Magnesium in PDB 1svt: Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7

The structure of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7, PDB code: 1svt was solved by C.Chaudhry, A.L.Horwich, A.T.Brunger, P.D.Adams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 2.81
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	255.546, 266.855, 187.049, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 27.4

The structure of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 also contains other interesting chemical elements:

Fluorine	(F)	21 atoms
Aluminium	(Al)	7 atoms
Potassium	(K)	7 atoms

The binding sites of Magnesium atom in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 (pdb code 1svt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7, PDB code: 1svt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


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 GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:2.0 occ:1.00 O1B A:ADP600 1.6 2.0 1.0 O2A A:ADP600 1.7 2.0 1.0 F1 A:AF3602 1.8 2.8 1.0 OD1 A:ASP87 2.3 2.0 1.0 PB A:ADP600 2.9 2.0 1.0 AL A:AF3602 2.9 7.2 1.0 PA A:ADP600 3.2 2.2 1.0 F2 A:AF3602 3.2 10.1 1.0 CG A:ASP87 3.2 2.4 1.0 OD2 A:ASP87 3.3 4.2 1.0 O3A A:ADP600 3.5 2.6 1.0 C5' A:ADP600 3.7 2.4 1.0 O3B A:ADP600 3.7 3.6 1.0 O5' A:ADP600 4.0 2.0 1.0 O2B A:ADP600 4.1 2.0 1.0 O A:SER151 4.4 2.6 1.0 O1A A:ADP600 4.4 2.0 1.0 N A:GLY88 4.5 2.0 1.0 CB A:ASP87 4.6 2.4 1.0 F3 A:AF3602 4.7 2.0 1.0 CA A:SER151 4.9 2.0 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


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 GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:2.0 occ:1.00 O2A B:ADP600 1.6 2.6 1.0 O1B B:ADP600 1.7 2.0 1.0 F1 B:AF3602 1.8 2.1 1.0 OD1 B:ASP87 2.6 2.0 1.0 PB B:ADP600 3.0 2.2 1.0 PA B:ADP600 3.1 3.2 1.0 AL B:AF3602 3.2 8.0 1.0 OD2 B:ASP87 3.3 4.1 1.0 CG B:ASP87 3.4 2.4 1.0 O3A B:ADP600 3.5 2.5 1.0 C5' B:ADP600 3.7 2.5 1.0 O5' B:ADP600 3.9 2.1 1.0 F2 B:AF3602 3.9 10.1 1.0 O3B B:ADP600 4.0 3.2 1.0 O2B B:ADP600 4.1 2.6 1.0 O1A B:ADP600 4.3 2.0 1.0 O B:SER151 4.3 2.4 1.0 N B:GLY88 4.7 2.0 1.0 CB B:ASP87 4.7 2.0 1.0 CA B:SER151 4.8 2.0 1.0 F3 B:AF3602 4.9 2.0 1.0 OD2 B:ASP398 5.0 8.1 1.0 C B:SER151 5.0 2.0 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


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 GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg601 b:2.0 occ:1.00 F1 C:AF3602 1.6 2.0 1.0 O1B C:ADP600 1.8 2.0 1.0 O2A C:ADP600 1.8 2.4 1.0 OD1 C:ASP87 2.3 2.9 1.0 AL C:AF3602 3.0 8.2 1.0 PB C:ADP600 3.0 2.5 1.0 CG C:ASP87 3.3 3.1 1.0 PA C:ADP600 3.3 2.0 1.0 OD2 C:ASP87 3.4 4.5 1.0 F2 C:AF3602 3.5 10.6 1.0 O3A C:ADP600 3.6 2.6 1.0 C5' C:ADP600 3.8 2.4 1.0 O3B C:ADP600 3.9 3.2 1.0 O5' C:ADP600 4.1 2.1 1.0 O C:SER151 4.3 2.4 1.0 O2B C:ADP600 4.3 2.3 1.0 O1A C:ADP600 4.5 2.0 1.0 N C:GLY88 4.6 2.0 1.0 CA C:SER151 4.7 2.0 1.0 OD2 C:ASP398 4.7 8.5 1.0 CB C:ASP87 4.8 2.4 1.0 F3 C:AF3602 4.8 2.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


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 GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg601 b:2.0 occ:1.00 O2A D:ADP600 1.5 2.0 1.0 O1B D:ADP600 1.6 2.0 1.0 F1 D:AF3602 1.7 2.0 1.0 OD1 D:ASP87 2.5 2.2 1.0 PB D:ADP600 2.8 2.5 1.0 PA D:ADP600 2.9 2.3 1.0 AL D:AF3602 2.9 8.1 1.0 F2 D:AF3602 3.1 10.1 1.0 O D:HOH611 3.1 51.0 1.0 O3A D:ADP600 3.3 2.1 1.0 C5' D:ADP600 3.5 2.4 1.0 CG D:ASP87 3.5 2.5 1.0 OD2 D:ASP87 3.6 3.5 1.0 O3B D:ADP600 3.7 3.4 1.0 O5' D:ADP600 3.7 2.0 1.0 O2B D:ADP600 4.0 2.3 1.0 O1A D:ADP600 4.1 2.0 1.0 N D:GLY88 4.5 2.0 1.0 O D:SER151 4.7 2.6 1.0 F3 D:AF3602 4.7 2.0 1.0 CB D:ASP87 4.9 2.4 1.0 C4' D:ADP600 4.9 2.1 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg601 b:2.0 occ:1.00 O1B E:ADP600 1.6 2.0 1.0 O2A E:ADP600 1.7 2.5 1.0 F1 E:AF3602 1.8 2.0 1.0 O E:HOH608 2.2 54.7 1.0 OD1 E:ASP87 2.4 2.3 1.0 PB E:ADP600 2.8 2.3 1.0 AL E:AF3602 2.9 8.2 1.0 PA E:ADP600 3.0 3.3 1.0 CG E:ASP87 3.3 2.9 1.0 O3A E:ADP600 3.3 2.7 1.0 F2 E:AF3602 3.4 9.8 1.0 OD2 E:ASP87 3.5 4.4 1.0 C5' E:ADP600 3.7 2.5 1.0 O3B E:ADP600 3.7 3.5 1.0 O5' E:ADP600 3.9 2.4 1.0 O2B E:ADP600 4.1 2.2 1.0 O1A E:ADP600 4.3 2.0 1.0 N E:GLY88 4.4 2.0 1.0 O E:SER151 4.5 2.2 1.0 F3 E:AF3602 4.7 2.0 1.0 CB E:ASP87 4.7 2.2 1.0 OD2 E:ASP398 4.9 8.3 1.0 CA E:SER151 5.0 2.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg601 b:2.0 occ:1.00 O2A F:ADP600 1.6 2.2 1.0 O1B F:ADP600 1.7 2.0 1.0 F1 F:AF3602 1.7 2.2 1.0 OD1 F:ASP87 2.4 2.5 1.0 AL F:AF3602 3.0 8.3 1.0 PB F:ADP600 3.0 2.0 1.0 PA F:ADP600 3.0 2.2 1.0 CG F:ASP87 3.3 2.8 1.0 OD2 F:ASP87 3.3 4.2 1.0 F2 F:AF3602 3.4 9.8 1.0 O3A F:ADP600 3.5 2.1 1.0 C5' F:ADP600 3.7 2.5 1.0 O3B F:ADP600 3.9 3.7 1.0 O5' F:ADP600 3.9 2.0 1.0 O1A F:ADP600 4.2 2.0 1.0 O2B F:ADP600 4.2 2.0 1.0 O F:SER151 4.5 2.3 1.0 N F:GLY88 4.6 2.0 1.0 F3 F:AF3602 4.7 2.0 1.0 CB F:ASP87 4.7 2.4 1.0 CA F:SER151 4.9 2.0 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of GROEL14-GROES7-(Adp-Alfx)7 within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg601 b:2.0 occ:1.00 F1 G:AF3602 1.6 2.4 1.0 O1B G:ADP600 1.7 2.0 1.0 O2A G:ADP600 1.7 2.4 1.0 OD1 G:ASP87 2.3 2.6 1.0 AL G:AF3602 2.9 8.0 1.0 PB G:ADP600 3.0 2.5 1.0 PA G:ADP600 3.1 2.0 1.0 CG G:ASP87 3.3 2.7 1.0 O3A G:ADP600 3.4 2.2 1.0 F2 G:AF3602 3.4 9.5 1.0 OD2 G:ASP87 3.4 3.8 1.0 O3B G:ADP600 3.9 3.7 1.0 C5' G:ADP600 3.9 2.5 1.0 O5' G:ADP600 4.0 2.0 1.0 O1A G:ADP600 4.3 2.0 1.0 O2B G:ADP600 4.3 2.0 1.0 O G:SER151 4.5 2.4 1.0 N G:GLY88 4.5 2.0 1.0 F3 G:AF3602 4.6 2.0 1.0 CB G:ASP87 4.7 2.2 1.0 OD2 G:ASP398 4.7 7.9 1.0 CA G:SER151 5.0 2.0 1.0

C.Chaudhry, A.L.Horwich, A.T.Brunger, P.D.Adams. Exploring the Structural Dynamics of the E.Coli Chaperonin Groel Using Translation-Libration-Screw Crystallographic Refinement of Intermediate States. J.Mol.Biol. V. 342 229 2004.
ISSN: ISSN 0022-2836
PubMed: 15313620
DOI: 10.1016/J.JMB.2004.07.015