Magnesium in PDB 3g3c: MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang

All present enzymatic activity of MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang:
3.1.11.2;

The structure of MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang, PDB code: 3g3c was solved by K.Lakomek, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 3.04
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	100.354, 79.337, 98.550, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 29.4

The binding sites of Magnesium atom in the MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang (pdb code 3g3c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang, PDB code: 3g3c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg267 b:64.1 occ:1.00 O3' I:DG9 2.2 77.7 1.0 O2 A:PO4266 2.4 80.4 1.0 OE2 A:GLU38 2.5 60.7 1.0 OD2 A:ASP247 3.1 61.9 1.0 CD A:GLU38 3.3 60.3 1.0 OE1 A:GLU38 3.3 60.4 1.0 OD1 A:ASN12 3.5 55.8 1.0 OD1 A:ASP247 3.6 63.4 1.0 C3' I:DG9 3.6 77.3 1.0 P A:PO4266 3.7 80.6 1.0 CG A:ASP247 3.8 62.6 1.0 CG A:ASN12 4.0 55.6 1.0 O3 A:PO4266 4.0 81.8 1.0 NE2 A:HIS248 4.1 59.9 1.0 OD1 A:ASN10 4.1 56.2 1.0 C2' I:DG9 4.3 77.5 1.0 CD2 A:HIS248 4.3 60.4 1.0 CB A:ASN12 4.4 55.4 1.0 O1 A:PO4266 4.5 79.8 1.0 C4' I:DG9 4.6 76.8 1.0 ND2 A:ASN12 4.7 55.7 1.0 O4 A:PO4266 4.7 80.6 1.0 C1' I:DG9 4.7 77.9 1.0 ND2 A:ASN10 4.7 55.6 1.0 CG A:ASN10 4.8 55.4 1.0 CG A:GLU38 4.8 59.0 1.0

Magnesium binding site 2 out of 2 in the MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of MTH0212 (Wt) in Complex with A 6BP Dsdna Containing A Single One Nucleotide Long 3'-Overhang within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg267 b:64.9 occ:1.00 O3' H:DA7 2.4 82.5 1.0 O4 B:PO4266 2.5 90.8 1.0 OE2 B:GLU38 2.9 67.7 1.0 OE1 B:GLU38 3.1 66.4 1.0 CD B:GLU38 3.2 66.9 1.0 OD1 B:ASN12 3.4 55.9 1.0 OD2 B:ASP247 3.4 61.9 1.0 OD1 B:ASP247 3.6 63.4 1.0 OD1 B:ASN10 3.7 56.3 1.0 CG B:ASN12 3.8 55.6 1.0 C3' H:DA7 3.9 82.3 1.0 P B:PO4266 3.9 91.1 1.0 CG B:ASP247 4.0 62.6 1.0 NE2 B:HIS248 4.1 60.0 1.0 CB B:ASN12 4.1 55.4 1.0 CD2 B:HIS248 4.3 60.5 1.0 O1 B:PO4266 4.3 91.7 1.0 CG B:ASN10 4.4 55.4 1.0 ND2 B:ASN10 4.4 55.6 1.0 CG B:GLU38 4.5 66.0 1.0 ND2 B:ASN12 4.6 55.7 1.0 C4' H:DA7 4.6 81.7 1.0 CA B:ASN12 4.6 55.3 1.0 C2' H:DA7 4.7 82.4 1.0 O3 B:PO4266 4.7 90.3 1.0 NZ B:LYS40 4.7 67.3 1.0 O2 B:PO4266 4.9 90.9 1.0 C1' H:DA7 4.9 82.7 1.0

K.Lakomek, A.Dickmanns, E.Ciirdaeva, L.Schomacher, R.Ficner. Crystal Structure Analysis of Dna Uridine Endonuclease MTH212 Bound to Dna J.Mol.Biol. V. 399 604 2010.
ISSN: ISSN 0022-2836
PubMed: 20434457
DOI: 10.1016/J.JMB.2010.04.044