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

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

Resolution Low / High (Å)	49.04 / 2.34
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	161.564, 185.585, 185.494, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22.1

The binding sites of Magnesium atom in the Crystal Structure of Cpn-Rls in Complex with Adp From Methanococcus Maripaludis (pdb code 3rus). 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-Rls in Complex with Adp From Methanococcus Maripaludis, PDB code: 3rus:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Cpn-Rls 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-Rls in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg544 b:30.8 occ:1.00 O1A A:ADP545 2.1 43.5 1.0 O A:HOH631 2.1 25.6 1.0 OD1 A:ASP91 2.2 32.5 1.0 O A:HOH641 2.2 32.1 1.0 O1B A:ADP545 2.3 43.0 1.0 O A:HOH552 2.3 28.9 1.0 CG A:ASP91 3.1 35.8 1.0 PB A:ADP545 3.3 30.9 1.0 OD2 A:ASP91 3.3 40.5 1.0 PA A:ADP545 3.4 32.3 1.0 O3B A:ADP545 3.7 35.6 1.0 O3A A:ADP545 3.7 46.4 1.0 O A:HOH571 4.0 30.0 1.0 N A:GLY92 4.1 21.7 1.0 O A:HOH562 4.2 36.0 1.0 O A:HOH557 4.2 35.0 1.0 NZ A:LYS161 4.3 45.2 1.0 O5' A:ADP545 4.3 46.4 1.0 OD2 A:ASP386 4.3 55.2 1.0 O A:HOH567 4.4 29.1 1.0 C5' A:ADP545 4.4 39.1 1.0 CE A:LYS161 4.4 40.8 1.0 O A:SER157 4.5 27.8 1.0 CB A:ASP91 4.5 29.6 1.0 O2A A:ADP545 4.6 43.3 1.0 O2B A:ADP545 4.7 42.2 1.0 CG A:ASP386 4.7 54.4 1.0 O A:HOH705 4.8 59.4 1.0 OG A:SER157 4.8 36.0 1.0 CA A:ASP91 4.9 24.6 1.0 CA A:GLY92 4.9 15.3 1.0 C A:ASP91 5.0 20.5 1.0 CB A:ASP386 5.0 36.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Cpn-Rls 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-Rls in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg544 b:31.3 occ:1.00 O1A B:ADP545 2.1 37.5 1.0 O B:HOH550 2.1 25.4 1.0 OD1 B:ASP91 2.2 40.9 1.0 O B:HOH551 2.3 30.4 1.0 O B:HOH549 2.3 28.0 1.0 O1B B:ADP545 2.4 52.9 1.0 PB B:ADP545 3.1 42.2 1.0 O3B B:ADP545 3.2 35.9 1.0 CG B:ASP91 3.3 42.9 1.0 PA B:ADP545 3.4 41.5 1.0 OD2 B:ASP91 3.6 46.9 1.0 O B:HOH625 3.6 54.8 1.0 O3A B:ADP545 3.6 53.6 1.0 OD2 B:ASP386 4.0 56.6 1.0 O B:HOH552 4.1 31.9 1.0 N B:GLY92 4.2 24.7 1.0 O B:HOH562 4.3 32.5 1.0 O B:HOH565 4.3 35.3 1.0 O5' B:ADP545 4.4 42.4 1.0 C5' B:ADP545 4.4 55.8 1.0 O2A B:ADP545 4.5 47.4 1.0 O B:SER157 4.5 30.1 1.0 O B:HOH599 4.5 46.1 1.0 O2B B:ADP545 4.6 36.9 1.0 CB B:ASP91 4.6 33.0 1.0 CG B:ASP386 4.6 48.9 1.0 O B:HOH661 4.6 51.0 1.0 CA B:ASP91 4.8 29.5 1.0 CA B:GLY92 5.0 25.0 1.0 CB B:ASP386 5.0 36.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Cpn-Rls 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-Rls in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg544 b:28.0 occ:1.00 O1A C:ADP545 2.0 38.3 1.0 O C:HOH680 2.1 35.4 1.0 O C:HOH612 2.2 30.4 1.0 O1B C:ADP545 2.2 38.8 1.0 OD1 C:ASP91 2.3 31.1 1.0 O C:HOH549 2.3 23.3 1.0 CG C:ASP91 3.1 37.0 1.0 PB C:ADP545 3.2 32.4 1.0 OD2 C:ASP91 3.3 38.1 1.0 PA C:ADP545 3.3 32.8 1.0 O3B C:ADP545 3.5 36.0 1.0 O3A C:ADP545 3.6 46.3 1.0 O C:HOH678 3.9 68.3 1.0 OD2 C:ASP386 4.0 54.3 1.0 O C:HOH555 4.0 27.1 1.0 N C:GLY92 4.2 23.4 1.0 O C:HOH557 4.2 38.9 1.0 O C:HOH562 4.2 37.9 1.0 O5' C:ADP545 4.3 51.0 1.0 CE C:LYS161 4.3 44.7 1.0 C5' C:ADP545 4.3 47.4 1.0 O C:SER157 4.4 31.2 1.0 O C:HOH574 4.4 38.6 1.0 O2A C:ADP545 4.5 46.9 1.0 CB C:ASP91 4.5 30.2 1.0 NZ C:LYS161 4.6 48.2 1.0 O2B C:ADP545 4.6 48.7 1.0 CG C:ASP386 4.7 46.2 1.0 OG C:SER157 4.9 35.8 1.0 CA C:GLY92 4.9 21.5 1.0 CA C:ASP91 4.9 25.6 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Cpn-Rls 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-Rls in Complex with Adp From Methanococcus Maripaludis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg544 b:39.4 occ:1.00 OD1 D:ASP91 2.2 43.8 1.0 O D:HOH665 2.2 32.5 1.0 O D:HOH664 2.2 29.2 1.0 O D:HOH640 2.3 30.9 1.0 O1A D:ADP545 2.3 44.0 1.0 O1B D:ADP545 2.6 41.7 1.0 CG D:ASP91 3.1 43.5 1.0 OD2 D:ASP91 3.3 44.2 1.0 PB D:ADP545 3.4 40.4 1.0 OD2 D:ASP386 3.4 63.6 1.0 O3B D:ADP545 3.5 42.7 1.0 PA D:ADP545 3.6 30.7 1.0 O D:HOH667 3.6 82.5 1.0 O3A D:ADP545 3.8 0.0 1.0 O D:HOH550 4.2 32.4 1.0 CE D:LYS161 4.2 43.1 1.0 N D:GLY92 4.2 31.3 1.0 O D:HOH666 4.3 32.9 1.0 NZ D:LYS161 4.3 42.0 1.0 CG D:ASP386 4.3 53.5 1.0 O D:HOH583 4.4 43.5 1.0 CB D:ASP91 4.5 36.9 1.0 O D:HOH552 4.5 32.9 1.0 O D:SER157 4.5 38.8 1.0 O2A D:ADP545 4.5 47.5 1.0 O5' D:ADP545 4.7 61.0 1.0 C5' D:ADP545 4.7 44.2 1.0 CA D:ASP91 4.8 31.7 1.0 CB D:ASP386 4.8 39.1 1.0 O2B D:ADP545 4.8 46.8 1.0 OG D:SER157 4.9 41.1 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