Magnesium in PDB 6sbj: X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Enzymatic activity of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
All present enzymatic activity of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed:
3.7.1.5;
4.1.1.112;
Protein crystallography data
The structure of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed, PDB code: 6sbj
was solved by
B.Rupp,
A.Naschberger,
A.K.H.Weiss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.65 /
2.22
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.401,
69.959,
107.557,
90.00,
92.25,
90.00
|
R / Rfree (%)
|
19.3 /
25.7
|
Other elements in 6sbj:
The structure of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
(pdb code 6sbj). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed, PDB code: 6sbj:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 6sbj
Go back to
Magnesium Binding Sites List in 6sbj
Magnesium binding site 1 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg301
b:15.9
occ:1.00
|
O
|
A:LYS21
|
2.3
|
10.9
|
1.0
|
O
|
B:LYS21
|
2.4
|
10.2
|
1.0
|
O
|
B:HOH423
|
2.5
|
3.7
|
1.0
|
OD1
|
A:ASN22
|
2.6
|
11.4
|
1.0
|
OD1
|
B:ASN22
|
2.7
|
9.3
|
1.0
|
O
|
A:HOH403
|
2.7
|
5.4
|
1.0
|
C
|
A:LYS21
|
3.2
|
11.3
|
1.0
|
C
|
B:LYS21
|
3.3
|
10.0
|
1.0
|
CG
|
A:ASN22
|
3.6
|
11.5
|
1.0
|
CG
|
B:ASN22
|
3.7
|
9.3
|
1.0
|
CA
|
A:ASN22
|
3.7
|
11.3
|
1.0
|
CA
|
B:ASN22
|
3.7
|
9.4
|
1.0
|
N
|
A:ASN22
|
3.8
|
11.5
|
1.0
|
N
|
B:ASN22
|
3.9
|
9.6
|
1.0
|
CB
|
A:ASN22
|
4.1
|
11.3
|
1.0
|
CB
|
B:ASN22
|
4.2
|
9.4
|
1.0
|
CA
|
A:LYS21
|
4.2
|
11.6
|
1.0
|
CA
|
B:LYS21
|
4.3
|
10.4
|
1.0
|
N
|
B:SER52
|
4.4
|
10.9
|
1.0
|
N
|
A:SER52
|
4.5
|
9.6
|
1.0
|
CB
|
A:LYS21
|
4.6
|
11.8
|
1.0
|
ND2
|
A:ASN22
|
4.6
|
11.7
|
1.0
|
CB
|
B:LYS21
|
4.6
|
10.6
|
1.0
|
ND2
|
B:ASN22
|
4.7
|
9.4
|
1.0
|
CA
|
B:PRO51
|
4.7
|
10.3
|
1.0
|
CA
|
A:PRO51
|
4.7
|
9.5
|
1.0
|
O
|
A:LYS50
|
4.9
|
8.8
|
1.0
|
O
|
B:LYS50
|
4.9
|
10.2
|
1.0
|
C
|
A:ASN22
|
4.9
|
11.1
|
1.0
|
CB
|
B:SER52
|
5.0
|
11.5
|
1.0
|
C
|
B:ASN22
|
5.0
|
9.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 6sbj
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Magnesium Binding Sites List in 6sbj
Magnesium binding site 2 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg302
b:9.8
occ:1.00
|
OE2
|
A:GLU76
|
1.8
|
8.9
|
1.0
|
O
|
A:HOH402
|
2.1
|
9.9
|
1.0
|
OE1
|
A:GLU74
|
2.1
|
16.5
|
1.0
|
O
|
A:HOH408
|
2.2
|
12.0
|
1.0
|
OD2
|
A:ASP105
|
2.2
|
11.6
|
1.0
|
O
|
A:HOH422
|
2.3
|
14.4
|
1.0
|
CD
|
A:GLU76
|
2.8
|
8.8
|
1.0
|
CG
|
A:ASP105
|
3.3
|
11.8
|
1.0
|
OE1
|
A:GLU76
|
3.3
|
8.9
|
1.0
|
CD
|
A:GLU74
|
3.4
|
19.7
|
1.0
|
CB
|
A:ASP105
|
3.6
|
12.4
|
1.0
|
O
|
A:VAL26
|
3.7
|
14.7
|
1.0
|
NZ
|
A:LYS126
|
4.1
|
21.3
|
1.0
|
CG
|
A:GLU76
|
4.1
|
8.7
|
1.0
|
OE2
|
A:GLU74
|
4.1
|
24.5
|
1.0
|
O
|
A:GLY27
|
4.1
|
24.7
|
1.0
|
CB
|
A:GLU74
|
4.3
|
14.2
|
1.0
|
CA
|
A:GLY194
|
4.4
|
9.5
|
1.0
|
OD1
|
A:ASP105
|
4.4
|
10.9
|
1.0
|
CG
|
A:GLU74
|
4.4
|
16.2
|
1.0
|
N
|
A:THR195
|
4.6
|
9.5
|
1.0
|
CZ
|
A:PHE48
|
4.6
|
23.2
|
1.0
|
CG2
|
A:THR195
|
4.7
|
10.0
|
1.0
|
CB
|
A:THR195
|
4.7
|
9.9
|
1.0
|
C
|
A:GLY194
|
4.7
|
9.5
|
1.0
|
O
|
A:HOH433
|
4.8
|
11.4
|
1.0
|
N
|
A:GLY194
|
4.9
|
9.2
|
1.0
|
O
|
A:HOH432
|
5.0
|
4.1
|
1.0
|
C
|
A:VAL26
|
5.0
|
15.4
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 6sbj
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Magnesium Binding Sites List in 6sbj
Magnesium binding site 3 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg301
b:12.3
occ:1.00
|
O
|
B:HOH436
|
1.9
|
13.0
|
1.0
|
OD2
|
B:ASP105
|
2.0
|
20.0
|
1.0
|
O
|
B:HOH422
|
2.0
|
14.2
|
1.0
|
OE1
|
B:GLU74
|
2.1
|
14.4
|
1.0
|
O
|
B:HOH410
|
2.1
|
4.4
|
1.0
|
OE2
|
B:GLU76
|
2.2
|
11.6
|
1.0
|
CG
|
B:ASP105
|
3.1
|
14.9
|
1.0
|
CD
|
B:GLU74
|
3.3
|
14.9
|
1.0
|
CD
|
B:GLU76
|
3.3
|
11.4
|
1.0
|
NZ
|
B:LYS126
|
3.6
|
15.0
|
1.0
|
CB
|
B:ASP105
|
3.6
|
14.8
|
1.0
|
OE1
|
B:GLU76
|
3.8
|
11.5
|
1.0
|
O
|
B:VAL26
|
3.8
|
20.4
|
1.0
|
OE2
|
B:GLU74
|
4.0
|
14.8
|
1.0
|
CZ
|
B:PHE48
|
4.1
|
11.5
|
1.0
|
OD1
|
B:ASP105
|
4.2
|
12.9
|
1.0
|
O
|
B:GLY27
|
4.3
|
57.1
|
1.0
|
CG
|
B:GLU74
|
4.4
|
14.0
|
1.0
|
CB
|
B:GLU74
|
4.5
|
13.6
|
1.0
|
CE2
|
B:PHE48
|
4.5
|
11.7
|
1.0
|
CG
|
B:GLU76
|
4.6
|
11.5
|
1.0
|
CA
|
B:GLY194
|
4.8
|
11.9
|
1.0
|
CE
|
B:LYS126
|
4.8
|
15.2
|
1.0
|
CG2
|
B:THR195
|
4.9
|
15.2
|
1.0
|
N
|
B:THR195
|
4.9
|
14.0
|
1.0
|
C
|
B:VAL26
|
5.0
|
19.7
|
1.0
|
CB
|
B:THR195
|
5.0
|
15.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 6sbj
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Magnesium Binding Sites List in 6sbj
Magnesium binding site 4 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg301
b:29.6
occ:1.00
|
OE1
|
C:GLU74
|
1.9
|
41.2
|
1.0
|
O
|
C:HOH402
|
2.2
|
20.3
|
1.0
|
OE2
|
C:GLU76
|
2.2
|
26.4
|
1.0
|
O
|
C:HOH412
|
2.2
|
17.9
|
1.0
|
OD2
|
C:ASP105
|
2.8
|
19.9
|
1.0
|
CD
|
C:GLU74
|
3.1
|
42.7
|
1.0
|
CD
|
C:GLU76
|
3.3
|
26.1
|
1.0
|
OE2
|
C:GLU74
|
3.8
|
43.6
|
1.0
|
O
|
C:GLY27
|
3.9
|
56.5
|
1.0
|
OE1
|
C:GLU76
|
3.9
|
24.5
|
1.0
|
CG
|
C:ASP105
|
3.9
|
21.8
|
1.0
|
O
|
C:VAL26
|
3.9
|
32.7
|
1.0
|
CG2
|
C:THR195
|
4.1
|
38.2
|
1.0
|
NZ
|
C:LYS126
|
4.2
|
31.3
|
1.0
|
CB
|
C:ASP105
|
4.2
|
24.2
|
1.0
|
CG
|
C:GLU74
|
4.2
|
39.0
|
1.0
|
CB
|
C:THR195
|
4.3
|
39.3
|
1.0
|
N
|
C:THR195
|
4.3
|
37.0
|
1.0
|
CB
|
C:GLU74
|
4.3
|
38.6
|
1.0
|
CA
|
C:GLY194
|
4.4
|
29.5
|
1.0
|
CG
|
C:GLU76
|
4.5
|
28.1
|
1.0
|
C
|
C:GLY194
|
4.6
|
32.6
|
1.0
|
C
|
C:GLY27
|
4.8
|
44.8
|
1.0
|
CZ
|
C:PHE48
|
4.9
|
19.4
|
1.0
|
CA
|
C:THR195
|
4.9
|
38.4
|
1.0
|
OD1
|
C:ASP105
|
5.0
|
20.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 6sbj
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Magnesium Binding Sites List in 6sbj
Magnesium binding site 5 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg301
b:23.4
occ:1.00
|
O
|
C:LYS21
|
2.2
|
25.9
|
1.0
|
O
|
D:LYS21
|
2.4
|
29.4
|
1.0
|
OD1
|
D:ASN22
|
2.5
|
17.5
|
1.0
|
O
|
C:HOH408
|
2.6
|
15.4
|
1.0
|
OD1
|
C:ASN22
|
2.6
|
23.1
|
1.0
|
O
|
D:HOH407
|
2.9
|
20.3
|
1.0
|
C
|
C:LYS21
|
3.2
|
26.7
|
1.0
|
C
|
D:LYS21
|
3.3
|
26.8
|
1.0
|
CG
|
D:ASN22
|
3.5
|
21.8
|
1.0
|
CG
|
C:ASN22
|
3.6
|
22.3
|
1.0
|
CA
|
C:ASN22
|
3.6
|
24.8
|
1.0
|
CA
|
D:ASN22
|
3.8
|
24.2
|
1.0
|
N
|
C:ASN22
|
3.8
|
26.2
|
1.0
|
N
|
D:ASN22
|
3.9
|
24.7
|
1.0
|
CB
|
C:ASN22
|
4.1
|
24.0
|
1.0
|
CB
|
D:ASN22
|
4.1
|
22.8
|
1.0
|
CA
|
C:LYS21
|
4.2
|
27.8
|
1.0
|
CA
|
D:LYS21
|
4.3
|
28.1
|
1.0
|
N
|
C:SER52
|
4.3
|
30.7
|
1.0
|
ND2
|
D:ASN22
|
4.4
|
21.8
|
1.0
|
CB
|
D:LYS21
|
4.5
|
34.0
|
1.0
|
CB
|
C:LYS21
|
4.6
|
28.4
|
1.0
|
ND2
|
C:ASN22
|
4.6
|
20.7
|
1.0
|
N
|
D:SER52
|
4.6
|
20.6
|
1.0
|
CA
|
C:PRO51
|
4.6
|
30.5
|
1.0
|
O
|
C:LYS50
|
4.8
|
24.5
|
1.0
|
C
|
C:ASN22
|
4.8
|
25.1
|
1.0
|
C
|
C:PRO51
|
4.9
|
30.0
|
1.0
|
CB
|
C:SER52
|
4.9
|
31.0
|
1.0
|
CA
|
D:PRO51
|
4.9
|
22.9
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 6sbj
Go back to
Magnesium Binding Sites List in 6sbj
Magnesium binding site 6 out
of 6 in the X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of X-Ray Structure of Mus Musculus Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) Apo-Form Uuncomplexed within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg302
b:22.8
occ:1.00
|
OE2
|
D:GLU76
|
2.0
|
17.9
|
1.0
|
O
|
D:HOH401
|
2.0
|
10.5
|
1.0
|
OE1
|
D:GLU74
|
2.1
|
34.4
|
1.0
|
OD2
|
D:ASP105
|
2.3
|
26.0
|
1.0
|
O
|
D:HOH419
|
2.5
|
30.2
|
1.0
|
CD
|
D:GLU76
|
3.1
|
17.3
|
1.0
|
CD
|
D:GLU74
|
3.4
|
38.6
|
1.0
|
CG
|
D:ASP105
|
3.4
|
22.2
|
1.0
|
OE1
|
D:GLU76
|
3.6
|
14.9
|
1.0
|
O
|
D:VAL26
|
3.6
|
40.3
|
1.0
|
CB
|
D:ASP105
|
3.8
|
20.1
|
1.0
|
NZ
|
D:LYS126
|
4.0
|
26.1
|
1.0
|
OE2
|
D:GLU74
|
4.1
|
58.9
|
1.0
|
O
|
D:GLY27
|
4.1
|
40.2
|
1.0
|
CG
|
D:GLU76
|
4.4
|
17.5
|
1.0
|
CZ
|
D:PHE48
|
4.4
|
20.5
|
1.0
|
CB
|
D:GLU74
|
4.4
|
29.1
|
1.0
|
CG
|
D:GLU74
|
4.5
|
33.2
|
1.0
|
CA
|
D:GLY194
|
4.5
|
19.1
|
1.0
|
OD1
|
D:ASP105
|
4.6
|
19.8
|
1.0
|
O
|
D:HOH412
|
4.6
|
11.8
|
1.0
|
CG2
|
D:THR195
|
4.6
|
25.2
|
1.0
|
N
|
D:THR195
|
4.6
|
21.7
|
1.0
|
CB
|
D:THR195
|
4.7
|
25.4
|
1.0
|
CE1
|
D:PHE48
|
4.8
|
20.7
|
1.0
|
C
|
D:GLY194
|
4.8
|
21.6
|
1.0
|
C
|
D:VAL26
|
4.8
|
32.9
|
1.0
|
|
Reference:
A.K.H.Weiss,
A.Naschberger,
E.Cappuccio,
C.Metzger,
L.Mottes,
M.Holzknecht,
J.Von Velsen,
M.W.Bowler,
B.Rupp,
P.Jansen-Durr.
Structural and Functional Comparison of Fumarylacetoacetate Domain Containing Protein 1 (FAHD1) in Human and Mouse. Biosci.Rep. 2020.
ISSN: ISSN 0144-8463
PubMed: 32068790
DOI: 10.1042/BSR20194431
Page generated: Tue Oct 1 17:50:56 2024
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