Magnesium in PDB 6umr: Structure of DUF89 - D291A Mutant

The structure of Structure of DUF89 - D291A Mutant, PDB code: 6umr was solved by J.J.Perry, N.Kenjic, T.N.Dennis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.49 / 2.21
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.260, 194.691, 114.940, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.7

The binding sites of Magnesium atom in the Structure of DUF89 - D291A Mutant (pdb code 6umr). 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 DUF89 - D291A Mutant, PDB code: 6umr:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of DUF89 - D291A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of DUF89 - D291A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:24.8 occ:1.00 O B:HOH789 1.7 22.1 1.0 O A:HOH749 1.8 21.4 1.0 O A:HOH652 2.0 17.2 1.0 O B:HOH666 2.0 24.0 1.0 O B:HOH689 2.4 17.9 1.0 O B:HOH655 2.4 13.3 1.0 O B:HOH657 3.5 24.0 1.0 O A:HOH811 4.0 25.5 1.0 NE2 A:GLN96 4.0 16.9 1.0 OE2 B:GLU93 4.1 24.4 1.0 O A:LEU99 4.1 16.5 1.0 O A:HOH639 4.2 27.9 1.0 O A:ASN100 4.3 22.0 1.0 O A:GLY104 4.3 16.5 1.0 OD1 B:ASP86 4.5 21.9 1.0 C A:ASN100 4.5 23.2 1.0 CA A:GLU101 4.5 21.8 1.0 OE1 B:GLU93 4.5 17.1 1.0 N A:GLU101 4.6 22.2 1.0 CD B:GLU93 4.7 17.9 1.0 C A:LEU99 4.9 19.6 1.0

Magnesium binding site 2 out of 2 in the Structure of DUF89 - D291A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of DUF89 - D291A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:24.5 occ:1.00 O A:HOH680 2.0 15.2 1.0 O A:HOH640 2.0 22.9 1.0 O B:HOH760 2.1 19.8 1.0 O B:HOH616 2.1 15.4 1.0 O A:HOH815 2.2 19.5 1.0 O B:HOH683 2.3 18.8 1.0 O A:HOH695 3.4 21.8 1.0 NE2 B:GLN96 3.5 15.7 1.0 O B:LEU99 3.8 20.9 1.0 OE1 A:GLU93 3.8 19.6 1.0 O B:GLY104 4.2 14.7 1.0 OE2 A:GLU93 4.2 17.9 1.0 O B:ASN100 4.4 19.3 1.0 CD A:GLU93 4.5 16.0 1.0 O B:HOH790 4.5 22.1 1.0 CD B:GLN96 4.6 18.1 1.0 OD1 A:ASP86 4.7 19.9 1.0 C B:ASN100 4.7 21.6 1.0 C B:LEU99 4.8 22.0 1.0 O B:GLN96 4.8 16.9 1.0 CG B:GLN96 4.9 18.3 1.0 CA B:GLU101 4.9 21.1 1.0

T.N.Dennis, N.Kenjic, A.S.Kang, J.D.Lowenson, J.S.Kirkwood, S.G.Clarke, J.J.P.Perry. Human ARMT1 Structure and Substrate Specificity Indicates That It Is A DUF89 Family Damage-Control Phosphatase. J.Struct.Biol. V. 212 07576 2020.
ISSN: ESSN 1095-8657
PubMed: 32682077
DOI: 10.1016/J.JSB.2020.107576