Magnesium in PDB 6umq: Structure of DUF89

The structure of Structure of DUF89, PDB code: 6umq 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)	66.49 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	90.140, 194.473, 114.201, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 22.4

The binding sites of Magnesium atom in the Structure of DUF89 (pdb code 6umq). 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 DUF89, PDB code: 6umq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of DUF89


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:11.9 occ:1.00 O A:HOH722 2.0 11.0 1.0 O A:HOH845 2.1 14.2 1.0 O B:HOH852 2.1 13.6 1.0 O B:HOH728 2.1 13.8 1.0 O A:HOH669 2.1 10.1 1.0 O B:HOH644 2.2 11.6 1.0 O A:LEU99 3.8 10.1 1.0 OE2 B:GLU93 4.0 20.2 1.0 NE2 A:GLN96 4.0 11.4 1.0 O B:HOH605 4.1 19.9 1.0 O A:ASN100 4.2 11.2 1.0 OE1 B:GLU93 4.3 10.9 1.0 OD1 B:ASP86 4.3 16.3 1.0 O A:HOH712 4.3 18.3 1.0 O A:HOH763 4.4 21.5 1.0 O A:GLY104 4.4 10.8 1.0 C A:ASN100 4.4 11.1 1.0 CA A:GLU101 4.6 11.8 1.0 CD B:GLU93 4.6 15.2 1.0 N A:GLU101 4.6 11.8 1.0 C A:LEU99 4.6 11.2 1.0 O B:HOH647 4.7 22.3 1.0 O A:GLN96 5.0 8.7 1.0

Magnesium binding site 2 out of 4 in the Structure of DUF89


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:9.2 occ:1.00 OD1 A:ASP291 2.0 6.2 1.0 OD1 A:ASP253 2.0 10.4 1.0 OD1 A:ASN254 2.1 10.4 1.0 O A:HOH728 2.1 10.4 1.0 O A:HOH653 2.1 9.4 1.0 O A:HOH811 2.2 10.2 1.0 CG A:ASP291 3.0 5.2 1.0 CG A:ASP253 3.1 12.8 1.0 CG A:ASN254 3.1 10.7 1.0 OD2 A:ASP291 3.4 9.4 1.0 OD2 A:ASP253 3.5 16.5 1.0 ND2 A:ASN254 3.6 20.9 1.0 O A:HOH733 3.7 16.0 1.0 N A:ASN254 4.2 6.4 1.0 CB A:ASN254 4.3 8.3 1.0 CB A:ASP291 4.3 7.7 1.0 O A:PHE288 4.3 8.6 1.0 O A:HOH893 4.3 23.9 1.0 C A:ASP253 4.4 9.1 1.0 CB A:ASP253 4.4 6.4 1.0 CA A:ASN254 4.4 8.9 1.0 N A:ASP291 4.4 6.5 1.0 CA A:ASP291 4.5 6.9 1.0 CA A:ASP253 4.6 6.2 1.0 CB A:SER290 4.7 10.7 1.0 CB A:PHE288 4.7 6.8 1.0 O A:HOH732 4.7 9.3 1.0 C A:SER290 4.8 8.1 1.0 O A:ASP253 4.8 7.1 1.0

Magnesium binding site 3 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of DUF89 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:11.7 occ:1.00 O A:HOH710 2.0 11.5 1.0 O B:HOH630 2.1 9.8 1.0 O B:HOH823 2.1 11.4 1.0 O A:HOH874 2.1 13.2 1.0 O A:HOH673 2.2 10.5 1.0 O A:HOH682 2.2 13.2 1.0 O B:LEU99 3.8 11.9 1.0 OE1 A:GLU93 3.9 20.1 1.0 NE2 B:GLN96 4.0 10.3 1.0 O A:HOH626 4.0 24.0 1.0 O B:ASN100 4.2 11.7 1.0 OE2 A:GLU93 4.3 12.0 1.0 O B:HOH640 4.3 16.6 1.0 OD1 A:ASP86 4.3 15.3 1.0 O B:GLY104 4.3 10.5 1.0 C B:ASN100 4.4 11.6 1.0 O B:HOH843 4.5 22.2 1.0 CA B:GLU101 4.5 13.1 1.0 CD A:GLU93 4.6 16.3 1.0 N B:GLU101 4.6 12.2 1.0 C B:LEU99 4.7 12.8 1.0 O A:HOH785 4.9 19.3 1.0 O B:GLN96 4.9 11.1 1.0

Magnesium binding site 4 out of 4 in the Structure of DUF89


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of DUF89 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:8.7 occ:1.00 OD1 B:ASP291 2.0 8.0 1.0 OD1 B:ASP253 2.1 10.1 1.0 O B:HOH655 2.1 10.5 1.0 OD1 B:ASN254 2.1 11.9 1.0 O B:HOH762 2.1 7.8 1.0 O B:HOH773 2.2 12.4 1.0 CG B:ASP291 3.0 9.5 1.0 CG B:ASP253 3.1 13.4 1.0 CG B:ASN254 3.2 15.8 1.0 OD2 B:ASP291 3.4 11.6 1.0 OD2 B:ASP253 3.5 15.8 1.0 O B:HOH735 3.6 13.9 1.0 ND2 B:ASN254 3.9 23.1 1.0 O B:PHE288 4.3 8.5 1.0 O B:HOH873 4.3 27.8 1.0 N B:ASN254 4.3 7.7 1.0 CB B:ASP291 4.3 8.6 1.0 CB B:ASN254 4.4 11.8 1.0 CB B:ASP253 4.4 8.1 1.0 C B:ASP253 4.4 10.8 1.0 N B:ASP291 4.4 10.3 1.0 CA B:ASN254 4.4 10.1 1.0 CA B:ASP291 4.5 8.3 1.0 CB B:PHE288 4.6 8.2 1.0 CA B:ASP253 4.6 9.4 1.0 O B:HOH714 4.7 10.6 1.0 O B:ASP253 4.8 9.2 1.0 C B:SER290 4.8 11.0 1.0 CB B:SER290 4.9 13.1 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