Magnesium in PDB 1iow: Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate

All present enzymatic activity of Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate:
6.3.2.4;

The structure of Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate, PDB code: 1iow was solved by J.R.Knox, P.C.Moews, C.Fan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.800, 51.700, 51.700, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 23.4

The binding sites of Magnesium atom in the Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate (pdb code 1iow). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate, PDB code: 1iow:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg330 b:3.9 occ:1.00 OE2 A:GLU270 1.9 8.3 1.0 O3B A:ADP310 2.0 5.5 1.0 O5P A:PHY320 2.0 7.8 1.0 O A:HOH401 2.2 4.3 1.0 OD1 A:ASN272 2.3 10.3 1.0 CD A:GLU270 2.5 11.0 1.0 OE1 A:GLU270 2.5 10.5 1.0 CG A:ASN272 3.2 9.6 1.0 PB A:ADP310 3.2 6.0 1.0 P2 A:PHY320 3.3 7.8 1.0 ND2 A:ASN272 3.4 7.6 1.0 O2B A:ADP310 3.4 10.6 1.0 MG A:MG331 3.6 11.3 1.0 O4P A:PHY320 3.7 6.0 1.0 NZ A:LYS97 3.9 7.4 1.0 CG A:GLU270 4.0 7.3 1.0 CA A:GLY149 4.0 7.0 1.0 O A:HOH406 4.0 8.3 1.0 O3A A:ADP310 4.1 5.7 1.0 O A:GLU148 4.1 7.8 1.0 O2P A:PHY320 4.2 4.9 1.0 O3P A:PHY320 4.3 5.8 1.0 O1B A:ADP310 4.3 6.9 1.0 O A:HOH404 4.4 2.0 1.0 N1 A:PHY320 4.5 5.3 1.0 CE A:LYS97 4.5 4.1 1.0 OD2 A:ASP257 4.6 12.0 1.0 CB A:ASN272 4.6 7.0 1.0 O A:HOH403 4.8 8.5 1.0 O2A A:ADP310 4.8 7.1 1.0 N A:SER150 4.8 6.6 1.0 C A:GLY149 5.0 7.3 1.0 CB A:GLU270 5.0 7.8 1.0 C A:GLU148 5.0 6.5 1.0

Magnesium binding site 2 out of 2 in the Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of Y216F D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphinate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg331 b:11.3 occ:1.00 O A:HOH407 1.9 13.4 1.0 O4P A:PHY320 2.0 6.0 1.0 OD2 A:ASP257 2.1 12.0 1.0 O2B A:ADP310 2.2 10.6 1.0 O2A A:ADP310 2.3 7.1 1.0 OE2 A:GLU270 2.5 8.3 1.0 P2 A:PHY320 3.2 7.8 1.0 CG A:ASP257 3.3 12.4 1.0 PB A:ADP310 3.3 6.0 1.0 PA A:ADP310 3.4 8.7 1.0 O5P A:PHY320 3.5 7.8 1.0 O3A A:ADP310 3.5 5.7 1.0 MG A:MG330 3.6 3.9 1.0 CD A:GLU270 3.6 11.0 1.0 O3B A:ADP310 3.7 5.5 1.0 O3P A:PHY320 4.0 5.8 1.0 ND2 A:ASN272 4.0 7.6 1.0 CG A:GLU270 4.0 7.3 1.0 NZ A:LYS215 4.1 4.4 1.0 OD1 A:ASP257 4.1 14.6 1.0 CB A:ASP257 4.1 10.8 1.0 O A:HOH408 4.2 10.8 1.0 O5' A:ADP310 4.3 7.8 1.0 NH2 A:ARG255 4.3 5.2 1.0 C5' A:ADP310 4.3 6.3 1.0 O3' A:ADP310 4.4 5.8 1.0 O1A A:ADP310 4.4 8.2 1.0 O2P A:PHY320 4.5 4.9 1.0 O1B A:ADP310 4.6 6.9 1.0 OE1 A:GLU270 4.7 10.5 1.0 OD1 A:ASN272 4.8 10.3 1.0 C3' A:ADP310 4.9 7.4 1.0 CG A:ASN272 4.9 9.6 1.0 CE A:LYS215 4.9 2.0 1.0

C.Fan, I.S.Park, C.T.Walsh, J.R.Knox. D-Alanine:D-Alanine Ligase: Phosphonate and Phosphinate Intermediates with Wild Type and the Y216F Mutant. Biochemistry V. 36 2531 1997.
ISSN: ISSN 0006-2960
PubMed: 9054558
DOI: 10.1021/BI962431T