Magnesium in PDB 6du3: Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide

All present enzymatic activity of Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide:
3.1.3.16;

The structure of Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide, PDB code: 6du3 was solved by N.T.Burkholder, J.E.Mayfield, X.Yu, S.Irani, D.K.Arce, F.Jiang, W.Matthews, Y.Xue, Y.J.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.20 / 2.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.414, 78.731, 63.001, 90.00, 112.42, 90.00
R / Rfree (%)	n/a / n/a

The binding sites of Magnesium atom in the Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide (pdb code 6du3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide, PDB code: 6du3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:30.0 occ:1.00 O C:HOH901 1.9 37.7 1.0 O2P C:SEP861 2.0 40.0 1.0 OD1 A:ASN207 2.0 31.0 1.0 OD1 A:ASN96 2.2 34.2 1.0 O A:ASP98 2.5 28.8 1.0 CG A:ASN207 2.7 29.1 1.0 ND2 A:ASN207 2.8 28.8 1.0 O C:HOH902 2.9 40.2 1.0 CG A:ASN96 3.4 30.0 1.0 P C:SEP861 3.4 53.3 1.0 O3P C:SEP861 3.7 48.8 1.0 C A:ASP98 3.7 27.2 1.0 OD1 A:ASP206 3.8 35.6 1.0 OG1 A:THR100 4.0 33.8 1.0 ND2 A:ASN96 4.1 26.4 1.0 CB A:ASN207 4.2 32.9 1.0 OE1 A:GLU99 4.2 32.6 1.0 CB A:GLU99 4.3 21.7 1.0 O1P C:SEP861 4.4 46.2 1.0 CB A:ASN96 4.5 30.6 1.0 N A:ASN207 4.5 26.8 1.0 OG C:SEP861 4.5 56.3 1.0 CB A:SER208 4.5 31.5 1.0 CA A:ASP98 4.6 30.6 1.0 N A:SER208 4.7 25.6 1.0 N A:GLU99 4.7 24.1 1.0 N A:ASP98 4.7 30.2 1.0 CG A:ASP206 4.7 34.0 1.0 C A:GLU99 4.7 28.3 1.0 N A:THR100 4.8 24.2 1.0 CA A:GLU99 4.8 29.4 1.0 CA A:ASN207 4.8 25.6 1.0 CB A:ASP98 4.8 29.0 1.0 C A:ASN207 5.0 29.0 1.0 OD2 A:ASP206 5.0 34.4 1.0

Magnesium binding site 2 out of 2 in the Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:30.0 occ:1.00 O2P D:SEP861 2.1 49.2 1.0 OD1 B:ASN96 2.1 38.3 1.0 O B:ASP98 2.2 37.1 1.0 O B:HOH402 2.2 46.7 1.0 OD1 B:ASN207 2.3 43.4 1.0 O D:HOH901 2.5 45.7 1.0 CG B:ASN207 3.2 41.3 1.0 CG B:ASN96 3.3 41.5 1.0 C B:ASP98 3.3 35.6 1.0 P D:SEP861 3.6 62.1 1.0 ND2 B:ASN207 3.6 43.6 1.0 OE1 B:GLU99 3.9 48.7 1.0 O1P D:SEP861 3.9 42.7 1.0 ND2 B:ASN96 4.0 39.8 1.0 OD1 B:ASP206 4.1 35.3 1.0 CA B:ASP98 4.1 31.9 1.0 OG1 B:THR100 4.1 34.9 1.0 CB B:ASP98 4.2 44.9 1.0 N B:ASP98 4.2 34.4 1.0 O3P D:SEP861 4.4 52.2 1.0 CB B:GLU99 4.4 35.2 1.0 N B:GLU99 4.4 34.3 1.0 CB B:ASN96 4.5 41.7 1.0 CB B:ASN207 4.5 36.8 1.0 N B:THR100 4.7 35.3 1.0 OG D:SEP861 4.7 73.0 1.0 CA B:GLU99 4.7 36.1 1.0 N B:ASN207 4.8 36.2 1.0 CD B:GLU99 4.8 40.5 1.0 C B:GLU99 4.8 39.1 1.0 CB B:SER208 5.0 44.2 1.0 CG B:ASP206 5.0 41.7 1.0

N.T.Burkholder, J.E.Mayfield, X.Yu, S.Irani, D.K.Arce, F.Jiang, W.L.Matthews, Y.Xue, Y.J.Zhang. Phosphatase Activity of Small C-Terminal Domain Phosphatase 1 (SCP1) Controls the Stability of the Key Neuronal Regulator RE1-Silencing Transcription Factor (Rest). J. Biol. Chem. V. 293 16851 2018.
ISSN: ESSN 1083-351X
PubMed: 30217818
DOI: 10.1074/JBC.RA118.004722