Manganese in PDB 6vtd: Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn

The structure of Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn, PDB code: 6vtd 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)	27.05 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	88.775, 88.775, 100.926, 90.00, 90.00, 90.00
R / Rfree (%)	24.6 / 30.6

The binding sites of Manganese atom in the Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn (pdb code 6vtd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn, PDB code: 6vtd:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Naegleria Gruberi Rna Ligase R149A Mutant with Atp 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 R149A Mutant with Atp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:81.2 occ:1.00 O2A A:ATP401 2.2 62.0 1.0 OD1 A:ASP146 2.6 86.8 1.0 O2B A:ATP401 3.1 79.1 1.0 PA A:ATP401 3.3 63.5 1.0 O3A A:ATP401 3.3 72.8 1.0 PB A:ATP401 3.3 80.8 1.0 O1B A:ATP401 3.4 83.6 1.0 CG A:ASP146 3.7 86.8 1.0 NZ A:LYS326 3.9 51.5 1.0 O A:GLN147 4.0 59.4 1.0 O1A A:ATP401 4.3 64.3 1.0 CB A:ASP146 4.4 84.0 1.0 N A:GLN147 4.5 68.9 1.0 O5' A:ATP401 4.5 61.5 1.0 NH2 A:ARG190 4.6 78.2 1.0 OD2 A:ASP146 4.6 89.1 1.0 CA A:ASP146 4.8 80.7 1.0 C A:GLN147 4.8 59.2 1.0 C5' A:ATP401 4.8 56.7 1.0 NZ A:LYS121 4.8 63.3 1.0 CE A:LYS326 4.9 48.6 1.0 O3B A:ATP401 4.9 85.7 1.0

Manganese binding site 2 out of 3 in the Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:0.5 occ:1.00 O A:HOH512 2.5 61.6 1.0 O A:HOH520 2.5 60.3 1.0 O2G A:ATP401 2.7 92.7 1.0 O1G A:ATP401 2.7 89.6 1.0 OD1 A:ASP172 2.8 70.6 1.0 PG A:ATP401 3.1 91.2 1.0 CG A:ASP172 3.7 69.2 1.0 O3G A:ATP401 3.8 93.0 1.0 OE2 A:GLU227 3.9 57.6 1.0 O A:GLY173 4.0 71.7 1.0 NZ A:LYS170 4.2 47.1 1.0 OE1 A:GLU312 4.2 60.1 1.0 CA A:ASP172 4.2 64.8 1.0 OE2 A:GLU312 4.3 58.8 1.0 OD2 A:ASP172 4.3 69.8 1.0 N A:GLY173 4.4 72.2 1.0 CB A:ASP172 4.5 66.9 1.0 O3B A:ATP401 4.5 85.7 1.0 CD A:GLU312 4.6 57.9 1.0 O A:LEU171 4.7 62.0 1.0 C A:ASP172 4.8 67.9 1.0 C A:GLY173 4.8 72.7 1.0 O4' A:ATP401 4.9 50.5 1.0

Manganese binding site 3 out of 3 in the Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Naegleria Gruberi Rna Ligase R149A Mutant with Atp and Mn within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn404 b:0.2 occ:1.00 O3G A:ATP401 2.2 93.0 1.0 O1B A:ATP401 2.4 83.6 1.0 O1A A:ATP401 3.3 64.3 1.0 PG A:ATP401 3.5 91.2 1.0 O A:HOH541 3.6 67.9 1.0 PB A:ATP401 3.7 80.8 1.0 O1G A:ATP401 3.9 89.6 1.0 O A:HOH512 3.9 61.6 1.0 O3B A:ATP401 3.9 85.7 1.0 OD2 A:ASP53 4.0 67.3 1.0 NZ A:LYS121 4.4 63.3 1.0 PA A:ATP401 4.4 63.5 1.0 O3A A:ATP401 4.4 72.8 1.0 NZ A:LYS326 4.6 51.5 1.0 O2G A:ATP401 4.7 92.7 1.0 O2B A:ATP401 4.9 79.1 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