Magnesium in PDB 5jmd: Heparinase III-BT4657 Gene Product, Methylated Lysines

The structure of Heparinase III-BT4657 Gene Product, Methylated Lysines, PDB code: 5jmd was solved by T.S.Ulaganathan, R.Shi, D.Yao, M.-L.Garron, M.Cherney, M.Cygler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.359, 80.412, 83.543, 90.00, 104.08, 90.00
R / Rfree (%)	21.9 / 25.8

The binding sites of Magnesium atom in the Heparinase III-BT4657 Gene Product, Methylated Lysines (pdb code 5jmd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Heparinase III-BT4657 Gene Product, Methylated Lysines, PDB code: 5jmd:

Magnesium binding site 1 out of 1 in the Heparinase III-BT4657 Gene Product, Methylated Lysines


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Heparinase III-BT4657 Gene Product, Methylated Lysines within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg701 b:54.3 occ:1.00 O A:HOH822 2.0 68.0 1.0 OE1 A:GLN433 2.1 58.2 1.0 OD2 A:ASP451 2.2 66.0 1.0 O A:HOH802 2.3 71.4 1.0 NE2 A:HIS476 2.3 67.0 1.0 CD A:GLN433 3.2 63.6 1.0 CE1 A:HIS476 3.2 69.9 1.0 CG A:ASP451 3.3 62.7 1.0 CD2 A:HIS476 3.3 65.1 1.0 NE2 A:GLN433 3.7 62.1 1.0 O A:GLY453 3.8 77.7 1.0 OD1 A:ASP451 3.8 55.9 1.0 N A:GLY453 3.9 68.0 1.0 O A:CYS352 4.0 76.0 1.0 OD2 A:ASP435 4.2 68.7 1.0 O A:HIS470 4.2 62.5 1.0 O A:SER354 4.3 80.4 1.0 ND1 A:HIS476 4.3 58.4 1.0 C A:GLY453 4.3 75.2 1.0 N A:SER354 4.3 62.2 1.0 CG A:HIS476 4.4 62.1 1.0 CA A:GLY453 4.4 72.1 1.0 CG A:GLN433 4.5 69.0 1.0 N A:SER452 4.5 73.6 1.0 CB A:ASP451 4.5 61.0 1.0 CB A:SER452 4.6 70.8 1.0 C A:SER452 4.7 68.2 1.0 CB A:GLN433 4.8 68.7 1.0 CA A:SER452 4.8 72.3 1.0 CA A:PHE353 4.9 61.9 1.0 C A:PHE353 4.9 57.9 1.0

T.Ulaganathan, R.Shi, D.Yao, R.X.Gu, M.L.Garron, M.Cherney, D.P.Tieleman, E.Sterner, G.Li, L.Li, R.J.Linhardt, M.Cygler. Conformational Flexibility of PL12 Family Heparinases: Structure and Substrate Specificity of Heparinase III From Bacteroides Thetaiotaomicron (BT4657). Glycobiology V. 27 176 2017.
ISSN: ESSN 1460-2423
PubMed: 27621378
DOI: 10.1093/GLYCOB/CWW096