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Manganese in PDB 6giu: Human Impase with L-690330

Enzymatic activity of Human Impase with L-690330

All present enzymatic activity of Human Impase with L-690330:
3.1.3.25; 3.1.3.94;

Protein crystallography data

The structure of Human Impase with L-690330, PDB code: 6giu was solved by L.V.Kraft, S.M.Roe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.35 / 1.39
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.290, 85.290, 151.510, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 16.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Impase with L-690330 (pdb code 6giu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Human Impase with L-690330, PDB code: 6giu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 6giu

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Manganese binding site 1 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:9.8
occ:1.00
 OE2 A:GLU70 2.1 10.3 1.0
O3 A:L69304 2.1 9.0 1.0
O A:HOH466 2.2 10.8 1.0
O A:HOH524 2.2 11.8 1.0
O6 A:L69304 2.2 10.4 1.0
O A:HOH541 2.3 11.6 1.0
HZ3 A:LYS36 3.1 12.8 1.0
CD A:GLU70 3.2 11.8 1.0
HG1 A:THR95 3.3 8.6 1.0
P1 A:L69304 3.3 9.6 1.0
P A:L69304 3.4 8.7 1.0
C6 A:L69304 3.7 9.3 1.0
OE1 A:GLU70 3.7 9.9 1.0
O5 A:L69304 3.8 9.2 1.0
HO3 A:GOL313 3.9 16.1 1.0
OD1 A:ASP41 3.9 13.0 1.0
HD3 A:LYS36 4.0 13.4 1.0
O1 A:L69304 4.0 8.0 1.0
O A:HOH658 4.0 21.1 1.0
NZ A:LYS36 4.0 11.4 1.0
C7 A:L69304 4.1 9.6 1.0
HG21 A:THR95 4.1 12.3 1.0
O A:LEU42 4.2 10.7 1.0
HZ2 A:LYS36 4.2 9.7 1.0
OG1 A:THR95 4.2 10.5 1.0
MN A:MN302 4.3 9.0 1.0
O3 A:GOL313 4.3 18.0 1.0
HG23 A:THR95 4.4 11.9 1.0
CG A:GLU70 4.4 11.3 1.0
OE2 A:GLU71 4.4 14.0 1.0
HG3 A:GLU70 4.5 11.8 1.0
HG2 A:GLU70 4.5 12.7 1.0
H31 A:GOL313 4.6 25.1 1.0
O2 A:L69304 4.6 8.9 1.0
HZ1 A:LYS36 4.6 11.4 1.0
O A:HOH411 4.7 26.4 1.0
O4 A:L69304 4.7 10.3 1.0
CG2 A:THR95 4.7 10.6 1.0
O A:HOH425 4.7 11.1 1.0
HE1 A:TRP219 4.8 11.5 1.0
CD A:LYS36 4.8 11.9 1.0
CE A:LYS36 4.9 12.1 1.0
HE2 A:LYS36 4.9 10.3 1.0
C3 A:GOL313 4.9 24.5 1.0

Manganese binding site 2 out of 7 in 6giu

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Manganese binding site 2 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:9.0
occ:1.00
 OE1 A:GLU70 2.1 9.9 1.0
O1 A:L69304 2.1 8.0 1.0
O A:HOH425 2.2 11.1 1.0
OD1 A:ASP90 2.2 9.2 1.0
O A:ILE92 2.2 9.3 1.0
CG A:ASP90 3.0 9.2 1.0
HA A:ASP93 3.1 9.6 1.0
HG23 A:THR95 3.1 11.9 1.0
OD2 A:ASP90 3.2 10.2 1.0
C A:ILE92 3.2 9.1 1.0
CD A:GLU70 3.2 11.8 1.0
H A:ILE92 3.2 11.3 1.0
P A:L69304 3.3 8.7 1.0
O3 A:L69304 3.3 9.0 1.0
HD2 A:PRO91 3.6 10.9 1.0
MN A:MN303 3.6 8.8 1.0
OE2 A:GLU70 3.7 10.3 1.0
O5 A:L69304 3.7 9.2 1.0
N A:ASP93 3.9 7.8 1.0
CA A:ASP93 4.0 7.5 1.0
CG2 A:THR95 4.0 10.6 1.0
HG21 A:THR95 4.0 12.3 1.0
N A:ILE92 4.1 9.1 1.0
HB A:ILE92 4.1 11.0 1.0
CA A:ILE92 4.2 9.2 1.0
O2 A:L69304 4.2 8.9 1.0
MN A:MN301 4.3 9.8 1.0
HG2 A:PRO91 4.3 12.1 1.0
HB3 A:GLU70 4.3 6.6 1.0
OE2 A:GLU71 4.3 14.0 1.0
H A:GLY94 4.4 9.2 1.0
HG22 A:THR95 4.4 10.4 1.0
CB A:ASP90 4.4 9.6 1.0
OD2 A:ASP47 4.4 16.7 1.0
HA A:ASP90 4.4 5.6 1.0
CG A:GLU70 4.4 11.3 1.0
HG1 A:THR95 4.5 8.6 1.0
HB2 A:GLU70 4.5 7.3 1.0
CD A:PRO91 4.5 9.8 1.0
HE1 A:TRP219 4.6 11.5 1.0
O A:HOH541 4.6 11.6 1.0
C6 A:L69304 4.6 9.3 1.0
P1 A:L69304 4.6 9.6 1.0
H A:THR95 4.6 9.5 1.0
CB A:GLU70 4.7 9.3 1.0
HB2 A:ASP93 4.7 8.1 1.0
CB A:ILE92 4.7 12.1 1.0
HD1 A:TRP219 4.8 11.1 1.0
N A:PRO91 4.8 8.8 1.0
OD1 A:ASP93 4.8 9.7 1.0
H A:ASP93 4.8 6.9 1.0
CA A:ASP90 4.8 8.5 1.0
O A:L69304 4.9 9.1 1.0
CB A:ASP93 4.9 8.4 1.0
C A:ASP90 4.9 9.3 1.0
N A:GLY94 4.9 8.3 1.0
HB3 A:ASP90 4.9 8.8 1.0
HG2 A:GLU70 4.9 12.7 1.0
CG A:PRO91 4.9 10.8 1.0
C A:ASP93 5.0 8.8 1.0
O6 A:L69304 5.0 10.4 1.0

Manganese binding site 3 out of 7 in 6giu

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Manganese binding site 3 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:8.8
occ:1.00
 OD1 A:ASP220 2.0 11.1 1.0
OD2 A:ASP90 2.1 10.2 1.0
OD1 A:ASP93 2.1 9.7 1.0
O1 A:L69304 2.2 8.0 1.0
O5 A:L69304 2.2 9.2 1.0
O A:L69304 2.3 9.1 1.0
HA A:ASP93 3.0 9.6 1.0
C6 A:L69304 3.0 9.3 1.0
P1 A:L69304 3.2 9.6 1.0
CG A:ASP220 3.2 10.7 1.0
P A:L69304 3.2 8.7 1.0
CG A:ASP93 3.2 10.3 1.0
CG A:ASP90 3.2 9.2 1.0
HD1 A:TRP219 3.3 11.1 1.0
C5 A:L69304 3.4 9.4 1.0
HE1 A:TRP219 3.5 11.5 1.0
MN A:MN302 3.6 9.0 1.0
HB2 A:ASP93 3.7 8.1 1.0
OD1 A:ASP90 3.8 9.2 1.0
CB A:ASP93 3.8 8.4 1.0
OD2 A:ASP220 3.8 9.3 1.0
O4 A:L69304 3.8 10.3 1.0
HA A:ASP220 3.8 8.1 1.0
CA A:ASP93 3.8 7.5 1.0
H A:GLY94 4.0 9.2 1.0
C4 A:L69304 4.1 8.8 1.0
CD1 A:TRP219 4.1 10.1 1.0
O2 A:L69304 4.1 8.9 1.0
OE1 A:GLU70 4.1 9.9 1.0
NE1 A:TRP219 4.1 9.4 1.0
OD2 A:ASP93 4.2 10.1 1.0
C A:L69304 4.3 8.3 1.0
CB A:ASP220 4.3 9.3 1.0
O3 A:L69304 4.3 9.0 1.0
HB2 A:ASP90 4.4 10.0 1.0
CB A:ASP90 4.4 9.6 1.0
O6 A:L69304 4.5 10.4 1.0
CA A:ASP220 4.5 8.3 1.0
C7 A:L69304 4.5 9.6 1.0
HB3 A:ASP220 4.5 10.3 1.0
O A:ILE92 4.6 9.3 1.0
N A:GLY94 4.7 8.3 1.0
HB3 A:ASP90 4.7 8.8 1.0
C A:ASP93 4.8 8.8 1.0
N A:ASP93 4.8 7.8 1.0
HB3 A:ALA196 4.9 5.6 1.0
HB3 A:ASP93 4.9 10.4 1.0
CD A:GLU70 4.9 11.8 1.0

Manganese binding site 4 out of 7 in 6giu

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Manganese binding site 4 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:8.9
occ:1.00
 OD1 B:ASP220 2.0 11.1 1.0
OD2 B:ASP90 2.1 10.7 1.0
OD1 B:ASP93 2.1 9.1 1.0
O4 B:L69305 2.2 8.3 1.0
O2 B:L69305 2.3 9.2 1.0
O B:L69305 2.3 8.5 1.0
HA B:ASP93 2.9 9.9 1.0
C6 B:L69305 3.0 8.7 1.0
P B:L69305 3.1 9.6 1.0
P1 B:L69305 3.2 8.6 1.0
CG B:ASP220 3.2 10.5 1.0
CG B:ASP93 3.2 10.3 1.0
CG B:ASP90 3.2 9.9 1.0
HD1 B:TRP219 3.3 12.4 1.0
C5 B:L69305 3.4 9.3 1.0
HE1 B:TRP219 3.5 11.8 1.0
MN B:MN302 3.6 9.0 1.0
HB2 B:ASP93 3.7 7.6 1.0
OD1 B:ASP90 3.8 10.1 1.0
CB B:ASP93 3.8 7.5 1.0
HA B:ASP220 3.8 8.9 1.0
OD2 B:ASP220 3.8 9.3 1.0
CA B:ASP93 3.8 7.2 1.0
O3 B:L69305 3.8 9.9 1.0
H B:GLY94 4.0 9.3 1.0
O6 B:L69305 4.0 9.1 1.0
CD1 B:TRP219 4.0 10.5 1.0
OE1 B:GLU70 4.1 9.9 1.0
C4 B:L69305 4.1 8.6 1.0
NE1 B:TRP219 4.1 9.9 1.0
OD2 B:ASP93 4.3 11.0 1.0
C B:L69305 4.3 8.9 1.0
O5 B:L69305 4.3 8.3 1.0
CB B:ASP220 4.3 9.5 1.0
CB B:ASP90 4.4 9.0 1.0
HB2 B:ASP90 4.4 11.2 1.0
O1 B:L69305 4.5 9.9 1.0
C7 B:L69305 4.5 8.7 1.0
CA B:ASP220 4.5 9.1 1.0
HB3 B:ASP220 4.6 9.0 1.0
O B:ILE92 4.6 8.9 1.0
HB3 B:ALA196 4.7 8.2 1.0
N B:GLY94 4.7 7.4 1.0
HB3 B:ASP90 4.7 9.8 1.0
C B:ASP93 4.8 8.4 1.0
N B:ASP93 4.8 7.8 1.0
HB3 B:ASP93 4.8 6.4 1.0
CD B:GLU70 4.8 10.3 1.0
N B:ASP220 5.0 9.6 1.0

Manganese binding site 5 out of 7 in 6giu

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Manganese binding site 5 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:9.0
occ:1.00
 OE1 B:GLU70 2.1 9.9 1.0
O4 B:L69305 2.1 8.3 1.0
O B:HOH416 2.1 10.6 1.0
OD1 B:ASP90 2.1 10.1 1.0
O B:ILE92 2.2 8.9 1.0
CG B:ASP90 3.0 9.9 1.0
HA B:ASP93 3.1 9.9 1.0
CD B:GLU70 3.2 10.3 1.0
C B:ILE92 3.2 9.3 1.0
OD2 B:ASP90 3.2 10.7 1.0
H B:ILE92 3.2 11.2 1.0
HG23 B:THR95 3.2 11.7 1.0
P1 B:L69305 3.3 8.6 1.0
O5 B:L69305 3.3 8.3 1.0
MN B:MN301 3.6 8.9 1.0
HD2 B:PRO91 3.6 10.4 1.0
OE2 B:GLU70 3.7 10.9 1.0
O2 B:L69305 3.7 9.2 1.0
N B:ASP93 3.9 7.8 1.0
HG21 B:THR95 3.9 9.2 1.0
CA B:ASP93 4.0 7.2 1.0
CG2 B:THR95 4.1 9.5 1.0
N B:ILE92 4.1 9.7 1.0
CA B:ILE92 4.2 9.2 1.0
HB B:ILE92 4.2 7.7 1.0
HG2 B:PRO91 4.2 12.4 1.0
O6 B:L69305 4.2 9.1 1.0
MN B:MN303 4.2 9.2 1.0
OE2 B:GLU71 4.3 11.9 1.0
HB3 B:GLU70 4.3 9.9 1.0
H B:GLY94 4.4 9.3 1.0
OD2 B:ASP47 4.4 15.1 1.0
HA B:ASP90 4.4 7.8 1.0
CB B:ASP90 4.4 9.0 1.0
CG B:GLU70 4.4 9.5 1.0
CD B:PRO91 4.5 10.0 1.0
O B:HOH541 4.5 9.6 1.0
HG1 B:THR95 4.5 8.2 1.0
HB2 B:GLU70 4.5 6.2 1.0
C6 B:L69305 4.5 8.7 1.0
HG22 B:THR95 4.5 11.2 1.0
HE1 B:TRP219 4.6 11.8 1.0
P B:L69305 4.6 9.6 1.0
H B:THR95 4.6 7.0 1.0
CB B:GLU70 4.7 9.5 1.0
HB2 B:ASP93 4.7 7.6 1.0
HD1 B:TRP219 4.8 12.4 1.0
CA B:ASP90 4.8 8.8 1.0
CB B:ILE92 4.8 10.3 1.0
N B:PRO91 4.8 8.9 1.0
OD1 B:ASP93 4.8 9.1 1.0
H B:ASP93 4.8 9.7 1.0
C B:ASP90 4.8 9.2 1.0
CB B:ASP93 4.9 7.5 1.0
O B:L69305 4.9 8.5 1.0
HG2 B:GLU70 4.9 8.9 1.0
CG B:PRO91 4.9 12.1 1.0
C B:ASP93 4.9 8.4 1.0
N B:GLY94 5.0 7.4 1.0
HB3 B:ASP90 5.0 9.8 1.0
O1 B:L69305 5.0 9.9 1.0
HG22 B:ILE92 5.0 15.2 1.0
HB2 B:ASP90 5.0 11.2 1.0

Manganese binding site 6 out of 7 in 6giu

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Manganese binding site 6 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:9.2
occ:1.00
 OE2 B:GLU70 2.1 10.9 1.0
O5 B:L69305 2.1 8.3 1.0
O B:HOH451 2.2 10.1 1.0
O1 B:L69305 2.2 9.9 1.0
O B:HOH541 2.2 9.6 1.0
O B:HOH466 2.3 10.7 1.0
HZ3 B:LYS36 3.0 13.6 1.0
CD B:GLU70 3.2 10.3 1.0
P B:L69305 3.3 9.6 1.0
HG1 B:THR95 3.3 8.2 1.0
P1 B:L69305 3.3 8.6 1.0
C6 B:L69305 3.7 8.7 1.0
OE1 B:GLU70 3.7 9.9 1.0
O2 B:L69305 3.8 9.2 1.0
HG21 B:THR95 3.9 9.2 1.0
HD3 B:LYS36 3.9 11.9 1.0
OD1 B:ASP41 4.0 13.3 1.0
O4 B:L69305 4.0 8.3 1.0
NZ B:LYS36 4.0 11.8 1.0
C7 B:L69305 4.0 8.7 1.0
O B:LEU42 4.1 9.6 1.0
O B:HOH647 4.1 24.1 1.0
MN B:MN302 4.2 9.0 1.0
OG1 B:THR95 4.3 9.7 1.0
O3 B:GOL312 4.3 20.1 1.0
OE2 B:GLU71 4.3 11.9 1.0
CG B:GLU70 4.4 9.5 1.0
HZ2 B:LYS36 4.4 9.6 1.0
HZ1 B:LYS36 4.4 12.9 1.0
HO3 B:GOL312 4.4 20.2 1.0
HG3 B:GLU70 4.5 10.6 1.0
HG2 B:GLU70 4.5 8.9 1.0
HG23 B:THR95 4.5 11.7 1.0
H32 B:GOL312 4.6 27.8 1.0
O B:HOH412 4.6 36.1 1.0
O6 B:L69305 4.6 9.1 1.0
O B:HOH416 4.6 10.6 1.0
O3 B:L69305 4.7 9.9 1.0
CG2 B:THR95 4.7 9.5 1.0
HE1 B:TRP219 4.7 11.8 1.0
CD B:LYS36 4.7 12.0 1.0
CE B:LYS36 4.8 11.4 1.0
HE2 B:LYS36 4.9 13.1 1.0
HD2 B:LYS36 4.9 12.4 1.0
C3 B:GOL312 4.9 27.3 1.0

Manganese binding site 7 out of 7 in 6giu

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Manganese binding site 7 out of 7 in the Human Impase with L-690330


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Impase with L-690330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:17.0
occ:0.44
 O B:HOH433 2.0 23.3 1.0
O B:HOH443 2.2 21.8 1.0
O B:HOH668 2.2 30.2 1.0
O B:HOH727 2.2 37.9 1.0
HB2 B:ASP153 3.6 14.5 1.0
HD2 B:LYS156 3.9 13.3 1.0
O B:HOH560 4.0 21.3 1.0
O B:HOH613 4.2 25.5 1.0
HE3 B:LYS156 4.2 17.1 1.0
HB3 B:ASP153 4.3 12.0 1.0
OE1 B:GLN151 4.4 14.2 1.0
CB B:ASP153 4.4 13.4 1.0
OD2 B:ASP153 4.6 16.7 1.0
O B:HOH679 4.7 37.6 1.0
HE2 B:LYS156 4.7 14.7 1.0
CE B:LYS156 4.8 15.6 1.0
CD B:LYS156 4.8 13.9 1.0
HE22 B:GLN151 4.9 17.2 1.0
H B:ASP153 5.0 10.5 1.0

Reference:

L.Kraft, S.M.Roe, R.Gill, J.R.Atack. Co-Crystallization of Human Inositol Monophosphatase with the Lithium Mimetic L-690,330. Acta Crystallogr D Struct V. 74 973 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289407
DOI: 10.1107/S2059798318010380
Page generated: Sun Oct 6 04:44:43 2024

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