Calcium in PDB 8gxd: L-Leucine Dehydrogenase From Exiguobacterium Sibiricum

All present enzymatic activity of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum:
1.4.1.9;

The structure of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum, PDB code: 8gxd was solved by X.Mu, Y.Nie, T.Wu, Y.Wang, N.Zhang, D.Yin, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.62 / 3.02
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	152.99, 152.99, 132.02, 90, 90, 90
R / Rfree (%)	21.3 / 25.5

The binding sites of Calcium atom in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum (pdb code 8gxd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum, PDB code: 8gxd:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:30.8 occ:1.00 OD1 A:ASP29 3.4 37.4 1.0 N A:LYS30 3.9 39.4 1.0 CA A:ASP29 4.0 38.3 1.0 O A:HIS28 4.1 35.6 1.0 CG A:ASP29 4.3 37.0 1.0 OH A:TYR111 4.5 24.9 1.0 C A:ASP29 4.5 37.9 1.0 CB A:ASP29 4.6 37.6 1.0 CB A:LYS30 4.8 42.8 1.0 C A:HIS28 4.9 36.1 1.0 N A:ASP29 4.9 37.8 1.0

Calcium binding site 2 out of 4 in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:51.8 occ:1.00 CE1 A:HIS28 3.6 36.6 1.0 O A:LYS30 3.7 39.6 1.0 CA A:GLY33 4.1 36.7 1.0 CA A:LYS30 4.3 41.4 1.0 NE2 A:HIS28 4.4 38.0 1.0 C A:LYS30 4.5 40.6 1.0 ND1 A:HIS28 4.5 36.3 1.0 O A:ASP29 4.7 36.1 1.0 N A:GLY33 4.8 35.7 1.0 CG A:LYS30 5.0 44.8 1.0

Calcium binding site 3 out of 4 in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:57.7 occ:1.00 NZ A:LYS77 3.5 40.1 1.0 OD1 A:ASN270 3.6 50.3 1.0 ND2 A:ASN270 3.6 51.1 1.0 CG A:ASN270 4.1 49.1 1.0 O A:ASN296 4.1 38.6 1.0 CE A:LYS77 4.2 40.6 1.0 OD1 A:ASN296 4.2 34.5 1.0 CG A:ASN296 4.7 32.9 1.0 O A:HOH530 4.8 24.4 1.0 CA A:GLY299 5.0 42.1 1.0

Calcium binding site 4 out of 4 in the L-Leucine Dehydrogenase From Exiguobacterium Sibiricum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of L-Leucine Dehydrogenase From Exiguobacterium Sibiricum within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:44.5 occ:1.00 O A:HOH510 3.8 20.7 1.0 O3 A:GOL402 4.0 62.5 1.0 CE2 A:PHE293 4.2 39.0 1.0 CD2 A:PHE293 4.2 38.7 1.0 CD1 A:TYR76 4.2 34.8 1.0 CA A:GLY73 4.3 32.1 1.0 OE2 A:GLU345 4.3 42.7 1.0 CG A:TYR76 4.5 34.3 1.0 CB A:TYR76 4.7 34.3 1.0 CE1 A:TYR76 4.8 35.1 1.0 N A:GLY73 4.9 31.2 1.0 O A:LYS72 4.9 31.0 1.0 O A:GLY73 5.0 31.9 1.0

T.Wu, Y.Wang, N.Zhang, D.Yin, Y.Xu, Y.Nie, X.Mu. Reshaping Substrate-Binding Pocket of Leucine Dehydrogenase For Bidirectionally Accessing Structurally Diverse Substrates Acs Catalysis V. 13 158 2023.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.2C04735