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Magnesium in PDB 6b64: Impase (AF2372) with 25 Mm Asp

Enzymatic activity of Impase (AF2372) with 25 Mm Asp

All present enzymatic activity of Impase (AF2372) with 25 Mm Asp:
3.1.3.11; 3.1.3.25;

Protein crystallography data

The structure of Impase (AF2372) with 25 Mm Asp, PDB code: 6b64 was solved by R.I.Goldstein, M.Roberts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.65 / 2.60
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 89.530, 89.530, 102.136, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 22.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Impase (AF2372) with 25 Mm Asp (pdb code 6b64). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Impase (AF2372) with 25 Mm Asp, PDB code: 6b64:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6b64

Go back to Magnesium Binding Sites List in 6b64
Magnesium binding site 1 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:20.8
occ:1.00
OD1 A:ASP82 2.1 23.9 1.0
O A:HOH613 2.1 30.1 1.0
O A:LEU84 2.1 22.5 1.0
OE1 A:GLU67 2.2 22.4 1.0
O2 A:SO4503 2.3 32.5 1.0
C A:LEU84 3.1 15.2 1.0
CG A:ASP82 3.1 18.2 1.0
MG A:MG506 3.3 26.5 1.0
CD A:GLU67 3.4 27.6 1.0
OD2 A:ASP82 3.5 25.9 1.0
O2 A:SO4504 3.5 44.0 1.0
S A:SO4503 3.6 39.5 1.0
N A:ASP85 3.7 20.9 1.0
CA A:ASP85 3.8 19.7 1.0
O1 A:SO4503 3.9 27.2 1.0
N A:LEU84 4.0 23.7 1.0
CA A:LEU84 4.1 19.9 1.0
OE2 A:GLU67 4.1 36.3 1.0
OG1 A:THR87 4.3 26.9 1.0
OE1 A:GLU68 4.3 28.9 1.0
OD1 A:ASP46 4.3 33.3 1.0
O3 A:SO4503 4.4 61.9 1.0
CB A:ASP82 4.4 17.7 1.0
CB A:GLU67 4.5 29.1 1.0
CD A:PRO83 4.5 20.7 1.0
CG A:GLU67 4.5 25.9 1.0
CB A:ASP85 4.5 16.6 1.0
O4 A:SO4503 4.6 54.8 1.0
CA A:ASP82 4.7 21.6 1.0
N A:PRO83 4.7 24.1 1.0
CB A:LEU84 4.8 17.3 1.0
S A:SO4504 4.8 79.6 1.0
OD1 A:ASP85 4.8 18.9 1.0
C A:ASP82 4.8 20.3 1.0
O3 A:SO4504 4.9 60.1 1.0
CG A:PRO83 5.0 26.5 1.0
NH2 A:ARG197 5.0 23.2 1.0
C A:ASP85 5.0 25.4 1.0

Magnesium binding site 2 out of 6 in 6b64

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Magnesium binding site 2 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:26.5
occ:1.00
OD2 A:ASP82 2.0 25.9 1.0
OD1 A:ASP85 2.0 18.9 1.0
O1 A:SO4503 2.1 27.2 1.0
OD1 A:ASP200 2.2 21.8 1.0
CG A:ASP82 3.0 18.2 1.0
CG A:ASP85 3.0 21.4 1.0
O2 A:SO4503 3.2 32.5 1.0
S A:SO4503 3.2 39.5 1.0
OD1 A:ASP82 3.3 23.9 1.0
MG A:MG505 3.3 20.8 1.0
CB A:ASP85 3.3 16.6 1.0
OXT A:ASP502 3.4 48.5 1.0
CG A:ASP200 3.4 25.1 1.0
CA A:ASP85 3.5 19.7 1.0
NH2 A:ARG197 3.7 23.2 1.0
C A:ASP502 4.1 46.0 1.0
OE1 A:GLU67 4.1 22.4 1.0
O3 A:SO4503 4.1 61.9 1.0
OD2 A:ASP85 4.2 25.5 1.0
O4 A:SO4503 4.2 54.8 1.0
OD2 A:ASP200 4.2 28.0 1.0
CB A:ASP82 4.3 17.7 1.0
CB A:ASP200 4.4 18.8 1.0
O A:LEU84 4.4 22.5 1.0
CA A:ASP200 4.4 13.4 1.0
N A:ASP85 4.5 20.9 1.0
N A:ASP502 4.6 21.2 1.0
C A:ASP85 4.6 25.4 1.0
O A:ASP502 4.6 46.4 1.0
N A:GLY86 4.6 18.4 1.0
CD2 A:TYR199 4.8 16.2 1.0
C A:LEU84 4.8 15.2 1.0
CZ A:ARG197 4.8 36.6 1.0
CE2 A:TYR199 4.9 25.5 1.0
N A:ASP200 5.0 16.9 1.0
O2 A:SO4504 5.0 44.0 1.0

Magnesium binding site 3 out of 6 in 6b64

Go back to Magnesium Binding Sites List in 6b64
Magnesium binding site 3 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg507

b:6.0
occ:1.00
OG1 A:THR40 2.4 21.6 1.0
O3 A:SO4504 2.4 60.1 1.0
OE2 A:GLU68 2.5 32.0 1.0
OD1 A:ASP38 2.6 27.1 1.0
O A:THR40 2.6 19.8 1.0
OE2 A:GLU67 2.7 36.3 1.0
O A:PRO41 2.7 24.0 1.0
C A:THR40 3.2 24.5 1.0
C A:PRO41 3.4 28.1 1.0
CD A:GLU68 3.4 29.5 1.0
CG A:ASP38 3.4 31.6 1.0
OE1 A:GLU68 3.6 28.9 1.0
CB A:THR40 3.6 32.2 1.0
OD2 A:ASP38 3.6 28.7 1.0
S A:SO4504 3.7 79.6 1.0
CD A:GLU67 3.8 27.6 1.0
CA A:THR40 3.9 20.2 1.0
N A:THR42 3.9 20.7 1.0
O1 A:SO4504 4.0 57.8 1.0
OG1 A:THR42 4.0 31.6 1.0
N A:PRO41 4.0 20.7 1.0
CA A:THR42 4.1 21.1 1.0
CA A:GLY36 4.1 22.1 1.0
N A:THR40 4.2 21.7 1.0
CA A:PRO41 4.3 22.4 1.0
CG A:GLU67 4.3 25.9 1.0
N A:GLY36 4.5 28.3 1.0
O4 A:SO4504 4.6 65.9 1.0
O2 A:SO4504 4.7 44.0 1.0
CB A:THR42 4.7 28.0 1.0
CG2 A:THR40 4.8 19.1 1.0
OE1 A:GLU67 4.8 22.4 1.0
CG A:GLU68 4.8 25.0 1.0
CB A:ASP38 4.8 20.8 1.0
OD2 A:ASP46 4.9 25.2 1.0

Magnesium binding site 4 out of 6 in 6b64

Go back to Magnesium Binding Sites List in 6b64
Magnesium binding site 4 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:6.5
occ:1.00
OG1 B:THR40 2.4 27.0 1.0
OE2 B:GLU68 2.5 33.7 1.0
OD1 B:ASP38 2.5 23.8 1.0
O B:THR40 2.6 23.4 1.0
O B:PRO41 2.6 19.9 1.0
O2 B:SO4306 2.7 41.1 1.0
CG B:ASP38 3.3 33.4 1.0
OE2 B:GLU67 3.3 33.4 1.0
C B:THR40 3.3 25.2 1.0
OD2 B:ASP38 3.4 32.3 1.0
CD B:GLU68 3.4 29.3 1.0
C B:PRO41 3.5 28.2 1.0
CB B:THR40 3.6 28.0 1.0
OE1 B:GLU68 3.7 23.1 1.0
O4 B:SO4306 3.8 41.3 1.0
S B:SO4306 3.9 78.8 1.0
CA B:THR40 3.9 21.8 1.0
CG B:GLU67 4.0 24.5 1.0
CD B:GLU67 4.0 27.9 1.0
CA B:GLY36 4.1 22.4 1.0
N B:THR42 4.1 22.9 1.0
OG1 B:THR42 4.1 26.9 1.0
N B:PRO41 4.2 22.6 1.0
N B:THR40 4.2 25.4 1.0
CA B:THR42 4.2 19.8 1.0
CA B:PRO41 4.4 18.5 1.0
N B:GLY36 4.4 24.1 1.0
O3 B:SO4306 4.6 38.3 1.0
CB B:ASP38 4.7 24.1 1.0
CG2 B:THR40 4.8 21.6 1.0
OD2 B:ASP46 4.8 22.4 1.0
CG B:GLU68 4.9 23.1 1.0
CB B:THR42 4.9 25.0 1.0
O B:GLU67 4.9 25.3 1.0
O1 B:SO4306 5.0 27.0 1.0

Magnesium binding site 5 out of 6 in 6b64

Go back to Magnesium Binding Sites List in 6b64
Magnesium binding site 5 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:18.7
occ:1.00
OD1 B:ASP82 2.0 31.2 1.0
OE1 B:GLU67 2.0 27.2 1.0
O B:HOH410 2.1 25.7 1.0
O4 B:SO4305 2.2 20.9 1.0
O B:LEU84 2.2 21.6 1.0
CG B:ASP82 2.9 19.9 1.0
O3 B:SO4306 3.0 38.3 1.0
OD2 B:ASP82 3.0 24.5 1.0
C B:LEU84 3.0 15.9 1.0
CD B:GLU67 3.2 27.9 1.0
MG B:MG310 3.3 35.6 1.0
N B:ASP85 3.6 21.4 1.0
CA B:ASP85 3.7 18.9 1.0
S B:SO4305 3.7 36.9 1.0
OE2 B:GLU67 3.7 33.4 1.0
N B:LEU84 4.0 19.0 1.0
OG1 B:THR87 4.1 26.3 1.0
CA B:LEU84 4.1 19.3 1.0
O3 B:SO4305 4.2 46.0 1.0
OD1 B:ASP85 4.3 19.8 1.0
CB B:ASP82 4.3 20.2 1.0
OE1 B:GLU68 4.3 23.1 1.0
S B:SO4306 4.4 78.8 1.0
CG B:GLU67 4.4 24.5 1.0
OD1 B:ASP46 4.4 31.6 1.0
O1 B:SO4305 4.4 41.3 1.0
CB B:ASP85 4.4 16.7 1.0
O2 B:SO4305 4.4 53.7 1.0
NH2 B:ARG197 4.4 40.6 1.0
CD B:PRO83 4.4 22.3 1.0
CB B:GLU67 4.5 27.7 1.0
CA B:ASP82 4.7 20.8 1.0
CB B:LEU84 4.8 19.9 1.0
C B:ASP82 4.8 20.8 1.0
N B:PRO83 4.8 25.8 1.0
C B:ASP85 4.8 23.4 1.0
O4 B:SO4306 4.9 41.3 1.0
CG B:ASP85 4.9 23.1 1.0
N B:GLY86 5.0 17.5 1.0

Magnesium binding site 6 out of 6 in 6b64

Go back to Magnesium Binding Sites List in 6b64
Magnesium binding site 6 out of 6 in the Impase (AF2372) with 25 Mm Asp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Impase (AF2372) with 25 Mm Asp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg310

b:35.6
occ:1.00
OD1 B:ASP200 2.0 30.0 1.0
NH2 B:ARG197 2.1 40.6 1.0
O3 B:SO4305 2.1 46.0 1.0
OD2 B:ASP82 2.3 24.5 1.0
OD1 B:ASP85 2.4 19.8 1.0
O4 B:SO4305 2.4 20.9 1.0
S B:SO4305 2.7 36.9 1.0
CG B:ASP200 3.1 25.8 1.0
MG B:MG309 3.3 18.7 1.0
CG B:ASP82 3.3 19.9 1.0
CZ B:ARG197 3.4 39.9 1.0
O2 B:SO4305 3.4 53.7 1.0
OE1 B:GLU67 3.6 27.2 1.0
OD2 B:ASP200 3.6 25.4 1.0
CG B:ASP85 3.6 23.1 1.0
OD1 B:ASP82 3.8 31.2 1.0
O1 B:SO4305 4.1 41.3 1.0
OXT B:ASP304 4.1 35.1 1.0
NE B:ARG197 4.1 51.3 1.0
C B:ASP304 4.2 41.8 1.0
NH1 B:ARG197 4.3 28.4 1.0
CB B:ASP85 4.3 16.7 1.0
CD B:GLU67 4.3 27.9 1.0
CA B:ASP85 4.3 18.9 1.0
CB B:ASP200 4.3 20.6 1.0
CD2 B:TYR199 4.4 26.3 1.0
CE2 B:TYR199 4.4 26.9 1.0
OE2 B:GLU67 4.4 33.4 1.0
CA B:ASP304 4.5 46.1 1.0
CA B:ASP200 4.5 18.4 1.0
O B:ASP304 4.6 27.4 1.0
CB B:ASP82 4.6 20.2 1.0
OD2 B:ASP85 4.6 24.4 1.0
O3 B:SO4306 4.7 38.3 1.0
N B:ASP304 4.7 50.1 1.0
O B:LEU84 4.9 21.6 1.0
N B:ASP200 4.9 15.4 1.0

Reference:

R.I.Goldstein, M.Roberts. Osmolyte Binding Capacity of A Dual Action Impase/Fbpase (AF2372) To Be Published.
Page generated: Mon Sep 30 19:34:24 2024

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