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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Hydroxynitrile Lyase From Linum Usitatissium Complexed with (R)-2-Hydroxy-2-Methylbutanenitrile, PDB code: 7vb6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7vb6

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Zinc binding site 1 out of 8 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 Zinc with other atoms in the Zn 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:Zn502

b:14.7
occ:1.00
 SG A:CYS121 2.3 14.0 1.0
SG A:CYS118 2.3 15.9 1.0
SG A:CYS115 2.4 15.2 1.0
SG A:CYS129 2.4 14.1 1.0
CB A:CYS121 3.3 16.7 1.0
CB A:CYS118 3.4 15.1 1.0
CB A:CYS129 3.4 14.3 1.0
CB A:CYS115 3.5 15.6 1.0
N A:CYS115 3.6 15.0 1.0
CA A:CYS129 3.7 13.5 1.0
N A:GLN116 3.9 17.6 1.0
CA A:CYS115 3.9 16.3 1.0
N A:CYS118 3.9 15.8 1.0
N A:GLN130 3.9 13.5 1.0
N A:CYS121 4.2 13.5 1.0
CA A:CYS118 4.2 15.2 1.0
C A:CYS129 4.2 13.7 1.0
C A:CYS115 4.3 17.5 1.0
CA A:CYS121 4.3 14.6 1.0
N A:THR117 4.5 17.4 1.0
N A:ASN131 4.6 15.4 1.0
C A:GLU114 4.6 14.8 1.0
OD1 A:ASN131 4.6 19.5 1.0
O A:HOH934 4.7 18.2 1.0
CA A:GLN116 4.8 20.1 1.0
O A:CYS118 4.8 14.8 1.0
C A:CYS118 4.9 14.1 1.0
CB A:ASN131 4.9 15.9 1.0
CA A:GLU114 4.9 14.7 1.0
N A:CYS129 5.0 12.6 1.0

Zinc binding site 2 out of 8 in 7vb6

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Zinc binding site 2 out of 8 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 Zinc with other atoms in the Zn 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
A:Zn503

b:14.6
occ:0.98
 NE2 A:HIS85 2.0 12.1 1.0
N1 A:5Z9505 2.2 14.3 1.0
SG A:CYS199 2.3 13.3 1.0
SG A:CYS63 2.3 12.8 1.0
CD2 A:HIS85 3.0 10.5 1.0
CE1 A:HIS85 3.0 14.1 1.0
CB A:CYS63 3.2 11.1 1.0
C5 A:5Z9505 3.3 14.9 1.0
C5N A:NAD501 3.5 12.3 1.0
CB A:CYS199 3.5 13.5 1.0
C4N A:NAD501 3.6 11.4 1.0
C6N A:NAD501 4.0 12.1 1.0
ND1 A:HIS85 4.1 12.0 1.0
CG A:HIS85 4.2 11.5 1.0
CB A:THR65 4.3 10.9 1.0
OE2 A:GLU86 4.3 15.2 1.0
O A:HOH804 4.3 15.5 1.0
C3N A:NAD501 4.4 12.3 1.0
OG1 A:THR65 4.5 11.4 1.0
CA A:CYS63 4.6 11.2 1.0
C3 A:5Z9505 4.7 14.4 1.0
N1N A:NAD501 4.7 12.3 1.0
O A:HOH689 4.8 13.8 1.0
CA A:CYS199 4.8 12.6 1.0
C2N A:NAD501 4.9 11.8 1.0

Zinc binding site 3 out of 8 in 7vb6

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Zinc binding site 3 out of 8 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 Zinc with other atoms in the Zn 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
B:Zn502

b:15.9
occ:1.00
 SG B:CYS115 2.3 17.1 1.0
SG B:CYS121 2.3 17.2 1.0
SG B:CYS118 2.4 15.4 1.0
SG B:CYS129 2.4 16.6 1.0
CB B:CYS129 3.3 15.4 1.0
CB B:CYS121 3.4 15.3 1.0
CB B:CYS118 3.4 15.5 1.0
CB B:CYS115 3.4 18.3 1.0
N B:CYS115 3.5 17.6 1.0
CA B:CYS129 3.7 15.6 1.0
CA B:CYS115 3.8 17.5 1.0
N B:GLN130 3.9 15.6 1.0
N B:CYS118 3.9 18.4 1.0
N B:GLN116 4.0 19.1 1.0
CA B:CYS118 4.2 17.5 1.0
C B:CYS129 4.2 14.6 1.0
C B:CYS115 4.3 18.7 1.0
N B:CYS121 4.3 15.5 1.0
CA B:CYS121 4.4 16.9 1.0
N B:ASN131 4.5 18.2 1.0
OD1 B:ASN131 4.5 23.3 1.0
C B:GLU114 4.6 16.6 1.0
O B:HOH928 4.6 22.1 1.0
N B:THR117 4.6 21.5 1.0
CB B:ASN131 4.8 20.8 1.0
CA B:GLU114 4.9 15.0 1.0
C B:CYS118 4.9 15.5 1.0
O B:CYS118 4.9 14.9 1.0
CA B:GLN116 5.0 22.8 1.0

Zinc binding site 4 out of 8 in 7vb6

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Zinc binding site 4 out of 8 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 Zinc with other atoms in the Zn 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
B:Zn503

b:12.8
occ:0.91
 NE2 B:HIS85 2.1 14.1 1.0
N1 B:5Z9505 2.2 11.9 1.0
SG B:CYS199 2.3 13.1 1.0
SG B:CYS63 2.3 12.5 1.0
CD2 B:HIS85 3.0 12.8 1.0
CE1 B:HIS85 3.1 13.8 1.0
CB B:CYS63 3.2 12.3 1.0
C5 B:5Z9505 3.3 14.8 1.0
C5N B:NAD501 3.5 11.4 1.0
CB B:CYS199 3.5 11.9 1.0
C4N B:NAD501 3.6 11.1 1.0
C6N B:NAD501 4.0 11.7 1.0
CG B:HIS85 4.2 12.3 1.0
ND1 B:HIS85 4.2 12.7 1.0
OE2 B:GLU86 4.3 14.3 1.0
CB B:THR65 4.3 12.5 1.0
O B:HOH715 4.4 14.9 1.0
C3N B:NAD501 4.5 11.6 1.0
OG1 B:THR65 4.6 13.7 1.0
CA B:CYS63 4.6 11.9 1.0
C3 B:5Z9505 4.7 15.6 1.0
N1N B:NAD501 4.8 11.8 1.0
O B:HOH639 4.8 11.4 1.0
CA B:CYS199 4.8 12.4 1.0
C2N B:NAD501 4.9 11.1 1.0

Zinc binding site 5 out of 8 in 7vb6

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Zinc binding site 5 out of 8 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 Zinc with other atoms in the Zn binding site number 5 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:Zn502

b:23.5
occ:1.00
 SG C:CYS121 2.3 23.1 1.0
SG C:CYS129 2.3 23.2 1.0
SG C:CYS115 2.3 28.4 1.0
SG C:CYS118 2.4 21.8 1.0
CB C:CYS121 3.3 23.3 1.0
CB C:CYS129 3.4 22.2 1.0
CB C:CYS118 3.4 23.7 1.0
CB C:CYS115 3.4 29.0 1.0
N C:CYS115 3.5 27.8 1.0
CA C:CYS129 3.7 21.3 1.0
CA C:CYS115 3.9 26.7 1.0
N C:CYS118 3.9 29.9 1.0
N C:GLN116 3.9 30.4 1.0
N C:GLN130 4.0 20.8 1.0
N C:CYS121 4.2 22.1 1.0
CA C:CYS118 4.2 25.7 1.0
C C:CYS129 4.2 20.3 1.0
C C:CYS115 4.3 30.7 1.0
CA C:CYS121 4.3 22.9 1.0
N C:ASN131 4.5 27.7 1.0
OD1 C:ASN131 4.6 33.1 1.0
C C:GLU114 4.6 27.4 1.0
N C:THR117 4.6 31.9 1.0
O C:HOH778 4.6 26.4 1.0
CB C:ASN131 4.8 29.1 1.0
CA C:GLU114 4.9 25.1 1.0
C C:CYS118 4.9 27.8 1.0
CA C:GLN116 4.9 33.2 1.0
O C:CYS118 5.0 24.9 1.0
N C:CYS129 5.0 20.1 1.0

Zinc binding site 6 out of 8 in 7vb6

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Zinc binding site 6 out of 8 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 Zinc with other atoms in the Zn binding site number 6 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:Zn503

b:23.1
occ:1.00
 NE2 C:HIS85 2.0 19.5 1.0
SG C:CYS63 2.3 22.5 1.0
SG C:CYS199 2.3 22.1 1.0
N1 C:5Z9505 2.4 19.2 1.0
CE1 C:HIS85 2.9 21.8 1.0
CD2 C:HIS85 3.0 21.1 1.0
CB C:CYS63 3.2 22.5 1.0
C5 C:5Z9505 3.4 22.7 1.0
CB C:CYS199 3.5 22.4 1.0
C5N C:NAD501 3.5 19.1 1.0
C4N C:NAD501 3.7 19.4 1.0
C6N C:NAD501 4.0 20.8 1.0
ND1 C:HIS85 4.1 20.8 1.0
CG C:HIS85 4.1 18.9 1.0
CB C:THR65 4.2 23.4 1.0
O C:HOH713 4.3 20.3 1.0
OE2 C:GLU86 4.4 24.5 1.0
C3N C:NAD501 4.5 19.1 1.0
OG1 C:THR65 4.6 20.1 1.0
CA C:CYS63 4.6 21.0 1.0
N1N C:NAD501 4.7 20.3 1.0
O C:HOH670 4.7 23.0 1.0
C3 C:5Z9505 4.8 23.4 1.0
CA C:CYS199 4.8 21.0 1.0
C2N C:NAD501 4.8 17.5 1.0
CG2 C:THR65 4.9 22.8 1.0

Zinc binding site 7 out of 8 in 7vb6

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Zinc binding site 7 out of 8 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 Zinc with other atoms in the Zn binding site number 7 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:Zn502

b:21.9
occ:0.85
 SG D:CYS121 2.2 27.0 1.0
SG D:CYS129 2.2 26.2 1.0
SG D:CYS115 2.3 25.2 1.0
SG D:CYS118 2.3 26.5 1.0
CB D:CYS129 3.2 26.4 1.0
CB D:CYS115 3.4 27.6 1.0
CB D:CYS121 3.4 28.1 1.0
CB D:CYS118 3.4 27.8 1.0
N D:CYS115 3.5 26.6 1.0
CA D:CYS129 3.6 23.9 1.0
CA D:CYS115 3.8 28.1 1.0
N D:GLN130 3.8 28.3 1.0
N D:GLN116 3.9 30.7 1.0
N D:CYS118 4.0 33.0 1.0
C D:CYS129 4.2 26.1 1.0
CA D:CYS118 4.2 27.6 1.0
C D:CYS115 4.3 29.4 1.0
N D:CYS121 4.3 26.3 1.0
CA D:CYS121 4.4 29.0 1.0
OD1 D:ASN131 4.5 33.0 1.0
N D:ASN131 4.5 31.4 1.0
C D:GLU114 4.6 25.8 1.0
N D:THR117 4.7 32.3 1.0
O D:HOH746 4.8 30.2 1.0
CA D:GLU114 4.9 26.1 1.0
C D:CYS118 4.9 26.7 1.0
CB D:ASN131 4.9 33.7 1.0
O D:CYS118 4.9 27.3 1.0
N D:CYS129 4.9 22.4 1.0
CA D:GLN116 5.0 31.7 1.0
CA D:GLN130 5.0 29.4 1.0

Zinc binding site 8 out of 8 in 7vb6

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Zinc binding site 8 out of 8 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 Zinc with other atoms in the Zn binding site number 8 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:Zn503

b:23.7
occ:1.00
 NE2 D:HIS85 2.1 18.9 1.0
SG D:CYS199 2.2 21.5 1.0
SG D:CYS63 2.3 22.7 1.0
N1 D:5Z9505 2.3 21.1 1.0
CE1 D:HIS85 3.0 21.1 1.0
CD2 D:HIS85 3.1 22.1 1.0
CB D:CYS63 3.2 23.6 1.0
C5 D:5Z9505 3.3 27.3 1.0
C5N D:NAD501 3.4 21.0 1.0
CB D:CYS199 3.5 19.3 1.0
C4N D:NAD501 3.6 19.5 1.0
C6N D:NAD501 3.9 19.2 1.0
ND1 D:HIS85 4.1 21.7 1.0
CB D:THR65 4.2 21.9 1.0
CG D:HIS85 4.2 22.0 1.0
O D:HOH750 4.3 19.5 1.0
OE2 D:GLU86 4.4 23.2 1.0
OG1 D:THR65 4.4 22.9 1.0
C3N D:NAD501 4.5 20.0 1.0
CA D:CYS63 4.6 22.9 1.0
O D:HOH647 4.7 16.7 1.0
N1N D:NAD501 4.7 18.9 1.0
C3 D:5Z9505 4.8 24.8 1.0
CA D:CYS199 4.8 18.6 1.0
C2N D:NAD501 4.8 18.4 1.0
CG2 D:THR65 4.9 23.1 1.0
C1 D:5Z9505 5.0 27.7 1.0
N D:ALA200 5.0 19.5 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: Wed Oct 30 12:37:17 2024

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