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Magnesium in PDB 7vb6: Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile

Enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile

All present enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile:
4.1.2.46;

Protein crystallography data

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile, PDB code: 7vb6 was solved by D.Zheng, M.Nakabayashi, Y.Asano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.85 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.178, 52.103, 169.85, 90, 94.8, 90
R / Rfree (%) 16.3 / 20.6

Other elements in 7vb6:

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile (pdb code 7vb6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile, PDB code: 7vb6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7vb6

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Magnesium binding site 1 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile


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 Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:14.1
occ:1.00
 O A:HOH803 2.0 12.4 1.0
O A:HOH739 2.1 16.3 1.0
OE1 A:GLU140 2.1 14.3 1.0
O A:HOH927 2.1 12.7 1.0
O A:HOH894 2.2 15.2 1.0
OE2 A:GLU52 2.2 15.5 1.0
CD A:GLU140 3.1 13.6 1.0
CD A:GLU52 3.2 14.1 1.0
OE2 A:GLU140 3.5 14.6 1.0
CG A:GLU52 3.6 13.6 1.0
CD A:PRO141 4.1 16.6 1.0
OD1 A:ASN50 4.2 15.8 1.0
O A:HOH982 4.2 26.1 1.0
O A:HOH936 4.2 31.6 1.0
NH2 A:ARG146 4.2 16.8 1.0
ND2 A:ASN50 4.2 15.5 1.0
O A:HOH933 4.2 16.9 1.0
OE1 A:GLU52 4.2 14.0 1.0
O A:HOH666 4.4 14.3 1.0
OD2 A:ASP175 4.4 16.4 1.0
CG A:GLU140 4.5 14.2 1.0
O A:HOH988 4.5 23.0 1.0
CB A:ASP175 4.6 12.4 1.0
CG A:ASN50 4.6 15.2 1.0
CG A:PRO141 4.8 18.7 1.0
CB A:GLU140 4.8 12.9 1.0
CA A:GLU140 5.0 14.2 1.0

Magnesium binding site 2 out of 4 in 7vb6

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Magnesium binding site 2 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile


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 Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:16.3
occ:1.00
 OE2 B:GLU52 2.1 16.1 1.0
O B:HOH822 2.1 16.7 1.0
O B:HOH785 2.1 20.0 1.0
OE1 B:GLU140 2.1 17.7 1.0
O B:HOH886 2.1 16.4 1.0
O B:HOH885 2.2 17.8 1.0
CD B:GLU52 3.1 15.1 1.0
CD B:GLU140 3.1 16.0 1.0
OE2 B:GLU140 3.5 16.0 1.0
CG B:GLU52 3.5 14.6 1.0
OD1 B:ASN50 4.2 20.0 1.0
OE1 B:GLU52 4.2 16.2 1.0
ND2 B:ASN50 4.2 20.1 1.0
O B:HOH898 4.2 20.6 1.0
CD B:PRO141 4.2 19.9 1.0
NH2 B:ARG146 4.3 18.6 1.0
O B:HOH985 4.3 27.6 1.0
O B:HOH720 4.3 36.6 1.0
O B:HOH668 4.4 14.3 1.0
CG B:GLU140 4.4 14.9 1.0
OD2 B:ASP175 4.5 18.5 1.0
O B:HOH966 4.6 20.9 1.0
CB B:ASP175 4.6 16.1 1.0
CG B:ASN50 4.7 21.0 1.0
CB B:GLU140 4.7 15.1 1.0
CG B:PRO141 4.9 22.2 1.0
CB B:GLU52 5.0 14.5 1.0
CA B:GLU140 5.0 15.7 1.0

Magnesium binding site 3 out of 4 in 7vb6

Go back to Magnesium Binding Sites List in 7vb6
Magnesium binding site 3 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile


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 Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg504

b:31.9
occ:1.00
 O C:HOH708 1.9 30.3 1.0
OE1 C:GLU140 2.1 28.2 1.0
O C:HOH704 2.1 27.2 1.0
O C:HOH710 2.2 32.4 1.0
OE2 C:GLU52 2.2 28.9 1.0
O C:HOH754 2.2 33.8 1.0
CD C:GLU52 3.1 31.8 1.0
CD C:GLU140 3.1 29.6 1.0
CG C:GLU52 3.4 30.4 1.0
OE2 C:GLU140 3.6 33.5 1.0
O C:HOH807 4.0 35.8 1.0
OD1 C:ASN50 4.0 38.8 1.0
OE1 C:GLU52 4.2 32.3 1.0
CD C:PRO141 4.2 36.4 1.0
ND2 C:ASN50 4.3 34.6 1.0
NH2 C:ARG146 4.4 29.8 1.0
CG C:GLU140 4.4 31.7 1.0
O C:HOH607 4.4 28.6 1.0
O C:HOH756 4.4 33.2 1.0
OD2 C:ASP175 4.5 30.0 1.0
CB C:ASP175 4.5 30.5 1.0
O C:HOH799 4.6 36.3 1.0
CG C:ASN50 4.6 34.5 1.0
CB C:GLU140 4.7 31.2 1.0
CB C:GLU52 4.9 30.9 1.0
CA C:ASP175 4.9 27.3 1.0
CA C:GLU140 5.0 34.6 1.0

Magnesium binding site 4 out of 4 in 7vb6

Go back to Magnesium Binding Sites List in 7vb6
Magnesium binding site 4 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile


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 Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg504

b:34.7
occ:1.00
 OE1 D:GLU140 1.9 37.7 1.0
O D:HOH788 1.9 25.3 1.0
O D:HOH648 2.1 31.4 1.0
O D:HOH649 2.2 37.5 1.0
OE2 D:GLU52 2.2 35.6 1.0
O D:HOH796 2.2 38.1 1.0
CD D:GLU140 2.9 38.2 1.0
CD D:GLU52 3.1 33.8 1.0
OE2 D:GLU140 3.3 34.6 1.0
CG D:GLU52 3.4 30.1 1.0
CG D:GLU140 4.2 38.9 1.0
CD D:PRO141 4.2 37.9 1.0
OE1 D:GLU52 4.2 35.2 1.0
ND2 D:ASN50 4.3 39.5 1.0
NH2 D:ARG146 4.3 39.1 1.0
OD1 D:ASN50 4.4 42.6 1.0
O D:HOH818 4.4 32.2 1.0
CB D:GLU140 4.5 39.0 1.0
O D:HOH660 4.5 29.3 1.0
OD2 D:ASP175 4.6 32.8 1.0
CB D:ASP175 4.7 26.3 1.0
CA D:GLU140 4.7 35.7 1.0
CG D:ASN50 4.8 38.8 1.0
CB D:GLU52 4.9 32.9 1.0
CG D:PRO141 5.0 38.0 1.0

Reference:

D.Zheng, M.Nakabayashi, Y.Asano. Structural Characterization of Linum Usitatissimum Hydroxynitrile Lyase: A New Cyanohydrin Decomposition Mechanism Involving A Cyano-Zinc Complex. J.Biol.Chem. V. 298 01650 2022.
ISSN: ESSN 1083-351X
PubMed: 35101448
DOI: 10.1016/J.JBC.2022.101650
Page generated: Thu Aug 14 16:54:42 2025

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