Magnesium in PDB 2zdg: Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8

All present enzymatic activity of Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8:
6.3.2.4;

The structure of Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8, PDB code: 2zdg was solved by Y.Kitamura, S.Yokoyama, S.Kuramitsu, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.40 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.104, 101.068, 197.542, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.2

The binding sites of Magnesium atom in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8 (pdb code 2zdg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8, PDB code: 2zdg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:34.3 occ:1.00 O C:HOH668 2.3 28.4 1.0 O2A C:ADP403 2.3 21.2 1.0 O C:HOH606 2.3 24.1 1.0 OE1 C:GLU282 2.4 33.6 1.0 O2B C:ADP403 2.4 28.0 1.0 O C:HOH667 2.4 28.8 1.0 OD2 C:ASP270 3.5 30.2 1.0 CD C:GLU282 3.5 36.1 1.0 PB C:ADP403 3.6 28.0 1.0 O C:HOH616 3.7 34.7 1.0 O3B C:ADP403 3.8 31.5 1.0 PA C:ADP403 3.8 22.5 1.0 NZ C:LYS228 3.9 32.0 1.0 ND2 C:ASN281 4.1 29.3 1.0 OE2 C:GLU282 4.1 35.7 1.0 O C:HOH706 4.1 44.1 1.0 O3A C:ADP403 4.3 27.3 1.0 ND2 C:ASN284 4.5 31.3 1.0 CG C:GLU282 4.5 34.0 1.0 NH2 C:ARG268 4.5 22.4 1.0 O1A C:ADP403 4.6 27.1 1.0 CG C:ASP270 4.6 27.2 1.0 O3' C:ADP403 4.6 24.2 1.0 OD1 C:ASN284 4.7 33.8 1.0 C5' C:ADP403 4.7 23.9 1.0 O1B C:ADP403 4.8 28.5 1.0 CE C:LYS228 4.8 34.5 1.0 O5' C:ADP403 4.8 24.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8


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 D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg602 b:49.9 occ:1.00 O D:HOH608 2.3 41.3 1.0 O2B D:ADP404 2.4 42.6 1.0 OE1 D:GLU282 2.5 39.6 1.0 O D:HOH647 2.5 32.2 1.0 O2A D:ADP404 2.5 52.9 1.0 O D:HOH646 2.6 37.8 1.0 O5' D:ADP404 3.5 52.8 1.0 CD D:GLU282 3.5 38.5 1.0 PA D:ADP404 3.6 47.9 1.0 OD2 D:ASP270 3.7 32.3 1.0 ND2 D:ASN281 3.7 34.5 1.0 PB D:ADP404 3.9 45.0 1.0 O D:HOH640 3.9 41.3 1.0 CB D:GLU282 4.2 31.4 1.0 OD1 D:ASN284 4.3 27.4 1.0 O3A D:ADP404 4.3 49.0 1.0 OE2 D:GLU282 4.3 41.2 1.0 CG D:GLU282 4.4 34.4 1.0 O3' D:ADP404 4.5 50.1 1.0 O3B D:ADP404 4.7 45.6 1.0 CG D:ASP270 4.7 30.6 1.0 NH2 D:ARG268 4.8 32.8 1.0 O1A D:ADP404 4.8 51.7 1.0 ND2 D:ASN284 4.8 28.7 1.0 O1B D:ADP404 4.9 47.5 1.0 C5' D:ADP404 4.9 50.3 1.0 CB D:ASP270 5.0 27.4 1.0 CG D:ASN281 5.0 33.3 1.0

Y.Kitamura, S.Yokoyama, S.Kuramitsu. Crystal Structure of D-Alanine:D-Alanine Ligase with Adp From Thermus Thermophius HB8 To Be Published.