Magnesium in PDB 2z4r: Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa

The structure of Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa, PDB code: 2z4r was solved by N.Fujikawa, S.Ozaki, W.Kagawa, S.-Y.Park, T.Katayama, H.Kurumizaka, S.Yokoyama, Riken Structuralgenomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.12 / 3.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.335, 221.787, 55.601, 90.00, 106.13, 90.00
R / Rfree (%)	23.1 / 26.4

The binding sites of Magnesium atom in the Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa (pdb code 2z4r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa, PDB code: 2z4r:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:45.0 occ:1.00 OG1 A:THR144 2.3 52.7 1.0 O3B A:ADP501 2.5 45.2 1.0 OD2 A:ASP202 2.8 56.3 1.0 OD1 A:ASP201 3.1 49.5 1.0 OD1 A:ASP202 3.3 56.4 1.0 CG A:ASP202 3.4 54.1 1.0 CB A:THR144 3.7 54.0 1.0 CG A:ASP201 3.8 50.6 1.0 PB A:ADP501 3.9 45.8 1.0 OD2 A:ASP201 3.9 49.5 1.0 N A:THR144 4.1 57.5 1.0 O1B A:ADP501 4.2 40.4 1.0 CA A:THR144 4.3 58.1 1.0 CE A:LYS143 4.4 28.3 1.0 CG2 A:THR144 4.5 52.4 1.0 O2B A:ADP501 4.5 44.2 1.0 CB A:LYS143 4.6 35.0 1.0 O2A A:ADP501 4.7 53.1 1.0 CB A:ASP202 4.7 50.3 1.0 N A:ASP202 4.8 56.4 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:45.0 occ:1.00 OG1 B:THR144 2.3 38.6 1.0 O3B B:ADP502 2.5 45.2 1.0 OD2 B:ASP202 2.8 48.9 1.0 OD1 B:ASP201 3.3 44.2 1.0 OD1 B:ASP202 3.3 50.5 1.0 CG B:ASP202 3.4 48.4 1.0 CB B:THR144 3.7 41.6 1.0 PB B:ADP502 3.8 44.3 1.0 CG B:ASP201 4.0 45.9 1.0 OD2 B:ASP201 4.1 42.6 1.0 O1B B:ADP502 4.2 43.3 1.0 N B:THR144 4.2 42.0 1.0 O2B B:ADP502 4.3 44.4 1.0 CA B:THR144 4.4 41.9 1.0 CG2 B:THR144 4.5 40.6 1.0 CE B:LYS143 4.5 37.5 1.0 O2A B:ADP502 4.6 50.2 1.0 CB B:LYS143 4.8 38.9 1.0 CB B:ASP202 4.8 45.3 1.0 NH2 B:ARG300 4.9 0.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Domain III From the Thermotoga Maritima Replication Initiation Protein Dnaa within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg502 b:48.3 occ:1.00 OG1 C:THR144 2.3 54.0 1.0 O3B C:ADP503 2.4 47.6 1.0 OD2 C:ASP202 2.8 52.5 1.0 OD1 C:ASP201 3.3 46.0 1.0 OD1 C:ASP202 3.3 50.4 1.0 CG C:ASP202 3.4 49.9 1.0 CB C:THR144 3.7 52.4 1.0 PB C:ADP503 3.8 51.7 1.0 CG C:ASP201 4.0 47.0 1.0 OD2 C:ASP201 4.1 45.2 1.0 O1B C:ADP503 4.2 48.3 1.0 N C:THR144 4.2 57.3 1.0 CA C:THR144 4.4 58.5 1.0 O2B C:ADP503 4.4 53.0 1.0 CG2 C:THR144 4.5 50.7 1.0 CE C:LYS143 4.6 37.3 1.0 O2A C:ADP503 4.6 52.6 1.0 CB C:ASP202 4.8 47.2 1.0 CB C:LYS143 4.9 44.0 1.0 NH2 C:ARG300 4.9 0.8 1.0

S.Ozaki, H.Kawakami, K.Nakamura, N.Fujikawa, W.Kagawa, S.-Y.Park, S.Yokoyama, H.Kurumizaka, T.Katayama. A Common Mechanism For the Atp-Dnaa-Dependent Formation of Open Complexes at the Replication Origin J.Biol.Chem. V. 283 8351 2008.
ISSN: ISSN 0021-9258
PubMed: 18216012
DOI: 10.1074/JBC.M708684200