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

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

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

Protein crystallography data

The structure of Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with Imidazole, PDB code: 5vlb 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) 38.52 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.752, 142.814, 105.357, 90.00, 120.16, 90.00
R / Rfree (%) 18.1 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Medicago Truncatula L-Histidinol Dehydrogenase in Complex with Imidazole (pdb code 5vlb). 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 Imidazole, PDB code: 5vlb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:31.9
occ:1.00
 OD2 A:ASP401 2.1 29.1 1.0
N1 A:IMD502 2.1 31.9 1.0
NE2 B:HIS460 2.1 29.7 1.0
NE2 A:HIS302 2.1 31.6 1.0
O A:HOH636 2.2 26.9 1.0
O A:HOH618 2.2 28.4 1.0
CG A:ASP401 2.9 28.7 1.0
C2 A:IMD502 2.9 31.5 1.0
CE1 A:HIS302 2.9 32.6 1.0
CE1 B:HIS460 3.0 28.8 1.0
CD2 B:HIS460 3.1 29.1 1.0
C5 A:IMD502 3.1 32.6 1.0
CD2 A:HIS302 3.2 31.8 1.0
OD1 A:ASP401 3.5 27.2 1.0
O A:HOH620 3.6 34.3 1.0
CB A:ASP401 4.0 27.4 1.0
N3 A:IMD502 4.1 31.6 1.0
ND1 A:HIS302 4.1 32.4 1.0
O A:HOH712 4.2 44.1 1.0
ND1 B:HIS460 4.2 28.9 1.0
OE2 A:GLU397 4.2 39.4 1.0
C4 A:IMD502 4.2 32.0 1.0
CG B:HIS460 4.2 29.1 1.0
CG A:HIS302 4.3 32.1 1.0
O A:SER298 4.8 37.6 1.0
CD A:GLU397 4.8 35.8 1.0

Zinc binding site 2 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:32.2
occ:1.00
 OD2 B:ASP401 2.0 30.5 1.0
NE2 B:HIS302 2.1 29.3 1.0
N1 A:IMD505 2.1 31.9 1.0
NE2 A:HIS460 2.1 29.8 1.0
O B:HOH642 2.2 30.4 1.0
O B:HOH656 2.2 26.0 1.0
CE1 B:HIS302 2.9 28.9 1.0
C2 A:IMD505 2.9 30.2 1.0
CG B:ASP401 2.9 30.0 1.0
CE1 A:HIS460 3.0 29.5 1.0
CD2 A:HIS460 3.1 29.2 1.0
CD2 B:HIS302 3.2 28.8 1.0
C5 A:IMD505 3.3 30.9 1.0
OD1 B:ASP401 3.5 30.7 1.0
CB B:ASP401 4.0 28.3 1.0
ND1 B:HIS302 4.0 29.4 1.0
N3 A:IMD505 4.1 28.8 1.0
ND1 A:HIS460 4.2 31.0 1.0
CG A:HIS460 4.2 30.3 1.0
CG B:HIS302 4.3 28.8 1.0
C4 A:IMD505 4.3 29.9 1.0
OE2 B:GLU397 4.3 34.8 1.0
O B:SER298 4.7 33.1 1.0
CD B:GLU397 4.9 32.4 1.0

Zinc binding site 3 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:46.7
occ:1.00
 OD2 C:ASP401 2.0 45.2 1.0
N1 C:IMD502 2.1 43.2 1.0
NE2 D:HIS460 2.1 50.7 1.0
NE2 C:HIS302 2.1 45.7 1.0
O D:HOH621 2.2 40.5 1.0
CG C:ASP401 2.8 42.4 1.0
C2 C:IMD502 2.9 43.8 1.0
CE1 C:HIS302 3.0 46.5 1.0
CE1 D:HIS460 3.0 50.0 1.0
CD2 D:HIS460 3.1 51.0 1.0
C5 C:IMD502 3.2 42.9 1.0
CD2 C:HIS302 3.2 45.6 1.0
OD1 C:ASP401 3.3 43.5 1.0
CB C:ASP401 3.9 39.8 1.0
N3 C:IMD502 4.1 43.2 1.0
ND1 C:HIS302 4.1 45.9 1.0
ND1 D:HIS460 4.2 51.0 1.0
OE2 C:GLU397 4.2 45.8 1.0
C4 C:IMD502 4.2 42.9 1.0
CG D:HIS460 4.2 51.5 1.0
CG C:HIS302 4.3 45.8 1.0
O C:SER298 4.7 48.3 1.0
CD C:GLU397 4.8 44.4 1.0
CG C:GLU397 5.0 42.3 1.0

Zinc binding site 4 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn504

b:49.8
occ:1.00
 OD2 D:ASP401 2.0 42.9 1.0
NE2 D:HIS302 2.1 48.1 1.0
N1 C:IMD505 2.1 48.6 1.0
NE2 C:HIS460 2.1 47.8 1.0
O C:HOH640 2.2 38.0 1.0
C2 C:IMD505 2.8 46.3 1.0
CE1 D:HIS302 3.0 47.6 1.0
CG D:ASP401 3.0 42.7 1.0
CE1 C:HIS460 3.0 47.4 1.0
CD2 C:HIS460 3.1 48.2 1.0
CD2 D:HIS302 3.1 47.7 1.0
C5 C:IMD505 3.2 47.6 1.0
OD1 D:ASP401 3.6 43.4 1.0
N3 C:IMD505 4.0 47.1 1.0
CB D:ASP401 4.1 42.1 1.0
ND1 D:HIS302 4.1 47.8 1.0
ND1 C:HIS460 4.2 51.0 1.0
C4 C:IMD505 4.2 46.8 1.0
CG D:HIS302 4.2 47.8 1.0
CG C:HIS460 4.2 49.2 1.0
OE2 D:GLU397 4.4 54.5 1.0
O D:SER298 4.8 46.5 1.0
CD D:GLU397 4.9 52.2 1.0

Zinc binding site 5 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:38.0
occ:1.00
 OD2 E:ASP401 2.0 33.9 1.0
NE2 F:HIS460 2.1 34.2 1.0
NE2 E:HIS302 2.1 37.2 1.0
N1 E:IMD502 2.1 36.5 1.0
O E:HOH615 2.2 35.5 1.0
O E:HOH625 2.2 31.2 1.0
CE1 E:HIS302 2.9 37.7 1.0
C2 E:IMD502 3.0 36.2 1.0
CG E:ASP401 3.0 32.4 1.0
CE1 F:HIS460 3.1 34.2 1.0
CD2 F:HIS460 3.1 34.5 1.0
C5 E:IMD502 3.2 36.3 1.0
CD2 E:HIS302 3.2 37.9 1.0
OD1 E:ASP401 3.6 33.0 1.0
CB E:ASP401 4.0 32.2 1.0
ND1 E:HIS302 4.1 37.9 1.0
OE2 E:GLU397 4.1 46.3 1.0
N3 E:IMD502 4.2 35.6 1.0
ND1 F:HIS460 4.2 35.2 1.0
CG F:HIS460 4.2 35.0 1.0
C4 E:IMD502 4.3 36.6 1.0
CG E:HIS302 4.3 38.6 1.0
O E:SER298 4.7 40.4 1.0
CD E:GLU397 4.8 41.2 1.0

Zinc binding site 6 out of 6 in 5vlb

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


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 Imidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn504

b:36.9
occ:1.00
 OD2 F:ASP401 2.0 33.7 1.0
N1 E:IMD505 2.1 34.9 1.0
NE2 E:HIS460 2.1 33.4 1.0
NE2 F:HIS302 2.1 34.5 1.0
O F:HOH639 2.2 36.3 1.0
O F:HOH631 2.2 33.9 1.0
CE1 F:HIS302 2.9 35.0 1.0
C2 E:IMD505 3.0 34.7 1.0
CG F:ASP401 3.0 31.8 1.0
CE1 E:HIS460 3.0 33.0 1.0
CD2 E:HIS460 3.1 32.4 1.0
C5 E:IMD505 3.2 35.5 1.0
CD2 F:HIS302 3.2 35.1 1.0
OD1 F:ASP401 3.5 35.5 1.0
CB F:ASP401 4.1 30.9 1.0
ND1 F:HIS302 4.1 36.1 1.0
N3 E:IMD505 4.1 35.2 1.0
ND1 E:HIS460 4.2 33.7 1.0
OE2 F:GLU397 4.2 37.9 1.0
CG E:HIS460 4.2 32.9 1.0
C4 E:IMD505 4.3 36.0 1.0
CG F:HIS302 4.3 37.5 1.0
CD F:GLU397 4.8 36.8 1.0
O F:SER298 5.0 36.2 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: Wed Dec 16 11:11:01 2020

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