3 1.0
OH A:TYR82 4.7 12.0 1.0
C A:GLY85 4.7 11.4 1.0
OE2 A:GLU149 4.8 12.7 1.0
NE2 A:HIS174 4.8 12.4 1.0

Magnesium binding site 2 out of 4 in 3p0x

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Magnesium binding site 2 out of 4 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate


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 From Brucella Melitensis, Bound to Magnesium Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg430

b:18.9
occ:1.00
 O B:HOH535 1.9 7.4 1.0
O B:HOH536 2.0 4.6 1.0
O7 B:ICT450 2.0 21.4 1.0
OD2 B:ASP147 2.0 12.2 1.0
O2 B:ICT450 2.1 23.4 1.0
O B:HOH486 2.1 4.9 1.0
C1 B:ICT450 2.9 23.2 1.0
C2 B:ICT450 3.0 22.9 1.0
CG B:ASP147 3.1 12.4 1.0
OD1 B:ASP147 3.6 12.4 1.0
C3 B:ICT450 3.8 24.1 1.0
OD2 B:ASP101 3.9 13.2 1.0
N B:TRP86 4.0 13.2 1.0
NZ B:LYS183 4.1 20.7 1.0
O1 B:ICT450 4.1 21.3 1.0
OD1 B:ASP101 4.1 14.1 1.0
N B:GLY85 4.1 12.4 1.0
CA B:GLY85 4.2 12.3 1.0
O5 B:ICT450 4.2 23.7 1.0
NH1 B:ARG222 4.4 19.5 1.0
C6 B:ICT450 4.4 23.1 1.0
CG B:GLU149 4.4 14.4 1.0
CE B:LYS183 4.4 21.5 1.0
CB B:ASP147 4.4 12.6 1.0
CG B:ASP101 4.5 13.3 1.0
OE2 B:GLU149 4.5 13.6 1.0
C B:GLY85 4.5 12.4 1.0
CE1 B:HIS174 4.6 17.0 1.0
OE1 B:GLU176 4.7 19.0 1.0
OH B:TYR82 4.8 16.6 1.0
CD B:GLU149 4.8 15.1 1.0
CB B:TRP86 5.0 13.1 1.0

Magnesium binding site 3 out of 4 in 3p0x

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Magnesium binding site 3 out of 4 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate


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 From Brucella Melitensis, Bound to Magnesium Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg430

b:19.3
occ:1.00
 OD2 C:ASP147 1.9 11.1 1.0
O7 C:ICT450 2.0 19.1 1.0
O C:HOH570 2.1 10.7 1.0
O C:HOH517 2.1 9.8 1.0
O2 C:ICT450 2.1 22.3 1.0
O C:HOH518 2.2 8.4 1.0
C1 C:ICT450 2.8 20.9 1.0
C2 C:ICT450 2.9 21.4 1.0
CG C:ASP147 3.1 11.0 1.0
OD1 C:ASP147 3.6 8.8 1.0
C3 C:ICT450 3.7 22.1 1.0
OD2 C:ASP101 3.8 12.9 1.0
O5 C:ICT450 3.9 23.7 1.0
O1 C:ICT450 4.0 19.1 1.0
N C:TRP86 4.1 12.6 1.0
N C:GLY85 4.1 12.7 1.0
C6 C:ICT450 4.2 21.6 1.0
NZ C:LYS183 4.2 18.3 1.0
NH1 C:ARG222 4.3 16.5 1.0
CA C:GLY85 4.3 12.6 1.0
CB C:ASP147 4.3 11.5 1.0
OD1 C:ASP101 4.3 13.0 1.0
CG C:ASP101 4.5 13.7 1.0
CG C:GLU149 4.5 13.6 1.0
CE1 C:HIS174 4.5 15.0 1.0
OH C:TYR82 4.5 12.9 1.0
CE C:LYS183 4.5 19.9 1.0
C C:GLY85 4.6 12.8 1.0
OE2 C:GLU149 4.7 14.8 1.0
OE2 C:GLU176 4.7 14.9 1.0
CB C:TRP86 4.9 13.3 1.0
CA C:TRP86 5.0 13.1 1.0
CD C:GLU149 5.0 14.1 1.0

Magnesium binding site 4 out of 4 in 3p0x

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Magnesium binding site 4 out of 4 in the Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate


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 From Brucella Melitensis, Bound to Magnesium Isocitrate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg430

b:20.3
occ:1.00
 O7 D:ICT450 2.0 23.7 1.0
OD2 D:ASP147 2.0 12.9 1.0
O D:HOH485 2.0 8.4 1.0
O D:HOH551 2.1 6.9 1.0
O2 D:ICT450 2.2 24.3 1.0
O D:HOH553 2.2 9.7 1.0
C1 D:ICT450 2.9 24.1 1.0
C2 D:ICT450 3.0 23.9 1.0
CG D:ASP147 3.2 11.8 1.0
OD1 D:ASP147 3.6 11.0 1.0
C3 D:ICT450 3.8 24.4 1.0
OD2 D:ASP101 3.9 13.6 1.0
OD1 D:ASP101 4.0 16.6 1.0
N D:TRP86 4.0 13.6 1.0
N D:GLY85 4.1 13.3 1.0
NZ D:LYS183 4.1 20.0 1.0
O5 D:ICT450 4.1 22.7 1.0
CA D:GLY85 4.1 13.2 1.0
O1 D:ICT450 4.1 23.6 1.0
CE D:LYS183 4.4 20.6 1.0
C6 D:ICT450 4.4 23.6 1.0
CG D:GLU149 4.4 14.6 1.0
CG D:ASP101 4.4 16.0 1.0
CB D:ASP147 4.4 11.9 1.0
NH1 D:ARG222 4.4 19.9 1.0
C D:GLY85 4.5 13.3 1.0
OE2 D:GLU149 4.5 14.1 1.0
CE1 D:HIS174 4.7 17.8 1.0
OH D:TYR82 4.7 15.9 1.0
OE1 D:GLU176 4.8 16.9 1.0
CD D:GLU149 4.8 14.9 1.0
CB D:TRP86 4.9 14.2 1.0
CA D:TRP86 5.0 13.7 1.0

Reference:

Ssgcid, A.Gardberg, T.Edwards, M.Gander, B.Staker, L.Stewart. Crystal Structure of Isocitrate Lyase From Brucella Melitensis, Bound to Magnesium Isocitrate To Be Published.
Page generated: Mon Dec 14 08:38:29 2020

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