Magnesium in PDB 1ym0: Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin

The structure of Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin, PDB code: 1ym0 was solved by F.Wang, C.Wang, M.Li, J.P.Zhang, L.L.Gui, X.M.An, W.R.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.20 / 2.06
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.353, 96.353, 150.809, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 19.2

The binding sites of Magnesium atom in the Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin (pdb code 1ym0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin, PDB code: 1ym0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:20.4 occ:1.00 O A:HOH507 2.0 16.9 1.0 O A:HOH504 2.0 15.9 1.0 O A:HOH508 2.1 17.9 1.0 O A:HOH505 2.1 19.7 1.0 O A:HOH506 2.1 20.3 1.0 O A:HOH503 2.1 15.2 1.0 O A:HOH547 4.0 22.4 1.0 O A:HOH621 4.1 28.4 1.0 O5 A:FUC2 4.1 23.8 1.0 O A:HOH550 4.2 22.9 1.0 O A:HOH551 4.3 23.3 1.0 O A:HOH564 4.3 25.6 1.0 O A:TYR133 4.3 17.7 1.0 O1 A:SO4501 4.3 27.1 1.0 O2 A:SO4501 4.5 24.3 1.0 O A:VAL131 4.6 16.9 1.0 C A:TYR133 4.6 17.3 1.0 CB A:TYR133 4.6 17.2 1.0 O4 A:FUC2 4.7 25.5 1.0 CD A:ARG134 4.7 16.6 1.0 C1 A:FUC2 4.7 22.9 1.0 S A:SO4501 4.9 24.4 1.0 N A:ARG134 5.0 17.5 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:25.5 occ:1.00 O A:ASP174A 2.0 25.0 1.0 OD1 A:ASP169 2.2 24.6 1.0 O A:TYR172 2.4 21.6 1.0 O A:ASP169 2.4 22.6 1.0 CG A:ASP169 3.1 24.5 1.0 C A:ASP174A 3.2 25.1 1.0 C A:ASP169 3.3 21.9 1.0 C A:TYR172 3.5 22.8 1.0 CA A:ASP169 3.5 21.7 1.0 CB A:TYR172 3.7 19.4 1.0 OD2 A:ASP169 3.9 27.6 1.0 CB A:ASP169 3.9 23.4 1.0 CA A:THR175 4.0 24.2 1.0 N A:THR175 4.0 24.1 1.0 CA A:TYR172 4.1 20.5 1.0 N A:ASP174A 4.1 27.6 1.0 CA A:ASP174A 4.3 25.7 1.0 N A:ILE176 4.4 22.6 1.0 N A:TYR172 4.5 19.5 1.0 N A:THR173 4.5 24.7 1.0 N A:ALA170 4.6 20.7 1.0 C A:THR175 4.6 22.6 1.0 CG1 A:ILE176 4.7 21.0 1.0 CA A:THR173 4.9 27.8 1.0 N A:ASP169 4.9 21.9 1.0 O A:CYS168 4.9 20.4 1.0 C A:THR173 5.0 29.2 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:41.8 occ:1.00 O A:HOH627 1.9 39.6 1.0 O A:HOH625 2.0 25.4 1.0 O A:HOH626 2.1 38.6 1.0 O A:HOH624 2.1 32.3 1.0 O A:HOH599 2.4 29.6 1.0 O A:HOH572 2.5 25.2 1.0 O A:HOH617 4.0 33.8 1.0 O A:HOH604 4.0 23.7 1.0 O A:HOH660 4.1 32.0 1.0 O A:HOH628 4.2 23.1 1.0 O A:HOH690 4.4 43.7 1.0 O A:HOH630 4.5 27.7 1.0 OD1 A:ASP129 4.6 19.0 1.0 O A:HOH708 4.6 36.0 1.0 OD2 A:ASP129 4.6 18.7 1.0

F.Wang, C.Wang, M.Li, J.P.Zhang, L.L.Gui, X.M.An, W.R.Chang. Crystal Structure of Earthworm Fibrinolytic Enzyme Component B: A Novel, Glycosylated Two-Chained Trypsin. J.Mol.Biol. V. 348 671 2005.
ISSN: ISSN 0022-2836
PubMed: 15826663
DOI: 10.1016/J.JMB.2005.02.055