Magnesium in PDB 7drm: Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp

The structure of Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp, PDB code: 7drm was solved by I.Song, J.Yu, W.Song, S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.83 / 3.28
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	92.432, 91.294, 100.308, 90, 101.16, 90
R / Rfree (%)	25.1 / 25.9

The binding sites of Magnesium atom in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp (pdb code 7drm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp, PDB code: 7drm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:56.1 occ:1.00 OE2 A:GLU282 1.8 79.6 1.0 O1A A:ADP401 2.1 82.2 1.0 OD2 A:ASP269 2.6 72.1 1.0 CD A:GLU282 2.9 69.2 1.0 O1B A:ADP401 2.9 75.3 1.0 CG A:ASP269 3.5 86.9 1.0 PA A:ADP401 3.6 75.3 1.0 CG A:GLU282 3.6 70.2 1.0 O3B A:ADP401 3.6 85.3 1.0 PB A:ADP401 3.7 76.1 1.0 OE1 A:GLU282 3.8 60.1 1.0 O3A A:ADP401 4.1 78.4 1.0 ND2 A:ASN284 4.1 74.5 1.0 CB A:ASP269 4.2 79.9 1.0 OD1 A:ASP269 4.3 93.2 1.0 NH2 A:ARG213 4.4 91.1 1.0 OD1 A:ASN284 4.4 94.4 1.0 O5' A:ADP401 4.4 74.7 1.0 C5' A:ADP401 4.5 83.8 1.0 MG A:MG403 4.6 75.0 1.0 O2A A:ADP401 4.6 77.7 1.0 CG A:ASN284 4.7 78.2 1.0 CB A:GLU282 5.0 68.3 1.0

Magnesium binding site 2 out of 4 in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:75.0 occ:1.00 O1B A:ADP401 2.5 75.3 1.0 OE1 A:GLU282 2.7 60.1 1.0 OD1 A:ASN284 3.1 94.4 1.0 CD A:GLU282 3.6 69.2 1.0 PB A:ADP401 3.6 76.1 1.0 OE2 A:GLU282 3.7 79.6 1.0 O2B A:ADP401 3.8 91.7 1.0 CG E:GLU25 4.1 108.1 1.0 CG A:ASN284 4.3 78.2 1.0 O3B A:ADP401 4.4 85.3 1.0 CA E:GLU25 4.5 111.1 1.0 MG A:MG402 4.6 56.1 1.0 N E:GLU25 4.7 108.4 1.0 CE A:LYS133 4.8 87.2 1.0 O3A A:ADP401 4.9 78.4 1.0 CB E:GLU25 4.9 107.9 1.0 NZ A:LYS133 5.0 76.4 1.0 CG A:GLU282 5.0 70.2 1.0 ND2 A:ASN284 5.0 74.5 1.0

Magnesium binding site 3 out of 4 in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:58.8 occ:1.00 OE2 C:GLU282 2.0 86.0 1.0 OD2 C:ASP269 2.1 85.0 1.0 O2A C:ADP401 2.2 72.4 1.0 CG C:ASP269 3.1 84.1 1.0 CD C:GLU282 3.1 76.6 1.0 O1B C:ADP401 3.4 78.3 1.0 O2B C:ADP401 3.6 79.3 1.0 PA C:ADP401 3.6 70.0 1.0 ND2 C:ASN284 3.8 83.5 1.0 CG C:GLU282 3.9 74.0 1.0 CB C:ASP269 3.9 77.1 1.0 PB C:ADP401 3.9 85.5 1.0 NH2 C:ARG213 4.0 91.1 1.0 OD1 C:ASP269 4.0 84.3 1.0 OE1 C:GLU282 4.1 71.9 1.0 C5' C:ADP401 4.2 79.6 1.0 O3A C:ADP401 4.3 80.4 1.0 O5' C:ADP401 4.5 67.4 1.0 O1A C:ADP401 4.6 74.6 1.0 CG C:ASN284 4.8 83.9 1.0 O3' C:ADP401 4.8 92.0 1.0 OD1 C:ASN284 4.9 91.8 1.0 C3' C:ADP401 4.9 79.6 1.0

Magnesium binding site 4 out of 4 in the Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Atp-Grasp Ligase Psnb Complexed with Minimal Precursor, Mg, and Adp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg403 b:77.4 occ:1.00 O1B C:ADP401 2.6 78.3 1.0 OD1 C:ASN284 2.9 91.8 1.0 OE1 C:GLU282 3.3 71.9 1.0 O3B C:ADP401 3.6 100.9 1.0 PB C:ADP401 3.6 85.5 1.0 CG C:ASN284 4.1 83.9 1.0 CD C:GLU282 4.1 76.6 1.0 OE2 C:GLU282 4.2 86.0 1.0 CB F:GLU25 4.3 100.3 1.0 O2B C:ADP401 4.4 79.3 1.0 CE C:LYS133 4.4 95.9 1.0 NZ C:LYS133 4.6 91.8 1.0 ND2 C:ASN284 4.7 83.5 1.0 O F:ALA21 4.7 102.8 1.0 O3A C:ADP401 4.9 80.4 1.0 CD F:GLU25 5.0 100.1 1.0

I.Song, Y.Kim, J.Yu, S.Go, H.Lee, W.Song, S.Kim. Molecular Mechanism Underlying Substrate Recognition of the Peptide Macrocyclase Psnb To Be Published.