Magnesium in PDB 4oi4: Yeast CLP1/PCF11 Complex

All present enzymatic activity of Yeast CLP1/PCF11 Complex:
2.7.1.78;

The structure of Yeast CLP1/PCF11 Complex, PDB code: 4oi4 was solved by A.Dikfidan, B.Loll, C.Zeymer, T.Clausen, A.Meinhart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.99 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.640, 95.770, 181.580, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.1

The binding sites of Magnesium atom in the Yeast CLP1/PCF11 Complex (pdb code 4oi4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Yeast CLP1/PCF11 Complex, PDB code: 4oi4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Yeast CLP1/PCF11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast CLP1/PCF11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:28.8 occ:1.00 O A:HOH698 2.1 29.2 1.0 O1G A:ATP501 2.1 41.4 1.0 OG1 A:THR137 2.1 29.6 1.0 O A:HOH687 2.2 29.2 1.0 O A:HOH613 2.2 26.1 1.0 O2B A:ATP501 2.2 39.2 1.0 CB A:THR137 3.3 29.7 1.0 PG A:ATP501 3.4 45.0 1.0 PB A:ATP501 3.4 37.8 1.0 O3B A:ATP501 3.5 41.4 1.0 O A:HOH611 4.0 29.0 1.0 OE1 A:GLN164 4.0 31.4 0.5 N A:THR137 4.1 30.5 1.0 CG A:GLN164 4.1 35.0 0.5 O2A A:ATP501 4.2 36.9 1.0 OD2 A:ASP161 4.2 35.0 1.0 CA A:THR137 4.2 29.6 1.0 CG2 A:THR137 4.3 28.4 1.0 O2G A:ATP501 4.3 45.0 1.0 OD2 A:ASP251 4.3 32.9 1.0 O1B A:ATP501 4.4 37.4 1.0 O3G A:ATP501 4.4 44.2 1.0 CD A:GLN164 4.4 36.2 0.5 OD1 A:ASP251 4.5 34.5 1.0 O3A A:ATP501 4.5 37.2 1.0 O A:THR252 4.7 34.2 1.0 OE1 A:GLN164 4.7 39.2 0.5 CB A:LYS136 4.8 32.3 1.0 PA A:ATP501 4.8 34.8 1.0 O A:HOH712 4.8 43.7 1.0 CG A:ASP251 4.8 32.4 1.0 CE A:LYS136 4.8 33.8 1.0 NE2 A:GLN164 4.9 35.4 0.5 O A:HOH643 4.9 39.6 1.0 CD A:GLN164 4.9 30.7 0.5 C A:LYS136 5.0 30.4 1.0

Magnesium binding site 2 out of 2 in the Yeast CLP1/PCF11 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast CLP1/PCF11 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:36.2 occ:1.00 OG1 C:THR137 2.1 34.6 1.0 O1B C:ATP501 2.1 41.7 1.0 O C:HOH651 2.2 35.1 1.0 O2G C:ATP501 2.2 41.7 1.0 O C:HOH667 2.2 38.8 1.0 O C:HOH668 2.2 34.3 1.0 CB C:THR137 3.3 35.8 1.0 PB C:ATP501 3.3 39.1 1.0 PG C:ATP501 3.4 44.6 1.0 O3B C:ATP501 3.6 40.9 1.0 O C:HOH614 4.0 29.8 1.0 N C:THR137 4.0 37.2 1.0 OD2 C:ASP251 4.2 37.7 1.0 O1A C:ATP501 4.2 39.4 1.0 CA C:THR137 4.2 35.4 1.0 O1G C:ATP501 4.2 43.2 1.0 OD2 C:ASP161 4.3 44.0 1.0 O2B C:ATP501 4.3 40.9 1.0 CG2 C:THR137 4.3 34.1 1.0 OE1 C:GLN164 4.3 43.6 1.0 OD1 C:ASP251 4.4 39.4 1.0 O3A C:ATP501 4.5 38.9 1.0 CE C:LYS136 4.5 43.2 1.0 O3G C:ATP501 4.6 43.7 1.0 O C:THR252 4.6 41.6 1.0 O C:HOH649 4.6 41.6 1.0 CB C:LYS136 4.7 39.2 1.0 CG C:ASP251 4.8 36.5 1.0 O C:HOH679 4.8 41.8 1.0 PA C:ATP501 4.8 37.7 1.0 CD C:GLN164 4.8 41.8 1.0 CG C:GLN164 4.9 38.9 1.0 NZ C:LYS136 5.0 47.8 1.0 C C:LYS136 5.0 37.0 1.0

A.Dikfidan, B.Loll, C.Zeymer, I.Magler, T.Clausen, A.Meinhart. Rna Specificity and Regulation of Catalysis in the Eukaryotic Polynucleotide Kinase CLP1. Mol.Cell V. 54 975 2014.
ISSN: ISSN 1097-2765
PubMed: 24813946
DOI: 10.1016/J.MOLCEL.2014.04.005