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Magnesium in PDB 2cw6: Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria

Enzymatic activity of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria

All present enzymatic activity of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria:
4.1.3.4;

Protein crystallography data

The structure of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria, PDB code: 2cw6 was solved by Z.Fu, J.A.Runquist, J.F.Hunt, H.M.Miziorko, J.-J.P.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.44 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 196.990, 117.080, 86.830, 90.00, 112.50, 90.00
R / Rfree (%) 22.6 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria (pdb code 2cw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria, PDB code: 2cw6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2cw6

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Magnesium binding site 1 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:35.7
occ:1.00
 NE2 A:HIS235 2.0 35.2 1.0
OD1 A:ASP42 2.1 31.1 1.0
OD1 A:ASN275 2.3 35.1 1.0
NE2 A:HIS233 2.5 29.2 1.0
O A:HOH763 2.6 50.6 1.0
O A:HOH920 2.8 51.0 1.0
CE1 A:HIS235 3.0 39.0 1.0
CG A:ASP42 3.0 29.4 1.0
CD2 A:HIS235 3.0 35.0 1.0
CG A:ASN275 3.3 32.7 1.0
OD2 A:ASP42 3.3 27.7 1.0
CE1 A:HIS233 3.4 28.0 1.0
CD2 A:HIS233 3.5 27.6 1.0
ND2 A:ASN275 3.6 31.4 1.0
ND1 A:HIS235 4.1 37.9 1.0
CG A:HIS235 4.2 35.2 1.0
CB A:ASP42 4.4 27.9 1.0
ND1 A:HIS233 4.5 28.3 1.0
CB A:ASN275 4.6 32.3 1.0
CG A:HIS233 4.6 27.6 1.0
CA A:ASN275 4.9 30.3 1.0

Magnesium binding site 2 out of 6 in 2cw6

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Magnesium binding site 2 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg404

b:48.2
occ:1.00
 NE2 B:HIS235 2.2 40.9 1.0
OD1 B:ASP42 2.2 41.7 1.0
NE2 B:HIS233 2.4 40.2 1.0
O B:HOH938 2.4 60.3 1.0
OD1 B:ASN275 2.5 43.1 1.0
O B:HOH712 2.6 57.1 1.0
CE1 B:HIS235 3.0 41.5 1.0
CG B:ASP42 3.1 41.4 1.0
CE1 B:HIS233 3.2 40.0 1.0
CD2 B:HIS235 3.2 38.5 1.0
OD2 B:ASP42 3.3 43.8 1.0
CD2 B:HIS233 3.4 38.9 1.0
CG B:ASN275 3.4 42.2 1.0
ND2 B:ASN275 3.7 42.7 1.0
ND1 B:HIS235 4.1 40.0 1.0
CG B:HIS235 4.2 36.7 1.0
ND1 B:HIS233 4.3 38.9 1.0
CG B:HIS233 4.5 37.3 1.0
CB B:ASP42 4.5 39.0 1.0
CB B:ASN275 4.8 39.6 1.0

Magnesium binding site 3 out of 6 in 2cw6

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Magnesium binding site 3 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:37.5
occ:1.00
 OD1 C:ASP42 2.2 37.4 1.0
NE2 C:HIS235 2.2 39.7 1.0
NE2 C:HIS233 2.3 29.0 1.0
O C:HOH898 2.3 43.0 1.0
OD1 C:ASN275 2.4 43.5 1.0
CE1 C:HIS233 3.0 31.2 1.0
CE1 C:HIS235 3.0 41.2 1.0
CG C:ASP42 3.1 37.8 1.0
CG C:ASN275 3.2 43.4 1.0
CD2 C:HIS235 3.2 37.9 1.0
ND2 C:ASN275 3.3 42.7 1.0
OD2 C:ASP42 3.3 36.9 1.0
CD2 C:HIS233 3.5 30.3 1.0
ND1 C:HIS235 4.1 41.0 1.0
ND1 C:HIS233 4.2 30.5 1.0
O C:HOH839 4.2 46.4 1.0
CG C:HIS235 4.3 38.5 1.0
CG C:HIS233 4.5 29.7 1.0
CB C:ASP42 4.5 37.0 1.0
CB C:ASN275 4.6 43.0 1.0

Magnesium binding site 4 out of 6 in 2cw6

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Magnesium binding site 4 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg405

b:55.4
occ:1.00
 NE2 D:HIS235 2.3 50.3 1.0
NE2 D:HIS233 2.3 47.1 1.0
O D:HOH777 2.4 65.2 1.0
OD1 D:ASP42 2.4 65.8 1.0
OD1 D:ASN275 2.5 56.5 1.0
CE1 D:HIS235 3.0 52.5 1.0
CE1 D:HIS233 3.1 47.3 1.0
CD2 D:HIS235 3.3 50.5 1.0
CG D:ASP42 3.3 64.5 1.0
CD2 D:HIS233 3.3 47.8 1.0
OD2 D:ASP42 3.6 65.5 1.0
CG D:ASN275 3.6 55.6 1.0
ND2 D:ASN275 4.1 55.2 1.0
ND1 D:HIS235 4.1 51.4 1.0
ND1 D:HIS233 4.2 46.8 1.0
CG D:HIS235 4.3 49.0 1.0
CG D:HIS233 4.3 46.5 1.0
CB D:ASP42 4.6 63.0 1.0
CB D:ASN275 4.9 53.8 1.0

Magnesium binding site 5 out of 6 in 2cw6

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Magnesium binding site 5 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:44.7
occ:1.00
 OD1 E:ASP42 2.2 44.1 1.0
NE2 E:HIS235 2.3 41.4 1.0
O E:HOH860 2.4 59.3 1.0
NE2 E:HIS233 2.5 36.5 1.0
OD1 E:ASN275 2.5 47.1 1.0
CG E:ASP42 3.1 42.0 1.0
CE1 E:HIS235 3.1 42.9 1.0
CE1 E:HIS233 3.1 37.9 1.0
CD2 E:HIS235 3.3 39.6 1.0
OD2 E:ASP42 3.3 42.6 1.0
CG E:ASN275 3.5 45.1 1.0
CD2 E:HIS233 3.6 36.7 1.0
ND2 E:ASN275 3.7 45.9 1.0
ND1 E:HIS233 4.3 36.9 1.0
ND1 E:HIS235 4.3 43.4 1.0
CG E:HIS235 4.4 38.9 1.0
CB E:ASP42 4.5 39.2 1.0
CG E:HIS233 4.5 35.5 1.0
CB E:ASN275 4.8 44.1 1.0

Magnesium binding site 6 out of 6 in 2cw6

Go back to Magnesium Binding Sites List in 2cw6
Magnesium binding site 6 out of 6 in the Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Human Hmg-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg406

b:64.1
occ:1.00
 OD1 F:ASP42 2.2 63.8 1.0
NE2 F:HIS233 2.4 50.1 1.0
NE2 F:HIS235 2.4 53.1 1.0
OD1 F:ASN275 2.6 54.2 1.0
CG F:ASP42 2.9 64.4 1.0
OD2 F:ASP42 2.9 64.7 1.0
CE1 F:HIS233 3.3 49.3 1.0
CE1 F:HIS235 3.3 53.0 1.0
CD2 F:HIS233 3.3 48.5 1.0
CD2 F:HIS235 3.5 51.6 1.0
CG F:ASN275 3.7 53.1 1.0
ND2 F:ASN275 4.1 53.0 1.0
CB F:ASP42 4.4 64.6 1.0
ND1 F:HIS233 4.4 49.8 1.0
ND1 F:HIS235 4.4 52.2 1.0
CG F:HIS233 4.5 48.2 1.0
CG F:HIS235 4.6 50.2 1.0
CB F:ASN275 4.9 52.7 1.0

Reference:

Z.Fu, J.A.Runquist, F.Forouhar, M.Hussain, J.F.Hunt, H.M.Miziorko, J.-J.P.Kim. Crystal Structure of Human 3-Hydroxy-3-Methylglutaryl-Coa Lyase: Insights Into Catalysis and the Molecular Basis For Hydroxymethylglutaric Aciduria J.Biol.Chem. V. 281 7526 2006.
ISSN: ISSN 0021-9258
PubMed: 16330550
DOI: 10.1074/JBC.M506880200
Page generated: Tue Aug 13 22:22:51 2024

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