Magnesium in PDB 5z68: Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway

The structure of Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway, PDB code: 5z68 was solved by Q.Tang, Y.-P.Liu, X.-X.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.86 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.118, 138.821, 179.567, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.5

The binding sites of Magnesium atom in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway (pdb code 5z68). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway, PDB code: 5z68:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg408 b:81.3 occ:1.00 O2B A:ATP401 2.4 61.1 1.0 O A:HOH520 2.8 82.2 1.0 OG A:SER37 2.9 68.5 1.0 O2A A:ATP401 3.3 63.0 1.0 CB A:SER37 3.3 57.8 1.0 N B:GLN284 3.3 67.2 1.0 PB A:ATP401 3.6 53.9 1.0 O A:HOH505 3.6 65.3 1.0 O2G A:ATP401 3.6 83.7 1.0 O3B A:ATP401 3.6 71.2 1.0 CB B:GLN284 3.8 74.3 1.0 NH1 A:ARG53 4.0 69.8 1.0 PG A:ATP401 4.0 1.0 1.0 CA B:SER283 4.1 59.3 1.0 O3A A:ATP401 4.1 50.6 1.0 O3G A:ATP401 4.1 0.6 1.0 PA A:ATP401 4.1 55.9 1.0 CA B:GLN284 4.2 67.2 1.0 C B:SER283 4.2 65.6 1.0 CG B:GLN284 4.2 76.9 1.0 OG B:SER283 4.3 73.1 1.0 CB B:SER283 4.4 66.8 1.0 CA A:SER37 4.6 54.1 1.0 N A:SER37 4.7 52.6 1.0 O1A A:ATP401 4.7 58.7 1.0 O1B A:ATP401 4.9 66.3 1.0

Magnesium binding site 2 out of 4 in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:77.7 occ:1.00 O B:HOH502 1.9 77.1 1.0 OG B:SER37 2.2 62.4 1.0 O3G B:ATP401 2.3 72.2 1.0 O B:HOH501 2.9 55.7 1.0 O1B B:ATP401 2.9 67.4 1.0 OD1 B:ASP315 3.0 60.9 1.0 CB B:SER37 3.5 67.0 1.0 PG B:ATP401 3.5 76.5 1.0 OD2 B:ASP316 3.5 81.4 0.8 OD2 B:ASP315 3.6 58.3 1.0 CG B:ASP315 3.7 63.0 1.0 O1G B:ATP401 3.7 77.7 1.0 CG B:ASP316 3.8 78.4 0.6 OD1 B:ASP316 3.8 79.3 0.5 N B:SER37 3.9 75.1 1.0 PB B:ATP401 4.0 71.6 1.0 O3B B:ATP401 4.1 89.0 1.0 CA B:SER37 4.1 70.6 1.0 CB B:LYS36 4.3 69.7 1.0 CE B:LYS36 4.4 78.3 1.0 CB B:ASP316 4.7 69.7 0.8 C B:LYS36 4.7 71.8 1.0 OG1 B:THR341 4.8 64.6 1.0 O2G B:ATP401 4.9 73.2 1.0 O3A B:ATP401 4.9 67.5 1.0

Magnesium binding site 3 out of 4 in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg406 b:70.0 occ:1.00 O2G C:ATP401 2.2 76.8 1.0 OG C:SER37 2.3 77.0 1.0 O C:HOH501 2.5 69.2 1.0 O2B C:ATP401 2.7 77.9 1.0 O3A C:ATP401 2.7 75.9 1.0 O C:HOH508 2.8 70.1 1.0 CB C:SER37 2.9 75.9 1.0 PB C:ATP401 3.3 75.4 1.0 PG C:ATP401 3.5 82.8 1.0 O3B C:ATP401 3.7 0.8 1.0 PA C:ATP401 3.8 71.2 1.0 NH2 C:ARG53 4.0 76.5 1.0 N C:SER37 4.0 70.4 1.0 CA C:SER37 4.0 74.0 1.0 O1A C:ATP401 4.1 73.1 1.0 O2A C:ATP401 4.1 83.8 1.0 N D:GLN284 4.2 72.8 1.0 CB D:SER283 4.2 75.6 1.0 O1G C:ATP401 4.4 84.3 1.0 OD2 C:ASP315 4.4 63.2 1.0 OD1 C:ASP315 4.4 74.6 1.0 CA D:SER283 4.5 70.2 1.0 O3G C:ATP401 4.6 84.2 1.0 O1B C:ATP401 4.7 77.6 1.0 CB D:GLN284 4.8 70.9 1.0 CG C:ASP315 4.8 73.8 1.0 OD2 C:ASP316 4.9 1.0 1.0 C D:SER283 4.9 72.8 1.0

Magnesium binding site 4 out of 4 in the Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Recombination Mediator Protein Recf-Atp in Recfor Pathway within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg408 b:77.1 occ:1.00 O1G D:ATP401 1.9 0.6 1.0 OG D:SER37 2.4 91.9 1.0 PG D:ATP401 2.8 0.4 0.7 O3B D:ATP401 3.0 0.1 1.0 O1B D:ATP401 3.1 93.4 1.0 O3G D:ATP401 3.3 0.2 1.0 CB D:SER37 3.3 83.3 1.0 O2A D:ATP401 3.6 89.6 1.0 PB D:ATP401 3.7 86.7 1.0 N C:GLN284 4.0 96.1 1.0 CB C:GLN284 4.1 0.2 1.0 OD2 D:ASP315 4.2 87.0 1.0 O2G D:ATP401 4.2 0.7 1.0 OD1 D:ASP315 4.3 92.1 1.0 OG C:SER283 4.3 93.3 1.0 O3A D:ATP401 4.5 78.6 1.0 OD1 D:ASP316 4.5 0.8 1.0 PA D:ATP401 4.6 82.0 1.0 OD2 D:ASP316 4.6 0.6 1.0 CA D:SER37 4.6 83.1 1.0 CG D:ASP315 4.6 90.6 1.0 CA C:GLN284 4.7 98.2 1.0 N D:SER37 4.7 87.7 1.0 NH1 D:ARG53 4.7 81.0 1.0 CG D:ASP316 4.8 0.7 1.0 CA C:SER283 4.9 90.8 1.0 O2B D:ATP401 4.9 95.3 1.0 C C:SER283 4.9 96.9 1.0

Q.Tang, Y.P.Liu, H.H.Shan, L.F.Tian, J.Z.Zhang, X.X.Yan. Atp-Dependent Conformational Change in Abc-Atpase Recf Serves As A Switch in Dna Repair. Sci Rep V. 8 2127 2018.
ISSN: ESSN 2045-2322
PubMed: 29391496
DOI: 10.1038/S41598-018-20557-0