Magnesium in PDB 6du2: Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide

The structure of Structure of SCP1 D96N Bound to Rest-PS861/4 Peptide, PDB code: 6du2 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)	39.46 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	125.335, 78.568, 62.883, 90.00, 112.13, 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 6du2). 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: 6du2:
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 1.8 42.9 1.0 OD1 A:ASN207 1.9 53.6 1.0 O1P C:SEP861 1.9 48.0 1.0 OD1 A:ASN96 2.2 45.9 1.0 O C:HOH902 2.2 52.9 1.0 O A:ASP98 2.6 41.7 1.0 CG A:ASN207 2.8 39.2 1.0 ND2 A:ASN207 3.0 48.2 1.0 P C:SEP861 3.2 56.6 1.0 CG A:ASN96 3.3 43.2 1.0 O2P C:SEP861 3.4 52.3 1.0 OD1 A:ASP206 3.7 47.7 1.0 C A:ASP98 3.8 39.5 1.0 OG A:SER208 4.0 61.4 1.0 ND2 A:ASN96 4.0 38.4 1.0 OE1 A:GLU99 4.1 51.3 1.0 CB A:ASN207 4.2 36.3 1.0 OG C:SEP861 4.2 64.3 1.0 OG1 A:THR100 4.2 49.2 1.0 CB A:GLU99 4.4 36.7 1.0 O3P C:SEP861 4.4 51.4 1.0 N A:ASN207 4.4 36.1 1.0 CB A:ASN96 4.5 36.2 1.0 N A:SER208 4.6 32.6 1.0 CG A:ASP206 4.6 48.3 1.0 CA A:ASP98 4.7 42.3 1.0 N A:GLU99 4.7 35.9 1.0 CA A:ASN207 4.7 34.7 1.0 N A:ASP98 4.7 39.4 1.0 CB A:SER208 4.8 48.0 1.0 N A:THR100 4.8 38.6 1.0 C A:GLU99 4.8 38.8 1.0 CA A:GLU99 4.9 40.2 1.0 CB A:ASP98 4.9 41.4 1.0 OD2 A:ASP206 4.9 49.4 1.0 C A:ASN207 4.9 41.7 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 O D:HOH901 1.9 43.9 1.0 OD1 B:ASN207 2.0 42.1 1.0 O D:HOH902 2.0 56.0 1.0 ND2 B:ASN96 2.2 46.0 1.0 O1P D:SEP861 2.2 56.0 1.0 O B:ASP98 2.2 45.1 1.0 CG B:ASN207 3.0 47.1 1.0 ND2 B:ASN207 3.3 48.1 1.0 C B:ASP98 3.4 47.6 1.0 CG B:ASN96 3.5 49.9 1.0 P D:SEP861 3.7 63.1 1.0 OD1 B:ASP206 3.7 54.7 1.0 OG1 B:THR100 4.0 36.8 1.0 OE1 B:GLU99 4.0 52.5 1.0 OD1 B:ASN96 4.1 55.4 1.0 CB B:GLU99 4.2 47.6 1.0 O2P D:SEP861 4.2 50.4 1.0 CA B:ASP98 4.3 50.4 1.0 CB B:ASN207 4.3 48.3 1.0 CB B:ASP98 4.4 49.5 1.0 O3P D:SEP861 4.4 49.2 1.0 N B:GLU99 4.4 41.5 1.0 N B:ASP98 4.5 49.6 1.0 CB B:ASN96 4.5 48.6 1.0 CA B:GLU99 4.6 48.2 1.0 N B:ASN207 4.6 43.4 1.0 N B:THR100 4.7 51.0 1.0 C B:GLU99 4.7 50.5 1.0 N B:SER208 4.8 45.8 1.0 CB B:SER208 4.8 51.3 1.0 OG D:SEP861 4.8 71.8 1.0 CG B:ASP206 4.8 53.7 1.0 CA B:ASN207 4.9 51.1 1.0 CD B:GLU99 4.9 46.9 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