Manganese in PDB 5cou: Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp

The structure of Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp, PDB code: 5cou 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)	24.10 / 1.90
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	54.969, 54.969, 100.308, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 24.7

The binding sites of Manganese atom in the Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp (pdb code 5cou). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp, PDB code: 5cou:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:17.0 occ:1.00 O A:HOH635 1.7 17.7 1.0 O A:HOH541 1.8 23.6 1.0 O3G A:ATP401 2.0 21.8 1.0 O A:HOH566 2.1 22.1 1.0 O2B A:ATP401 2.1 18.0 1.0 O A:HOH671 2.1 19.7 1.0 PG A:ATP401 3.2 20.8 1.0 PB A:ATP401 3.3 20.6 1.0 O3B A:ATP401 3.6 22.5 1.0 O A:HOH595 3.7 36.3 1.0 O2A A:ATP401 3.9 19.4 1.0 O1G A:ATP401 4.0 19.1 1.0 O A:HOH763 4.0 28.3 1.0 O3A A:ATP401 4.1 19.7 1.0 NH2 A:ARG149 4.2 19.8 1.0 OD2 A:ASP53 4.2 23.6 1.0 O A:HOH767 4.3 34.5 1.0 O A:HOH657 4.4 18.8 1.0 PA A:ATP401 4.4 19.9 1.0 O A:HOH518 4.4 20.7 1.0 O2G A:ATP401 4.5 20.4 1.0 O1B A:ATP401 4.6 22.5 1.0 O1A A:ATP401 4.7 21.4 1.0 O A:HOH527 4.7 48.5 1.0 NZ A:LYS121 5.0 35.9 1.0

Manganese binding site 2 out of 2 in the Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure and Mechanism of A Eukaryal Nick-Sealing Rna Ligase K170M+Atp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn403 b:16.2 occ:1.00 O A:HOH590 1.8 20.5 1.0 O A:HOH657 1.9 18.8 1.0 O A:HOH518 2.1 20.7 1.0 O1A A:ATP401 2.1 21.4 1.0 O A:HOH538 2.1 16.2 1.0 O A:HOH572 2.2 19.7 1.0 PA A:ATP401 3.6 19.9 1.0 OE2 A:GLU227 4.0 18.6 1.0 O2B A:ATP401 4.1 18.0 1.0 OE2 A:GLU312 4.1 21.8 1.0 OE1 A:GLU312 4.1 24.1 1.0 O2A A:ATP401 4.3 19.4 1.0 O4' A:ATP401 4.3 19.1 1.0 C4' A:ATP401 4.3 19.6 1.0 O3A A:ATP401 4.4 19.7 1.0 OD1 A:ASP172 4.4 26.9 1.0 CE A:MET170 4.4 18.3 1.0 O A:HOH774 4.5 28.0 1.0 O A:GLY173 4.6 21.6 1.0 O5' A:ATP401 4.6 18.0 1.0 CD A:GLU312 4.6 23.1 1.0 O A:HOH635 4.6 17.7 1.0 C1' A:ATP401 4.6 18.6 1.0 O A:LEU171 4.7 19.4 1.0 PB A:ATP401 4.8 20.6 1.0 O A:HOH671 4.8 19.7 1.0 O A:HOH658 4.9 25.6 1.0 N A:GLY173 4.9 22.6 1.0 CA A:ASP172 5.0 22.0 1.0

M.C.Unciuleac, Y.Goldgur, S.Shuman. Structure and Two-Metal Mechanism of A Eukaryal Nick-Sealing Rna Ligase. Proc.Natl.Acad.Sci.Usa V. 112 13868 2015.
ISSN: ESSN 1091-6490
PubMed: 26512110
DOI: 10.1073/PNAS.1516536112