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Zinc in PDB 5vlc: Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol

Enzymatic activity of Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol

All present enzymatic activity of Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol:
1.1.1.23;

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol, PDB code: 5vlc was solved by M.Ruszkowski, Z.Dauter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 102.859, 139.201, 102.692, 90.00, 119.18, 90.00
R / Rfree (%) 17.9 / 22.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol (pdb code 5vlc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol, PDB code: 5vlc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5vlc

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Zinc binding site 1 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:30.2
occ:1.00
 OD2 B:ASP401 2.0 25.5 1.0
ND1 B:HSO502 2.1 29.0 1.0
OE1 B:GLN299 2.1 28.6 1.0
N B:HSO502 2.1 28.9 1.0
NE2 B:HIS302 2.1 29.8 1.0
NE2 A:HIS460 2.1 28.6 1.0
CD B:GLN299 3.0 30.0 1.0
CG B:ASP401 3.0 28.5 1.0
CG B:HSO502 3.0 29.5 1.0
CE1 B:HIS302 3.0 31.4 1.0
CE1 B:HSO502 3.1 29.7 1.0
CE1 A:HIS460 3.1 28.9 1.0
CD2 A:HIS460 3.1 28.5 1.0
CA B:HSO502 3.1 30.2 1.0
CD2 B:HIS302 3.1 30.8 1.0
NE2 B:GLN299 3.3 31.7 1.0
CB B:HSO502 3.4 29.6 1.0
OD1 B:ASP401 3.7 27.8 1.0
CB B:ASP401 4.0 28.3 1.0
OE2 B:GLU397 4.0 31.1 1.0
CD2 B:HSO502 4.2 29.4 1.0
ND1 B:HIS302 4.2 32.7 1.0
NE2 B:HSO502 4.2 30.0 1.0
ND1 A:HIS460 4.2 29.9 1.0
CG A:HIS460 4.3 29.6 1.0
CG B:HIS302 4.3 32.7 1.0
CG B:GLN299 4.5 30.1 1.0
C B:HSO502 4.6 30.4 1.0
OG B:SER277 4.6 44.6 1.0
O B:SER298 4.9 31.9 1.0

Zinc binding site 2 out of 6 in 5vlc

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Zinc binding site 2 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:26.0
occ:1.00
 OD2 A:ASP401 2.0 23.4 1.0
OE1 A:GLN299 2.1 26.4 1.0
N A:HSO501 2.1 24.9 1.0
ND1 A:HSO501 2.1 24.3 1.0
NE2 B:HIS460 2.1 24.0 1.0
NE2 A:HIS302 2.1 25.6 1.0
CG A:ASP401 3.0 25.4 1.0
CD A:GLN299 3.0 27.6 1.0
CE1 A:HSO501 3.0 24.1 1.0
CE1 B:HIS460 3.0 24.4 1.0
CE1 A:HIS302 3.0 26.8 1.0
CG A:HSO501 3.1 24.6 1.0
CD2 B:HIS460 3.1 24.1 1.0
CA A:HSO501 3.1 25.6 1.0
CD2 A:HIS302 3.2 25.8 1.0
NE2 A:GLN299 3.3 29.2 1.0
CB A:HSO501 3.5 24.8 1.0
OD1 A:ASP401 3.6 23.9 1.0
CB A:ASP401 4.0 24.7 1.0
OE2 A:GLU397 4.1 29.3 1.0
CD2 A:HSO501 4.2 24.1 1.0
ND1 B:HIS460 4.2 24.4 1.0
NE2 A:HSO501 4.2 25.1 1.0
ND1 A:HIS302 4.2 27.4 1.0
CG B:HIS460 4.2 24.9 1.0
CG A:HIS302 4.3 26.7 1.0
CG A:GLN299 4.5 26.7 1.0
C A:HSO501 4.5 26.4 1.0
O A:SER298 4.9 30.3 1.0
O A:HSO501 5.0 30.5 1.0
CD A:GLU397 5.0 29.1 1.0

Zinc binding site 3 out of 6 in 5vlc

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Zinc binding site 3 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:37.4
occ:1.00
 OE1 C:GLN299 2.0 38.4 1.0
OD2 C:ASP401 2.1 35.8 1.0
N C:HSO502 2.1 35.5 1.0
ND1 C:HSO502 2.1 37.0 1.0
NE2 D:HIS460 2.1 39.6 1.0
NE2 C:HIS302 2.1 37.7 1.0
CD C:GLN299 3.0 38.9 1.0
CG C:ASP401 3.0 35.1 1.0
CE1 D:HIS460 3.0 39.7 1.0
CE1 C:HIS302 3.0 38.4 1.0
CG C:HSO502 3.1 37.0 1.0
CE1 C:HSO502 3.1 39.0 1.0
CA C:HSO502 3.1 36.0 1.0
CD2 D:HIS460 3.2 38.7 1.0
CD2 C:HIS302 3.2 39.0 1.0
NE2 C:GLN299 3.3 39.9 1.0
CB C:HSO502 3.5 36.0 1.0
OD1 C:ASP401 3.6 34.3 1.0
OE2 C:GLU397 4.0 36.5 1.0
CB C:ASP401 4.0 34.1 1.0
ND1 D:HIS460 4.1 40.7 1.0
ND1 C:HIS302 4.2 37.6 1.0
CD2 C:HSO502 4.2 36.0 1.0
NE2 C:HSO502 4.3 37.6 1.0
CG D:HIS460 4.3 40.2 1.0
CG C:HIS302 4.3 39.0 1.0
CG C:GLN299 4.4 39.7 1.0
C C:HSO502 4.5 36.4 1.0
OG C:SER277 4.6 45.6 1.0
O C:SER298 4.8 41.2 1.0
CD C:GLU397 4.9 37.0 1.0
O C:HSO502 4.9 38.1 1.0

Zinc binding site 4 out of 6 in 5vlc

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Zinc binding site 4 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:39.1
occ:1.00
 OE1 D:GLN299 2.1 39.6 1.0
OD2 D:ASP401 2.1 35.6 1.0
NE2 C:HIS460 2.1 41.4 1.0
ND1 D:HSO502 2.1 35.8 1.0
N D:HSO502 2.1 36.1 1.0
NE2 D:HIS302 2.1 42.6 1.0
CE1 C:HIS460 2.9 43.8 1.0
CG D:ASP401 3.0 35.4 1.0
CE1 D:HSO502 3.0 35.6 1.0
CE1 D:HIS302 3.0 43.6 1.0
CD D:GLN299 3.1 39.6 1.0
CG D:HSO502 3.1 36.5 1.0
CD2 D:HIS302 3.2 44.3 1.0
CD2 C:HIS460 3.2 42.3 1.0
CA D:HSO502 3.2 36.3 1.0
NE2 D:GLN299 3.4 40.9 1.0
CB D:HSO502 3.5 35.9 1.0
OD1 D:ASP401 3.6 35.5 1.0
CB D:ASP401 4.0 34.9 1.0
ND1 C:HIS460 4.1 45.4 1.0
OE2 D:GLU397 4.1 44.4 1.0
NE2 D:HSO502 4.2 35.5 1.0
ND1 D:HIS302 4.2 44.9 1.0
CD2 D:HSO502 4.2 36.0 1.0
CG C:HIS460 4.2 44.3 1.0
CG D:HIS302 4.3 45.6 1.0
CG D:GLN299 4.5 40.5 1.0
C D:HSO502 4.5 38.5 1.0
O D:SER298 4.9 44.6 1.0
OG D:SER277 4.9 53.2 1.0
CA D:GLN299 5.0 41.7 1.0

Zinc binding site 5 out of 6 in 5vlc

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Zinc binding site 5 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:45.5
occ:1.00
 OE1 E:GLN299 2.0 38.6 1.0
OD2 E:ASP401 2.1 47.0 1.0
ND1 E:HSO502 2.1 44.4 1.0
NE2 F:HIS460 2.1 49.6 1.0
N E:HSO502 2.1 44.6 1.0
NE2 E:HIS302 2.1 50.8 1.0
CE1 F:HIS460 2.9 49.4 1.0
CG E:ASP401 3.0 44.6 1.0
CE1 E:HIS302 3.0 51.3 1.0
CD E:GLN299 3.0 40.8 1.0
CG E:HSO502 3.0 45.2 1.0
CA E:HSO502 3.1 44.0 1.0
CE1 E:HSO502 3.1 44.4 1.0
CD2 E:HIS302 3.2 52.1 1.0
CD2 F:HIS460 3.3 49.6 1.0
NE2 E:GLN299 3.4 40.1 1.0
CB E:HSO502 3.5 45.1 1.0
OD1 E:ASP401 3.5 44.2 1.0
OE2 E:GLU397 4.0 41.5 1.0
CB E:ASP401 4.1 45.2 1.0
ND1 F:HIS460 4.1 50.3 1.0
ND1 E:HIS302 4.2 52.3 1.0
CD2 E:HSO502 4.2 45.9 1.0
NE2 E:HSO502 4.3 44.4 1.0
CG F:HIS460 4.3 50.0 1.0
CG E:HIS302 4.3 52.5 1.0
CG E:GLN299 4.4 41.2 1.0
C E:HSO502 4.5 45.1 1.0
O E:SER298 4.8 45.7 1.0
OG E:SER277 4.9 50.0 1.0
CD E:GLU397 4.9 41.9 1.0
CA E:GLN299 5.0 45.2 1.0

Zinc binding site 6 out of 6 in 5vlc

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Zinc binding site 6 out of 6 in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol


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 Medicago Truncatula L-Histidinol Dehydrogenase in Complex with L-Histidinol within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:46.3
occ:1.00
 OE1 F:GLN299 2.0 43.0 1.0
OD2 F:ASP401 2.0 41.3 1.0
ND1 F:HSO501 2.1 48.8 1.0
NE2 F:HIS302 2.1 46.1 1.0
N F:HSO501 2.1 47.2 1.0
NE2 E:HIS460 2.1 50.1 1.0
CD F:GLN299 3.0 43.9 1.0
CG F:ASP401 3.0 43.6 1.0
CE1 F:HIS302 3.0 47.2 1.0
CE1 E:HIS460 3.1 51.2 1.0
CE1 F:HSO501 3.1 50.4 1.0
CG F:HSO501 3.1 49.0 1.0
CA F:HSO501 3.1 48.2 1.0
CD2 F:HIS302 3.2 46.8 1.0
CD2 E:HIS460 3.2 50.0 1.0
NE2 F:GLN299 3.3 45.5 1.0
CB F:HSO501 3.5 47.0 1.0
OD1 F:ASP401 3.7 39.8 1.0
CB F:ASP401 4.0 43.0 1.0
OE2 F:GLU397 4.0 44.9 1.0
ND1 F:HIS302 4.2 46.8 1.0
CD2 F:HSO501 4.2 48.3 1.0
ND1 E:HIS460 4.2 52.0 1.0
NE2 F:HSO501 4.2 51.1 1.0
CG F:HIS302 4.3 48.4 1.0
CG E:HIS460 4.3 51.2 1.0
CG F:GLN299 4.4 44.9 1.0
C F:HSO501 4.5 48.4 1.0
CD F:GLU397 4.8 44.0 1.0
OG F:SER277 4.9 54.4 1.0
O F:SER298 4.9 51.5 1.0
CB F:GLN299 5.0 45.8 1.0

Reference:

M.Ruszkowski, Z.Dauter. Structures of Medicago Truncatula L-Histidinol Dehydrogenase Show Rearrangements Required For Nad(+) Binding and the Cofactor Positioned to Accept A Hydride. Sci Rep V. 7 10476 2017.
ISSN: ESSN 2045-2322
PubMed: 28874718
DOI: 10.1038/S41598-017-10859-0
Page generated: Mon Oct 28 13:04:03 2024

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