Magnesium in PDB 5d1p: Archaeal Atp-Dependent Rna Ligase - Form 2

The structure of Archaeal Atp-Dependent Rna Ligase - Form 2, PDB code: 5d1p was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.37 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.500, 115.304, 91.567, 90.00, 104.55, 90.00
R / Rfree (%)	19.2 / 24.1

The binding sites of Magnesium atom in the Archaeal Atp-Dependent Rna Ligase - Form 2 (pdb code 5d1p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Archaeal Atp-Dependent Rna Ligase - Form 2, PDB code: 5d1p:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Archaeal Atp-Dependent Rna Ligase - Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Archaeal Atp-Dependent Rna Ligase - Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:45.8 occ:1.00 O A:HOH648 2.0 40.0 1.0 O A:HOH624 2.2 33.7 1.0 O A:HOH694 2.2 32.0 1.0 O A:HOH622 2.2 33.6 1.0 O2P A:APK97 2.3 49.2 1.0 O A:HOH658 2.3 30.8 1.0 P A:APK97 3.2 56.2 1.0 NZ A:APK97 3.2 41.7 1.0 O4' A:APK97 3.9 45.2 1.0 OE2 A:GLU151 3.9 36.8 1.0 O1P A:APK97 3.9 45.1 1.0 OE2 A:GLU231 3.9 32.2 1.0 C1' A:APK97 4.3 44.9 1.0 C4' A:APK97 4.3 46.6 1.0 O A:GLY100 4.4 34.9 1.0 O A:HOH734 4.4 49.2 1.0 OE1 A:GLU231 4.4 33.5 1.0 O A:HOH702 4.5 37.9 1.0 O A:MET98 4.5 27.2 1.0 OD1 A:ASN99 4.5 28.4 1.0 O5' A:APK97 4.5 50.2 1.0 CD A:GLU231 4.6 35.3 1.0 CE A:APK97 4.7 40.0 1.0 O A:HOH626 4.8 36.6 1.0 N A:GLY100 4.8 31.2 1.0 O A:HOH707 4.8 38.3 1.0 CA A:ASN99 5.0 32.0 1.0 CD A:GLU151 5.0 34.0 1.0

Magnesium binding site 2 out of 2 in the Archaeal Atp-Dependent Rna Ligase - Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Archaeal Atp-Dependent Rna Ligase - Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:37.5 occ:1.00 O B:HOH713 2.0 34.2 1.0 O2P B:APK97 2.0 43.5 1.0 O B:HOH614 2.0 34.0 1.0 O B:HOH662 2.0 30.8 1.0 O B:HOH620 2.2 31.6 1.0 O B:HOH630 2.3 25.4 1.0 P B:APK97 3.4 52.3 1.0 NZ B:APK97 3.6 33.2 1.0 OE1 B:GLU231 3.9 33.5 1.0 O1P B:APK97 4.1 41.9 1.0 OE2 B:GLU151 4.1 29.9 1.0 OE2 B:GLU231 4.2 30.9 1.0 OD1 B:ASN99 4.3 26.2 1.0 O4' B:APK97 4.3 37.3 1.0 O B:HOH722 4.3 38.6 1.0 C4' B:APK97 4.5 37.1 1.0 CD B:GLU231 4.5 31.8 1.0 O B:HOH648 4.6 37.0 1.0 O B:HOH720 4.6 39.9 1.0 O B:GLY100 4.6 31.7 1.0 O5' B:APK97 4.6 41.8 1.0 O B:HOH708 4.6 40.0 1.0 O B:MET98 4.7 26.1 1.0 C1' B:APK97 4.7 35.6 1.0 CA B:ASN99 4.9 29.1 1.0

H.Gu, S.Yoshinari, R.Ghosh, A.V.Ignatochkina, P.D.Gollnick, K.S.Murakami, C.K.Ho. Structural and Mutational Analysis of Archaeal Atp-Dependent Rna Ligase Identifies Amino Acids Required For Rna Binding and Catalysis. Nucleic Acids Res. V. 44 2337 2016.
ISSN: ESSN 1362-4962
PubMed: 26896806
DOI: 10.1093/NAR/GKW094