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Magnesium in PDB 6sbi: X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate

Enzymatic activity of X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate

All present enzymatic activity of X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate:
3.7.1.5; 4.1.1.112;

Protein crystallography data

The structure of X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate, PDB code: 6sbi 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) 44.37 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.603, 103.348, 86.597, 90.00, 90.21, 90.00
R / Rfree (%) 18.7 / 23.4

Other elements in 6sbi:

The structure of X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate also contains other interesting chemical elements:

Potassium (K) 2 atoms
Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate (pdb code 6sbi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate, PDB code: 6sbi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6sbi

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Magnesium binding site 1 out of 4 in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate


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 Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:20.5
occ:1.00
 O A:HOH404 2.1 13.7 1.0
OE2 A:GLU76 2.1 19.5 1.0
OD2 A:ASP105 2.1 22.1 1.0
O1 A:OXL306 2.1 24.8 1.0
OE1 A:GLU74 2.1 29.3 1.0
O2 A:OXL306 2.1 33.6 1.0
C1 A:OXL306 2.8 33.1 1.0
C2 A:OXL306 2.8 39.3 1.0
CD A:GLU76 3.1 18.4 1.0
CG A:ASP105 3.2 21.0 1.0
CD A:GLU74 3.3 31.5 1.0
OE1 A:GLU76 3.5 17.6 1.0
NZ A:LYS126 3.7 38.4 1.0
CB A:ASP105 3.8 21.0 1.0
OE2 A:GLU74 3.9 34.3 1.0
O3 A:OXL306 4.0 36.5 1.0
O4 A:OXL306 4.0 42.4 1.0
CZ A:PHE48 4.2 31.7 1.0
O A:VAL26 4.2 23.3 1.0
OD1 A:ASP105 4.2 18.4 1.0
CG A:GLU76 4.4 18.2 1.0
CG A:GLU74 4.4 29.7 1.0
CB A:GLU74 4.5 28.3 1.0
CA A:GLY194 4.5 23.8 1.0
N A:THR195 4.6 29.1 1.0
CB A:THR195 4.7 35.9 1.0
CE A:LYS126 4.7 33.5 1.0
CE1 A:PHE48 4.7 31.7 1.0
CG2 A:THR195 4.7 37.5 1.0
C A:GLY194 4.8 26.2 1.0

Magnesium binding site 2 out of 4 in 6sbi

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Magnesium binding site 2 out of 4 in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate


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 Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:22.5
occ:1.00
 O B:HOH405 1.8 7.3 1.0
OD2 B:ASP105 2.1 21.6 1.0
OE1 B:GLU74 2.1 22.0 1.0
OE2 B:GLU76 2.1 22.2 1.0
O4 B:OXL304 2.1 34.0 1.0
O3 B:OXL304 2.1 29.8 1.0
C1 B:OXL304 2.8 36.0 1.0
C2 B:OXL304 2.8 38.6 1.0
CD B:GLU76 3.1 22.3 1.0
CG B:ASP105 3.2 18.5 1.0
CD B:GLU74 3.3 23.1 1.0
OE1 B:GLU76 3.5 23.6 1.0
NZ B:LYS126 3.7 26.2 1.0
CB B:ASP105 3.8 16.6 1.0
OE2 B:GLU74 3.9 25.1 1.0
O1 B:OXL304 4.0 35.1 1.0
O2 B:OXL304 4.0 36.7 1.0
OD1 B:ASP105 4.2 18.1 1.0
CZ B:PHE48 4.3 28.3 1.0
O B:VAL26 4.3 21.8 1.0
CG B:GLU76 4.4 20.2 1.0
CG B:GLU74 4.4 21.0 1.0
CB B:GLU74 4.5 19.4 1.0
CA B:GLY194 4.5 29.5 1.0
N B:THR195 4.5 42.6 1.0
CB B:THR195 4.6 45.7 1.0
CG2 B:THR195 4.7 49.7 1.0
CE B:LYS126 4.7 26.6 1.0
CE1 B:PHE48 4.8 25.8 1.0
C B:GLY194 4.8 33.3 1.0

Magnesium binding site 3 out of 4 in 6sbi

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Magnesium binding site 3 out of 4 in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate


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 Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:28.3
occ:1.00
 O C:HOH401 2.1 7.9 1.0
OD2 C:ASP105 2.1 21.4 1.0
OE1 C:GLU74 2.1 31.1 1.0
O4 C:OXL306 2.1 42.7 1.0
OE2 C:GLU76 2.1 23.9 1.0
O3 C:OXL306 2.1 35.1 1.0
C1 C:OXL306 2.8 46.3 1.0
C2 C:OXL306 2.8 51.7 1.0
CD C:GLU76 3.1 22.3 1.0
CG C:ASP105 3.2 18.3 1.0
CD C:GLU74 3.3 31.5 1.0
OE1 C:GLU76 3.5 24.6 1.0
NZ C:LYS126 3.6 31.5 1.0
CB C:ASP105 3.8 18.0 1.0
OE2 C:GLU74 3.9 32.6 1.0
O1 C:OXL306 4.0 41.6 1.0
O2 C:OXL306 4.0 52.1 1.0
OD1 C:ASP105 4.2 16.9 1.0
CZ C:PHE48 4.2 25.9 1.0
O C:VAL26 4.3 25.6 1.0
CG C:GLU76 4.4 21.2 1.0
CG C:GLU74 4.4 28.9 1.0
CB C:GLU74 4.5 26.0 1.0
CA C:GLY194 4.5 25.1 1.0
N C:THR195 4.6 31.2 1.0
CE C:LYS126 4.6 35.1 1.0
CB C:THR195 4.7 34.1 1.0
CG2 C:THR195 4.7 34.6 1.0
CE1 C:PHE48 4.7 27.3 1.0
C C:GLY194 4.9 26.5 1.0

Magnesium binding site 4 out of 4 in 6sbi

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Magnesium binding site 4 out of 4 in the X-Ray Structure of Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate


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 Murine Fumarylacetoacetate Hydrolase Domain Containing Protein 1 (FAHD1) in Complex with Inhibitor Oxalate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:24.2
occ:1.00
 O D:HOH403 1.9 13.0 1.0
OD2 D:ASP105 2.1 23.5 1.0
O2 D:OXL303 2.1 34.8 1.0
OE1 D:GLU74 2.1 26.8 1.0
O3 D:OXL303 2.1 37.1 1.0
OE2 D:GLU76 2.1 23.9 1.0
C2 D:OXL303 2.8 43.5 1.0
C1 D:OXL303 2.8 46.3 1.0
CD D:GLU76 3.2 22.6 1.0
CG D:ASP105 3.2 24.5 1.0
CD D:GLU74 3.3 24.2 1.0
OE1 D:GLU76 3.6 21.6 1.0
NZ D:LYS126 3.6 19.3 1.0
CB D:ASP105 3.8 24.6 1.0
OE2 D:GLU74 3.9 22.0 1.0
O4 D:OXL303 4.0 46.4 1.0
O1 D:OXL303 4.0 44.8 1.0
OD1 D:ASP105 4.2 21.9 1.0
CZ D:PHE48 4.2 30.1 1.0
O D:VAL26 4.3 19.5 1.0
CG D:GLU74 4.4 25.2 1.0
CG D:GLU76 4.4 22.5 1.0
CB D:GLU74 4.5 26.1 1.0
CA D:GLY194 4.6 22.8 1.0
N D:THR195 4.6 29.9 1.0
CE D:LYS126 4.6 19.5 1.0
CB D:THR195 4.7 29.8 1.0
CE1 D:PHE48 4.7 28.9 1.0
CG2 D:THR195 4.7 27.7 1.0
C D:GLY194 4.9 26.9 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 in Human and Mouse. Biosci.Rep. V. 40 2020.
ISSN: ISSN 0144-8463
PubMed: 32068790
DOI: 10.1042/BSR20194431
Page generated: Tue Oct 1 17:50:39 2024

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