Calcium in PDB 4mmi: Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus

All present enzymatic activity of Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus:
4.2.2.8;

The structure of Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus, PDB code: 4mmi was solved by Y.Maruyama, Y.Nakamichi, B.Mikami, K.Murata, W.Hashimoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.94 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.674, 102.897, 149.247, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.9

The binding sites of Calcium atom in the Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus (pdb code 4mmi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus, PDB code: 4mmi:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:65.5 occ:1.00 O A:HOH801 2.3 44.4 1.0 OE1 A:GLU245 2.5 56.3 1.0 O A:HOH858 2.5 59.7 1.0 CD A:GLU245 3.3 53.0 1.0 ND1 A:HIS241 3.4 84.3 1.0 OE2 A:GLU245 3.4 52.0 1.0 CB A:HIS241 3.6 77.0 1.0 CG A:HIS241 3.7 84.6 1.0 CB A:PRO189 4.0 52.4 1.0 CB A:ALA236 4.1 55.3 1.0 N A:LEU190 4.2 51.0 1.0 CE1 A:HIS241 4.3 87.6 1.0 CG A:PRO189 4.5 52.5 1.0 CD2 A:HIS241 4.7 85.7 1.0 CD A:PRO189 4.7 51.0 1.0 CG A:GLU245 4.7 53.3 1.0 C A:PRO189 4.7 50.5 1.0 CB A:LEU190 4.8 52.1 1.0 CA A:PRO189 4.8 50.7 1.0 CA A:LEU190 4.8 51.6 1.0 N A:ALA236 4.9 55.4 1.0 CA A:ALA236 4.9 56.1 1.0 NE2 A:HIS241 5.0 90.1 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Heparan Sulfate Lyase Hepc Mutant From Pedobacter Heparinus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:38.8 occ:1.00 O A:HOH851 2.0 45.5 1.0 O A:HOH849 2.2 57.8 1.0 O A:HOH850 2.3 47.5 1.0 OD2 A:ASP444 2.3 49.9 1.0 NE2 A:HIS469 2.3 50.2 1.0 NE2 A:GLN426 2.3 49.9 1.0 CG A:ASP444 3.1 46.4 1.0 CD2 A:HIS469 3.2 52.3 1.0 OD1 A:ASP444 3.2 46.4 1.0 CD A:GLN426 3.3 53.1 1.0 CE1 A:HIS469 3.3 51.0 1.0 OE1 A:GLN426 3.5 54.7 1.0 N A:GLY446 3.9 50.2 1.0 O A:MET345 4.0 52.3 1.0 N A:GLY347 4.1 50.6 1.0 O A:GLY446 4.2 53.2 1.0 O A:TYR463 4.2 52.6 1.0 OD2 A:ASP428 4.4 46.1 1.0 CG A:HIS469 4.4 50.1 1.0 ND1 A:HIS469 4.4 50.7 1.0 CA A:GLY446 4.5 51.5 1.0 CB A:ASP444 4.5 49.9 1.0 N A:ALA445 4.5 50.3 1.0 O A:GLY347 4.5 47.1 1.0 CG A:GLN426 4.6 53.5 1.0 C A:GLY446 4.7 52.0 1.0 CA A:GLY347 4.7 49.5 1.0 CB A:ALA445 4.8 48.8 1.0 CA A:PHE346 4.9 46.8 1.0 C A:PHE346 4.9 48.0 1.0 C A:ALA445 4.9 49.2 1.0 CB A:GLN426 4.9 52.5 1.0 CA A:ALA445 5.0 51.4 1.0

W.Hashimoto, Y.Maruyama, Y.Nakamichi, B.Mikami, K.Murata. Crystal Structure of Pedobacter Heparinus Heparin Lyase Hep III with the Active Site in A Deep Cleft Biochemistry V. 53 777 2014.
ISSN: ISSN 0006-2960
PubMed: 24437462
DOI: 10.1021/BI4012463