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Magnesium in PDB 5d1o: Archaeal Atp-Dependent Rna Ligase - Form 1

Protein crystallography data

The structure of Archaeal Atp-Dependent Rna Ligase - Form 1, PDB code: 5d1o 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) 27.71 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.250, 114.870, 91.290, 90.00, 104.42, 90.00
R / Rfree (%) 20.6 / 26.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Archaeal Atp-Dependent Rna Ligase - Form 1 (pdb code 5d1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Archaeal Atp-Dependent Rna Ligase - Form 1, PDB code: 5d1o:

Magnesium binding site 1 out of 1 in 5d1o

Go back to Magnesium Binding Sites List in 5d1o
Magnesium binding site 1 out of 1 in the Archaeal Atp-Dependent Rna Ligase - Form 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg504

b:43.2
occ:1.00
O B:HOH605 2.5 39.5 1.0
O2P B:APK97 2.7 66.5 1.0
OE2 B:GLU151 2.9 37.4 1.0
O B:MET98 3.3 34.0 1.0
O4' B:APK97 3.4 43.3 1.0
NZ B:APK97 3.4 45.0 1.0
OE2 B:GLU231 3.5 40.2 1.0
C1' B:APK97 3.6 45.8 1.0
P B:APK97 3.8 56.0 1.0
CD B:GLU151 3.9 32.3 1.0
C4' B:APK97 4.1 39.6 1.0
CA B:ASN99 4.2 34.5 1.0
OE1 B:GLU231 4.3 41.1 1.0
C B:MET98 4.3 34.1 1.0
N B:GLY100 4.3 26.6 1.0
CD B:GLU231 4.3 44.2 1.0
OE1 B:GLU151 4.3 33.5 1.0
C8 B:APK97 4.4 38.4 1.0
N9 B:APK97 4.4 36.6 1.0
O B:GLY100 4.4 38.2 1.0
OD1 B:ASN99 4.4 31.6 1.0
O2' B:APK97 4.6 44.6 1.0
CE B:APK97 4.6 38.9 1.0
N B:ASN99 4.7 35.5 1.0
C2' B:APK97 4.7 41.4 1.0
C B:ASN99 4.8 28.9 1.0
O5' B:APK97 4.8 49.5 1.0
CG B:APK97 4.9 33.9 1.0
O1P B:APK97 4.9 38.6 1.0
CG B:GLU151 5.0 30.4 1.0
C B:GLY100 5.0 29.0 1.0

Reference:

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
Page generated: Mon Dec 14 20:09:44 2020

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