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Magnesium in PDB 7vb3: Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum

Enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum

All present enzymatic activity of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum:
4.1.2.46;

Protein crystallography data

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum, PDB code: 7vb3 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) 84.07 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 94.12, 52.18, 168.51, 90, 95.01, 90
R / Rfree (%) 15.6 / 18.3

Other elements in 7vb3:

The structure of Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum 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 Usitatissimum (pdb code 7vb3). 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 Usitatissimum, PDB code: 7vb3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7vb3

Go back to Magnesium Binding Sites List in 7vb3
Magnesium binding site 1 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum


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 Usitatissimum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg508

b:9.9
occ:1.00
 O A:HOH800 2.0 12.2 1.0
OE1 A:GLU140 2.0 12.5 1.0
OE2 A:GLU52 2.1 12.9 1.0
O A:HOH819 2.1 15.2 1.0
O A:HOH742 2.1 13.1 1.0
O A:HOH912 2.2 12.7 1.0
CD A:GLU52 3.0 12.1 1.0
CD A:GLU140 3.1 12.8 1.0
CG A:GLU52 3.4 12.3 1.0
OE2 A:GLU140 3.4 13.8 1.0
ND2 A:ASN50 4.1 15.8 1.0
OD1 A:ASN50 4.1 14.8 1.0
NH2 A:ARG146 4.1 15.7 1.0
CD A:PRO141 4.1 15.1 1.0
OE1 A:GLU52 4.2 13.3 1.0
O A:HOH741 4.3 12.7 1.0
O A:HOH919 4.3 16.0 1.0
O A:HOH1019 4.3 21.3 1.0
CG A:GLU140 4.4 12.9 1.0
OD2 A:ASP175 4.4 14.2 1.0
O A:HOH1008 4.5 16.6 1.0
CB A:ASP175 4.6 11.8 1.0
CG A:ASN50 4.6 14.3 1.0
CB A:GLU140 4.7 13.0 1.0
CG A:PRO141 4.8 17.1 1.0
CB A:GLU52 4.9 11.8 1.0
CA A:ASP175 5.0 11.0 1.0
CA A:GLU140 5.0 12.0 1.0

Magnesium binding site 2 out of 4 in 7vb3

Go back to Magnesium Binding Sites List in 7vb3
Magnesium binding site 2 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum


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 Usitatissimum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg508

b:10.8
occ:1.00
 OE1 B:GLU140 2.0 15.1 1.0
O B:HOH709 2.1 14.7 1.0
O B:HOH787 2.1 13.9 1.0
O B:HOH851 2.1 13.5 1.0
OE2 B:GLU52 2.1 14.6 1.0
O B:HOH899 2.2 15.1 1.0
CD B:GLU140 3.1 15.3 1.0
CD B:GLU52 3.1 12.9 1.0
CG B:GLU52 3.4 13.0 1.0
OE2 B:GLU140 3.4 15.3 1.0
OD1 B:ASN50 4.1 15.4 1.0
CD B:PRO141 4.2 17.1 1.0
ND2 B:ASN50 4.2 17.6 1.0
OE1 B:GLU52 4.2 13.4 1.0
NH2 B:ARG146 4.2 16.2 1.0
O B:HOH929 4.3 18.3 1.0
O B:HOH663 4.3 12.9 1.0
O B:HOH994 4.4 24.4 1.0
CG B:GLU140 4.4 15.3 1.0
OD2 B:ASP175 4.5 17.5 1.0
O B:HOH847 4.5 32.1 1.0
O B:HOH972 4.5 19.7 1.0
CG B:ASN50 4.6 15.4 1.0
CB B:ASP175 4.6 11.5 1.0
CB B:GLU140 4.7 15.0 1.0
CG B:PRO141 4.9 19.8 1.0
CB B:GLU52 4.9 13.8 1.0
CA B:GLU140 5.0 15.0 1.0
N B:ASP175 5.0 11.2 1.0
CA B:ASP175 5.0 11.3 1.0

Magnesium binding site 3 out of 4 in 7vb3

Go back to Magnesium Binding Sites List in 7vb3
Magnesium binding site 3 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum


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 Usitatissimum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg505

b:17.4
occ:1.00
 OE1 C:GLU140 2.0 21.2 1.0
O C:HOH713 2.0 21.4 1.0
O C:HOH641 2.1 22.6 1.0
O C:HOH707 2.1 26.4 1.0
O C:HOH861 2.2 20.9 1.0
OE2 C:GLU52 2.2 24.6 1.0
CD C:GLU140 3.0 22.1 1.0
CD C:GLU52 3.1 26.3 1.0
OE2 C:GLU140 3.4 21.7 1.0
CG C:GLU52 3.4 24.6 1.0
OD1 C:ASN50 4.1 23.0 1.0
ND2 C:ASN50 4.1 22.5 1.0
CD C:PRO141 4.2 26.0 1.0
OE1 C:GLU52 4.2 26.3 1.0
O C:HOH896 4.2 34.9 1.0
NH2 C:ARG146 4.3 23.5 1.0
O C:HOH856 4.3 26.9 1.0
CG C:GLU140 4.3 23.0 1.0
O C:HOH899 4.4 33.1 1.0
OD2 C:ASP175 4.4 22.8 1.0
O C:HOH668 4.4 20.4 1.0
CG C:ASN50 4.6 22.1 1.0
CB C:ASP175 4.6 21.7 1.0
CB C:GLU140 4.7 23.4 1.0
CG C:PRO141 4.9 29.5 1.0
CB C:GLU52 4.9 22.7 1.0
CA C:GLU140 5.0 24.5 1.0
CG C:ASP175 5.0 21.4 1.0

Magnesium binding site 4 out of 4 in 7vb3

Go back to Magnesium Binding Sites List in 7vb3
Magnesium binding site 4 out of 4 in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissimum


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 Usitatissimum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg506

b:16.7
occ:1.00
 OE1 D:GLU140 2.0 25.0 1.0
OE2 D:GLU52 2.1 20.4 1.0
O D:HOH721 2.1 21.6 1.0
O D:HOH763 2.1 20.7 1.0
O D:HOH726 2.2 19.8 1.0
O D:HOH805 2.2 24.3 1.0
CD D:GLU140 3.0 27.5 1.0
CD D:GLU52 3.0 18.4 1.0
OE2 D:GLU140 3.4 23.3 1.0
CG D:GLU52 3.4 20.3 1.0
ND2 D:ASN50 4.1 25.0 1.0
OD1 D:ASN50 4.2 23.5 1.0
OE1 D:GLU52 4.2 18.7 1.0
CD D:PRO141 4.2 25.1 1.0
NH2 D:ARG146 4.2 25.6 1.0
O D:HOH893 4.3 28.2 1.0
O D:HOH919 4.3 28.0 1.0
CG D:GLU140 4.3 24.1 1.0
O1 D:GOL505 4.3 34.6 1.0
O D:HOH663 4.3 19.1 1.0
OD2 D:ASP175 4.4 22.5 1.0
CB D:ASP175 4.5 17.7 1.0
CG D:ASN50 4.6 22.8 1.0
CB D:GLU140 4.7 24.6 1.0
C1 D:GOL505 4.8 41.8 1.0
CB D:GLU52 4.9 19.2 1.0
CA D:ASP175 4.9 17.3 1.0
CA D:GLU140 4.9 22.3 1.0
N D:ASP175 5.0 19.1 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 16:53:52 2025

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