Manganese in PDB 6vt8: Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn

The structure of Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn, PDB code: 6vt8 was solved by M.C.Unciuleac, Y.Goldgur, S.Shuman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.41 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	54.941, 54.941, 100.602, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 23.3

The binding sites of Manganese atom in the Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn (pdb code 6vt8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn, PDB code: 6vt8:

Manganese binding site 1 out of 1 in the Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Naegleria Gruberi Rna Ligase E312A Mutant with Amp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:28.9 occ:1.00 O A:HOH625 2.1 34.6 1.0 O A:HOH662 2.1 25.4 1.0 O1P A:AMP401 2.1 23.3 1.0 O A:HOH721 2.4 26.3 1.0 O A:HOH674 2.4 31.1 1.0 O A:HOH564 2.5 23.5 1.0 P A:AMP401 3.4 29.0 1.0 NZ A:LYS170 3.6 24.4 1.0 O A:HOH597 4.0 43.9 1.0 O4' A:AMP401 4.1 22.3 1.0 OE2 A:GLU227 4.1 22.6 1.0 C4' A:AMP401 4.3 23.8 1.0 O A:HOH764 4.4 37.7 1.0 O2P A:AMP401 4.4 28.3 1.0 O5' A:AMP401 4.5 24.6 1.0 OD1 A:ASP172 4.5 30.4 1.0 O A:HOH728 4.5 38.6 1.0 C1' A:AMP401 4.5 20.4 1.0 O A:GLY173 4.6 25.4 1.0 O A:HOH703 4.6 25.8 1.0 O A:HOH682 4.7 31.8 1.0 O A:HOH759 4.8 45.8 1.0 O A:LEU171 4.8 22.5 1.0 O A:HOH516 4.9 30.6 1.0

M.C.Unciuleac, Y.Goldgur, S.Shuman. Caveat Mutator: Alanine Substitutions For Conserved Amino Acids in Rna Ligase Elicit Unexpected Rearrangements of the Active Site For Lysine Adenylylation Nucleic Acids Res. 2020.
ISSN: ESSN 1362-4962