Magnesium in PDB 1iov: Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate

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

The structure of Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate, PDB code: 1iov 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 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	98.600, 51.000, 51.200, 90.00, 90.00, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate (pdb code 1iov). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate, PDB code: 1iov:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg330 b:29.2 occ:1.00 OD2 A:ASP257 1.9 2.0 1.0 O4P A:POB321 2.0 5.8 1.0 O2A A:ADP310 2.1 2.0 1.0 O3B A:ADP310 2.4 2.3 1.0 OE2 A:GLU270 2.8 4.0 1.0 CG A:ASP257 3.1 2.0 1.0 PA A:ADP310 3.3 2.0 1.0 P2 A:POB321 3.4 6.5 1.0 PB A:ADP310 3.5 2.0 1.0 O3A A:ADP310 3.6 2.0 1.0 CD A:GLU270 3.7 4.0 1.0 NZ A:LYS215 3.7 3.1 1.0 OD1 A:ASP257 3.8 2.0 1.0 CG A:GLU270 3.9 4.2 1.0 CB A:ASP257 4.0 2.0 1.0 O3' A:ADP310 4.0 2.0 1.0 O5' A:ADP310 4.0 2.0 1.0 C5' A:ADP310 4.0 2.0 1.0 O A:HOH510 4.2 2.0 1.0 O6P A:POB321 4.2 6.2 1.0 O5P A:POB321 4.2 6.5 1.0 O A:HOH507 4.3 28.2 1.0 MG A:MG331 4.4 2.0 1.0 O2B A:ADP310 4.4 2.0 1.0 NH2 A:ARG255 4.4 2.0 1.0 O1B A:ADP310 4.5 2.0 1.0 O3P A:POB321 4.5 5.7 1.0 C3' A:ADP310 4.5 2.0 1.0 O1A A:ADP310 4.6 2.0 1.0 ND2 A:ASN272 4.6 4.0 1.0 CE A:LYS215 4.7 3.0 1.0 C4' A:ADP310 4.8 2.0 1.0 OE1 A:GLU270 4.8 3.9 1.0

Magnesium binding site 2 out of 3 in the Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg331 b:2.0 occ:1.00 OE2 A:GLU270 2.1 4.0 1.0 O5P A:POB321 2.2 6.5 1.0 OD1 A:ASN272 2.3 4.3 1.0 O2B A:ADP310 2.4 2.0 1.0 CD A:GLU270 2.8 4.0 1.0 OE1 A:GLU270 2.8 3.9 1.0 O3B A:ADP310 2.9 2.3 1.0 O A:HOH536 2.9 2.0 1.0 PB A:ADP310 3.3 2.0 1.0 CG A:ASN272 3.3 4.1 1.0 P2 A:POB321 3.3 6.5 1.0 CA A:GLY149 3.4 5.5 1.0 O4P A:POB321 3.5 5.8 1.0 ND2 A:ASN272 3.6 4.0 1.0 O A:GLU148 3.7 5.7 1.0 N1' A:POB321 4.1 5.5 1.0 O3P A:POB321 4.2 5.7 1.0 CE A:LYS97 4.2 4.6 1.0 CG A:GLU270 4.2 4.2 1.0 MG A:MG332 4.2 34.9 1.0 O A:HOH522 4.3 29.7 1.0 O3A A:ADP310 4.3 2.0 1.0 MG A:MG330 4.4 29.2 1.0 O1B A:ADP310 4.4 2.0 1.0 N A:SER150 4.4 5.1 1.0 N A:GLY149 4.4 5.2 1.0 C A:GLY149 4.4 5.3 1.0 C A:GLU148 4.5 5.4 1.0 O6P A:POB321 4.5 6.2 1.0 CB A:ASN272 4.7 3.6 1.0 O2A A:ADP310 4.8 2.0 1.0 O A:ALA271 4.9 3.3 1.0 NZ A:LYS97 5.0 4.2 1.0

Magnesium binding site 3 out of 3 in the Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Complex of D-Ala:D-Ala Ligase with Adp and A Phosphoryl Phosphonate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg332 b:34.9 occ:1.00 O A:ALA271 2.3 3.3 1.0 O A:SER94 2.5 4.5 1.0 O A:HOH522 3.1 29.7 1.0 OE1 A:GLU270 3.2 3.9 1.0 C A:SER94 3.3 5.1 1.0 C A:ALA271 3.5 3.4 1.0 O A:HOH535 3.8 22.9 1.0 CA A:MET95 3.8 5.9 1.0 N A:MET95 3.8 5.6 1.0 OD1 A:ASN272 3.8 4.3 1.0 CE A:MET95 4.0 7.4 1.0 CG A:ASN272 4.1 4.1 1.0 CA A:ASN272 4.1 3.4 1.0 CB A:SER94 4.2 5.2 1.0 N A:ASN272 4.2 3.2 1.0 MG A:MG331 4.2 2.0 1.0 CA A:SER94 4.3 5.4 1.0 O A:HOH520 4.4 11.5 1.0 CD A:GLU270 4.4 4.0 1.0 N A:ALA271 4.5 4.0 1.0 O A:HOH536 4.5 2.0 1.0 C A:MET95 4.6 6.0 1.0 CA A:ALA271 4.6 3.5 1.0 ND2 A:ASN272 4.6 4.0 1.0 CB A:ASN272 4.7 3.6 1.0 CB A:MET95 4.8 6.8 1.0 OE2 A:GLU68 4.8 2.6 1.0 O A:MET95 4.9 6.3 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