Manganese in PDB 6gj0: Human Impase with Mn
Enzymatic activity of Human Impase with Mn
Protein crystallography data
The structure of Human Impase with Mn, PDB code: 6gj0
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)
|
42.47 /
1.73
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.940,
84.940,
152.510,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.1 /
21
|
Manganese Binding Sites:
The binding sites of Manganese atom in the Human Impase with Mn
(pdb code 6gj0). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the
Human Impase with Mn, PDB code: 6gj0:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
Manganese binding site 1 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 1 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn301
b:18.0
occ:1.00
|
OE2
|
A:GLU70
|
2.1
|
17.4
|
1.0
|
O
|
A:HOH429
|
2.2
|
21.7
|
1.0
|
O
|
A:HOH456
|
2.2
|
16.9
|
1.0
|
O2S
|
A:MES307
|
2.2
|
16.7
|
1.0
|
O
|
A:HOH432
|
2.2
|
18.6
|
1.0
|
O1S
|
A:MES307
|
2.4
|
17.5
|
1.0
|
S
|
A:MES307
|
2.8
|
23.7
|
1.0
|
CD
|
A:GLU70
|
3.2
|
16.6
|
1.0
|
OE1
|
A:GLU70
|
3.6
|
14.1
|
1.0
|
O3S
|
A:MES307
|
3.9
|
13.5
|
1.0
|
O
|
A:LEU42
|
3.9
|
16.0
|
1.0
|
O
|
A:HOH622
|
3.9
|
35.7
|
1.0
|
NZ
|
A:LYS36
|
3.9
|
17.2
|
1.0
|
MN
|
A:MN302
|
4.0
|
14.0
|
1.0
|
C8
|
A:MES307
|
4.0
|
10.9
|
1.0
|
OD1
|
A:ASP41
|
4.1
|
22.1
|
1.0
|
O
|
A:HOH528
|
4.1
|
20.5
|
1.0
|
OE2
|
A:GLU71
|
4.2
|
15.6
|
1.0
|
O
|
A:HOH585
|
4.4
|
39.4
|
1.0
|
OG1
|
A:THR95
|
4.4
|
16.1
|
1.0
|
CG
|
A:GLU70
|
4.5
|
14.5
|
1.0
|
O
|
A:HOH492
|
4.5
|
13.2
|
1.0
|
C5
|
A:MES307
|
4.5
|
42.7
|
1.0
|
CD
|
A:LYS36
|
4.7
|
21.8
|
1.0
|
O
|
A:HOH574
|
4.8
|
37.4
|
1.0
|
C7
|
A:MES307
|
4.9
|
36.6
|
1.0
|
CE
|
A:LYS36
|
4.9
|
24.1
|
1.0
|
O
|
A:HOH514
|
4.9
|
17.3
|
1.0
|
CB
|
A:THR95
|
4.9
|
15.1
|
1.0
|
N4
|
A:MES307
|
5.0
|
33.2
|
1.0
|
|
Manganese binding site 2 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 2 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn302
b:14.0
occ:1.00
|
OE1
|
A:GLU70
|
2.1
|
14.1
|
1.0
|
OD1
|
A:ASP90
|
2.2
|
13.1
|
1.0
|
O
|
A:ILE92
|
2.2
|
13.8
|
1.0
|
O3S
|
A:MES307
|
2.2
|
13.5
|
1.0
|
O
|
A:HOH492
|
2.2
|
13.2
|
1.0
|
O1S
|
A:MES307
|
2.3
|
17.5
|
1.0
|
S
|
A:MES307
|
2.8
|
23.7
|
1.0
|
CG
|
A:ASP90
|
3.1
|
15.2
|
1.0
|
C
|
A:ILE92
|
3.2
|
14.0
|
1.0
|
CD
|
A:GLU70
|
3.2
|
16.6
|
1.0
|
OD2
|
A:ASP90
|
3.3
|
16.4
|
1.0
|
OE2
|
A:GLU70
|
3.6
|
17.4
|
1.0
|
MN
|
A:MN303
|
3.7
|
16.0
|
1.0
|
O2S
|
A:MES307
|
3.8
|
16.7
|
1.0
|
N
|
A:ASP93
|
3.9
|
11.7
|
1.0
|
C8
|
A:MES307
|
3.9
|
10.9
|
1.0
|
CA
|
A:ASP93
|
3.9
|
12.3
|
1.0
|
MN
|
A:MN301
|
4.0
|
18.0
|
1.0
|
OG1
|
A:THR95
|
4.0
|
16.1
|
1.0
|
N
|
A:ILE92
|
4.0
|
14.7
|
1.0
|
CA
|
A:ILE92
|
4.1
|
13.4
|
1.0
|
O
|
A:HOH528
|
4.1
|
20.5
|
1.0
|
OE2
|
A:GLU71
|
4.3
|
15.6
|
1.0
|
OD2
|
A:ASP47
|
4.3
|
17.1
|
1.0
|
CD
|
A:PRO91
|
4.4
|
13.6
|
1.0
|
CB
|
A:ASP90
|
4.4
|
13.6
|
1.0
|
CG
|
A:GLU70
|
4.5
|
14.5
|
1.0
|
O
|
A:HOH456
|
4.5
|
16.9
|
1.0
|
CB
|
A:GLU70
|
4.6
|
14.2
|
1.0
|
CB
|
A:ILE92
|
4.7
|
15.6
|
1.0
|
N
|
A:PRO91
|
4.7
|
12.7
|
1.0
|
CA
|
A:ASP90
|
4.8
|
10.9
|
1.0
|
CG
|
A:PRO91
|
4.8
|
13.0
|
1.0
|
OD1
|
A:ASP93
|
4.8
|
15.9
|
1.0
|
C
|
A:ASP90
|
4.8
|
12.9
|
1.0
|
CB
|
A:ASP93
|
4.9
|
11.1
|
1.0
|
N
|
A:GLY94
|
4.9
|
13.7
|
1.0
|
C
|
A:ASP93
|
5.0
|
14.3
|
1.0
|
|
Manganese binding site 3 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 3 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mn303
b:16.0
occ:1.00
|
OD1
|
A:ASP220
|
2.0
|
18.7
|
1.0
|
O3S
|
A:MES307
|
2.1
|
13.5
|
1.0
|
OD2
|
A:ASP90
|
2.1
|
16.4
|
1.0
|
OD1
|
A:ASP93
|
2.1
|
15.9
|
1.0
|
O1
|
A:GOL304
|
2.3
|
20.1
|
1.0
|
O
|
A:HOH528
|
2.5
|
20.5
|
1.0
|
CG
|
A:ASP93
|
3.2
|
16.8
|
1.0
|
CG
|
A:ASP220
|
3.2
|
16.6
|
1.0
|
CG
|
A:ASP90
|
3.3
|
15.2
|
1.0
|
S
|
A:MES307
|
3.4
|
23.7
|
1.0
|
C1
|
A:GOL304
|
3.7
|
39.8
|
1.0
|
O2S
|
A:MES307
|
3.7
|
16.7
|
1.0
|
MN
|
A:MN302
|
3.7
|
14.0
|
1.0
|
O2
|
A:GOL304
|
3.8
|
20.6
|
1.0
|
OD1
|
A:ASP90
|
3.8
|
13.1
|
1.0
|
CB
|
A:ASP93
|
3.8
|
11.1
|
1.0
|
CA
|
A:ASP93
|
3.9
|
12.3
|
1.0
|
OD2
|
A:ASP220
|
3.9
|
16.0
|
1.0
|
O
|
A:HOH446
|
3.9
|
24.1
|
1.0
|
C7
|
A:MES307
|
4.0
|
36.6
|
1.0
|
CD1
|
A:TRP219
|
4.1
|
13.5
|
1.0
|
OE1
|
A:GLU70
|
4.1
|
14.1
|
1.0
|
C8
|
A:MES307
|
4.1
|
10.9
|
1.0
|
OD2
|
A:ASP93
|
4.2
|
15.3
|
1.0
|
NE1
|
A:TRP219
|
4.3
|
14.1
|
1.0
|
CB
|
A:ASP220
|
4.3
|
15.1
|
1.0
|
C2
|
A:GOL304
|
4.4
|
27.7
|
1.0
|
O1S
|
A:MES307
|
4.5
|
17.5
|
1.0
|
CB
|
A:ASP90
|
4.5
|
13.6
|
1.0
|
CA
|
A:ASP220
|
4.5
|
15.2
|
1.0
|
O
|
A:ILE92
|
4.7
|
13.8
|
1.0
|
N
|
A:GLY94
|
4.7
|
13.7
|
1.0
|
C
|
A:ASP93
|
4.8
|
14.3
|
1.0
|
CD
|
A:GLU70
|
4.9
|
16.6
|
1.0
|
N
|
A:ASP93
|
4.9
|
11.7
|
1.0
|
|
Manganese binding site 4 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 4 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn301
b:17.7
occ:1.00
|
OD1
|
B:ASP220
|
2.0
|
20.8
|
1.0
|
O1S
|
B:MES307
|
2.0
|
16.8
|
1.0
|
OD1
|
B:ASP93
|
2.2
|
15.6
|
1.0
|
OD2
|
B:ASP90
|
2.2
|
13.7
|
1.0
|
O3
|
B:GOL304
|
2.3
|
21.3
|
1.0
|
O
|
B:HOH517
|
2.4
|
20.7
|
1.0
|
CG
|
B:ASP93
|
3.2
|
17.2
|
1.0
|
CG
|
B:ASP220
|
3.2
|
19.8
|
1.0
|
CG
|
B:ASP90
|
3.3
|
13.2
|
1.0
|
S
|
B:MES307
|
3.3
|
22.6
|
1.0
|
C3
|
B:GOL304
|
3.6
|
30.9
|
1.0
|
O2S
|
B:MES307
|
3.7
|
18.3
|
1.0
|
MN
|
B:MN302
|
3.7
|
14.4
|
1.0
|
OD1
|
B:ASP90
|
3.8
|
13.4
|
1.0
|
CB
|
B:ASP93
|
3.8
|
14.4
|
1.0
|
CA
|
B:ASP93
|
3.9
|
12.6
|
1.0
|
O2
|
B:GOL304
|
3.9
|
21.1
|
1.0
|
O
|
B:HOH413
|
3.9
|
25.1
|
1.0
|
OD2
|
B:ASP220
|
3.9
|
19.6
|
1.0
|
C8
|
B:MES307
|
4.0
|
10.5
|
1.0
|
OE1
|
B:GLU70
|
4.2
|
14.3
|
1.0
|
OD2
|
B:ASP93
|
4.2
|
15.4
|
1.0
|
CD1
|
B:TRP219
|
4.2
|
15.4
|
1.0
|
CB
|
B:ASP220
|
4.3
|
16.9
|
1.0
|
C2
|
B:GOL304
|
4.3
|
28.1
|
1.0
|
NE1
|
B:TRP219
|
4.4
|
15.1
|
1.0
|
O3S
|
B:MES307
|
4.4
|
17.2
|
1.0
|
CA
|
B:ASP220
|
4.5
|
16.0
|
1.0
|
CB
|
B:ASP90
|
4.5
|
16.6
|
1.0
|
O
|
B:ILE92
|
4.7
|
12.4
|
1.0
|
N
|
B:GLY94
|
4.7
|
14.0
|
1.0
|
C
|
B:ASP93
|
4.8
|
14.1
|
1.0
|
CD
|
B:GLU70
|
4.9
|
17.0
|
1.0
|
N
|
B:ASP93
|
4.9
|
13.1
|
1.0
|
|
Manganese binding site 5 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 5 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn302
b:14.4
occ:1.00
|
OD1
|
B:ASP90
|
2.1
|
13.4
|
1.0
|
OE1
|
B:GLU70
|
2.1
|
14.3
|
1.0
|
O
|
B:HOH472
|
2.2
|
15.1
|
1.0
|
O
|
B:ILE92
|
2.2
|
12.4
|
1.0
|
O1S
|
B:MES307
|
2.3
|
16.8
|
1.0
|
O3S
|
B:MES307
|
2.4
|
17.2
|
1.0
|
S
|
B:MES307
|
2.8
|
22.6
|
1.0
|
CG
|
B:ASP90
|
3.1
|
13.2
|
1.0
|
CD
|
B:GLU70
|
3.1
|
17.0
|
1.0
|
C
|
B:ILE92
|
3.2
|
14.0
|
1.0
|
OD2
|
B:ASP90
|
3.4
|
13.7
|
1.0
|
OE2
|
B:GLU70
|
3.5
|
17.4
|
1.0
|
MN
|
B:MN301
|
3.7
|
17.7
|
1.0
|
O2S
|
B:MES307
|
3.8
|
18.3
|
1.0
|
N
|
B:ASP93
|
3.9
|
13.1
|
1.0
|
MN
|
B:MN303
|
3.9
|
18.2
|
1.0
|
CA
|
B:ASP93
|
3.9
|
12.6
|
1.0
|
OG1
|
B:THR95
|
4.0
|
13.8
|
1.0
|
N
|
B:ILE92
|
4.0
|
14.0
|
1.0
|
O
|
B:HOH517
|
4.1
|
20.7
|
1.0
|
CA
|
B:ILE92
|
4.1
|
11.4
|
1.0
|
C8
|
B:MES307
|
4.1
|
10.5
|
1.0
|
OE2
|
B:GLU71
|
4.3
|
18.9
|
1.0
|
OD2
|
B:ASP47
|
4.3
|
19.9
|
1.0
|
CD
|
B:PRO91
|
4.4
|
16.6
|
1.0
|
CG
|
B:GLU70
|
4.4
|
13.4
|
1.0
|
CB
|
B:ASP90
|
4.5
|
16.6
|
1.0
|
O
|
B:HOH447
|
4.5
|
15.5
|
1.0
|
CB
|
B:GLU70
|
4.6
|
15.8
|
1.0
|
CB
|
B:ILE92
|
4.7
|
12.8
|
1.0
|
N
|
B:PRO91
|
4.7
|
16.2
|
1.0
|
CG
|
B:PRO91
|
4.8
|
17.7
|
1.0
|
CA
|
B:ASP90
|
4.8
|
14.4
|
1.0
|
C
|
B:ASP90
|
4.8
|
13.1
|
1.0
|
OD1
|
B:ASP93
|
4.8
|
15.6
|
1.0
|
CB
|
B:ASP93
|
4.9
|
14.4
|
1.0
|
N
|
B:GLY94
|
4.9
|
14.0
|
1.0
|
C
|
B:ASP93
|
4.9
|
14.1
|
1.0
|
|
Manganese binding site 6 out
of 6 in 6gj0
Go back to
Manganese Binding Sites List in 6gj0
Manganese binding site 6 out
of 6 in the Human Impase with Mn
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 Mn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mn303
b:18.2
occ:1.00
|
OE2
|
B:GLU70
|
2.0
|
17.4
|
1.0
|
O
|
B:HOH428
|
2.1
|
19.4
|
1.0
|
O2S
|
B:MES307
|
2.1
|
18.3
|
1.0
|
O
|
B:HOH447
|
2.2
|
15.5
|
1.0
|
O
|
B:HOH436
|
2.3
|
20.9
|
1.0
|
O3S
|
B:MES307
|
2.4
|
17.2
|
1.0
|
S
|
B:MES307
|
2.8
|
22.6
|
1.0
|
CD
|
B:GLU70
|
3.2
|
17.0
|
1.0
|
OE1
|
B:GLU70
|
3.6
|
14.3
|
1.0
|
O1S
|
B:MES307
|
3.8
|
16.8
|
1.0
|
MN
|
B:MN302
|
3.9
|
14.4
|
1.0
|
O
|
B:LEU42
|
3.9
|
15.8
|
1.0
|
NZ
|
B:LYS36
|
3.9
|
18.2
|
1.0
|
O
|
B:HOH578
|
4.0
|
34.4
|
1.0
|
OD1
|
B:ASP41
|
4.1
|
23.2
|
1.0
|
C8
|
B:MES307
|
4.1
|
10.5
|
1.0
|
OE2
|
B:GLU71
|
4.1
|
18.9
|
1.0
|
O
|
B:HOH517
|
4.1
|
20.7
|
1.0
|
O
|
B:HOH496
|
4.2
|
29.6
|
1.0
|
OG1
|
B:THR95
|
4.3
|
13.8
|
1.0
|
C7
|
B:MES307
|
4.3
|
26.1
|
1.0
|
O
|
B:HOH472
|
4.4
|
15.1
|
1.0
|
CG
|
B:GLU70
|
4.4
|
13.4
|
1.0
|
CD
|
B:LYS36
|
4.6
|
24.8
|
1.0
|
O
|
B:HOH559
|
4.7
|
36.8
|
1.0
|
CB
|
B:THR95
|
4.8
|
13.2
|
1.0
|
CE
|
B:LYS36
|
4.8
|
27.9
|
1.0
|
O
|
B:HOH501
|
4.9
|
16.2
|
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 04:44:44 2024
|