Magnesium in PDB 3ruq: Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis

The structure of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis, PDB code: 3ruq was solved by J.H.Pereira, C.Y.Ralston, N.R.Douglas, R.Kumar, R.P.Mcandrew, K.M.Knee, J.Frydman, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	162.164, 185.002, 184.769, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 21.5

The binding sites of Magnesium atom in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis (pdb code 3ruq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis, PDB code: 3ruq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


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 Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg544 b:32.5 occ:1.00 O A:HOH546 2.0 40.6 1.0 OD1 A:ASP91 2.1 69.3 1.0 O2A A:ADP545 2.2 45.8 1.0 O A:HOH559 2.2 49.6 1.0 O3B A:ADP545 2.3 45.4 1.0 CG A:ASP91 2.8 64.0 1.0 OD2 A:ASP91 2.9 62.8 1.0 PB A:ADP545 3.5 32.3 1.0 PA A:ADP545 3.5 35.6 1.0 O A:HOH560 3.5 54.4 1.0 O3A A:ADP545 3.9 46.8 1.0 O1B A:ADP545 4.0 37.0 1.0 O A:SER157 4.2 40.8 1.0 N A:GLY92 4.2 38.8 1.0 C5' A:ADP545 4.2 45.9 1.0 O5' A:ADP545 4.2 44.7 1.0 NZ A:LYS161 4.3 65.9 1.0 CB A:ASP91 4.3 47.9 1.0 CE A:LYS161 4.4 54.5 1.0 OD2 A:ASP386 4.6 78.1 1.0 O A:HOH561 4.7 61.0 1.0 OG A:SER157 4.7 51.8 1.0 O1A A:ADP545 4.7 44.6 1.0 O2B A:ADP545 4.8 38.9 1.0 CA A:ASP91 4.9 38.5 1.0 CA A:SER157 4.9 36.6 1.0 CA A:GLY92 4.9 39.8 1.0 CG A:ASP386 5.0 94.8 1.0 C A:SER157 5.0 44.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


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 Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg544 b:33.1 occ:1.00 OD1 B:ASP91 2.1 57.4 1.0 O3B B:ADP545 2.2 53.2 1.0 O2A B:ADP545 2.3 38.4 1.0 O B:HOH555 2.3 59.0 1.0 O B:HOH546 2.5 34.8 1.0 O B:HOH554 2.7 57.5 1.0 CG B:ASP91 2.8 56.0 1.0 OD2 B:ASP91 2.8 56.7 1.0 PB B:ADP545 3.4 44.6 1.0 PA B:ADP545 3.6 43.6 1.0 O1B B:ADP545 3.7 38.4 1.0 O3A B:ADP545 3.8 51.1 1.0 N B:GLY92 4.1 47.1 1.0 C5' B:ADP545 4.1 51.9 1.0 CB B:ASP91 4.2 44.5 1.0 O B:SER157 4.2 41.1 1.0 O5' B:ADP545 4.3 43.5 1.0 NZ B:LYS161 4.3 77.7 1.0 O B:HOH547 4.4 47.6 1.0 CE B:LYS161 4.5 69.5 1.0 OD2 B:ASP386 4.6 85.1 1.0 O2B B:ADP545 4.7 39.9 1.0 CA B:ASP91 4.8 34.5 1.0 OG B:SER157 4.8 56.9 1.0 O1A B:ADP545 4.8 47.3 1.0 CA B:GLY92 4.8 44.8 1.0 C B:ASP91 4.9 41.0 1.0 CA B:SER157 5.0 34.8 1.0 CG B:ASP386 5.0 0.0 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


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 Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg544 b:40.5 occ:1.00 OD1 C:ASP91 2.1 50.9 1.0 O C:HOH558 2.2 48.8 1.0 O2A C:ADP545 2.2 42.4 1.0 O C:HOH546 2.2 46.2 1.0 O C:HOH559 2.6 34.9 1.0 O3B C:ADP545 2.6 39.1 1.0 CG C:ASP91 3.1 48.0 1.0 OD2 C:ASP91 3.3 60.7 1.0 PB C:ADP545 3.4 36.2 1.0 PA C:ADP545 3.5 37.4 1.0 O1B C:ADP545 3.6 41.8 1.0 OD2 C:ASP386 3.7 86.2 1.0 O3A C:ADP545 3.8 49.8 1.0 CE C:LYS161 4.0 64.4 1.0 NZ C:LYS161 4.1 52.8 1.0 O C:HOH547 4.2 48.8 1.0 N C:GLY92 4.3 34.4 1.0 CG C:ASP386 4.3 98.4 1.0 O C:SER157 4.4 40.6 1.0 CB C:ASP91 4.5 26.8 1.0 O5' C:ADP545 4.6 51.2 1.0 O1A C:ADP545 4.6 48.9 1.0 O C:HOH560 4.6 59.6 1.0 CB C:ASP386 4.7 94.3 1.0 C5' C:ADP545 4.7 49.0 1.0 CA C:ASP91 4.8 31.2 1.0 O2B C:ADP545 4.9 45.0 1.0 OG C:SER157 4.9 54.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Cpn-Wt in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg544 b:44.7 occ:1.00 O2A D:ADP545 2.0 49.2 1.0 O D:HOH553 2.1 61.9 1.0 O D:HOH546 2.2 44.2 1.0 O D:HOH554 2.2 62.3 1.0 OD1 D:ASP91 2.2 59.5 1.0 O1B D:ADP545 2.4 42.5 1.0 CG D:ASP91 3.1 55.3 1.0 OD2 D:ASP91 3.2 53.0 1.0 PA D:ADP545 3.4 34.3 1.0 PB D:ADP545 3.4 43.9 1.0 O3B D:ADP545 3.7 44.4 1.0 O3A D:ADP545 3.7 0.3 1.0 CE D:LYS161 4.1 55.1 1.0 NZ D:LYS161 4.1 59.7 1.0 N D:GLY92 4.2 41.9 1.0 OD2 D:ASP386 4.3 95.2 1.0 C5' D:ADP545 4.3 50.3 1.0 O D:SER157 4.3 46.2 1.0 O D:HOH547 4.3 37.4 1.0 O5' D:ADP545 4.4 58.6 1.0 O1A D:ADP545 4.4 49.1 1.0 CB D:ASP91 4.5 42.1 1.0 CG D:ASP386 4.8 99.7 1.0 O2B D:ADP545 4.8 48.2 1.0 O D:HOH555 4.9 53.8 1.0 CA D:ASP91 4.9 36.6 1.0 OG D:SER157 4.9 58.1 1.0 CA D:GLY92 5.0 43.6 1.0

J.H.Pereira, C.Y.Ralston, N.R.Douglas, R.Kumar, T.Lopez, R.P.Mcandrew, K.M.Knee, J.A.King, J.Frydman, P.D.Adams. Mechanism of Nucleotide Sensing in Group II Chaperonins. Embo J. V. 31 731 2012.
ISSN: ISSN 0261-4189
PubMed: 22193720
DOI: 10.1038/EMBOJ.2011.468