Magnesium in PDB 1pcq: Crystal Structure of Groel-Groes

The structure of Crystal Structure of Groel-Groes, PDB code: 1pcq was solved by C.Chaudhry, G.W.Farr, M.J.Todd, H.S.Rye, A.T.Brunger, P.D.Adams, A.L.Horwich, P.B.Sigler, 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 (%)	26.2 / 27.8

The structure of Crystal Structure of Groel-Groes 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 Groel-Groes (pdb code 1pcq). 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 Groel-Groes, PDB code: 1pcq:
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 Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:2.1 occ:1.00 F1 A:AF3602 1.8 7.3 1.0 O2A A:ADP600 1.8 2.2 1.0 O1B A:ADP600 1.8 2.0 1.0 OD1 A:ASP87 2.5 2.4 1.0 PA A:ADP600 2.9 2.9 1.0 PB A:ADP600 3.0 2.6 1.0 O5' A:ADP600 3.1 3.4 1.0 OD2 A:ASP87 3.2 2.6 1.0 CG A:ASP87 3.3 2.8 1.0 O3A A:ADP600 3.4 3.8 1.0 AL A:AF3602 3.5 12.2 1.0 O3B A:ADP600 3.8 2.9 1.0 O1A A:ADP600 4.2 2.0 1.0 O2B A:ADP600 4.3 2.0 1.0 O A:SER151 4.4 2.4 1.0 C5' A:ADP600 4.5 4.4 1.0 N A:GLY88 4.5 2.0 1.0 F2 A:AF3602 4.7 8.7 1.0 CB A:ASP87 4.8 2.8 1.0 F3 A:AF3602 4.8 5.5 1.0 CA A:SER151 4.8 2.0 1.0 OD2 A:ASP398 4.9 9.2 1.0 C3' A:ADP600 5.0 6.1 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg701 b:2.0 occ:1.00 F1 B:AF3702 1.8 7.5 1.0 O2A B:ADP700 1.8 2.2 1.0 O1B B:ADP700 2.1 2.0 1.0 OD1 B:ASP87 2.4 2.4 1.0 PA B:ADP700 3.0 2.7 1.0 OD2 B:ASP87 3.1 2.9 1.0 CG B:ASP87 3.2 3.0 1.0 PB B:ADP700 3.3 2.5 1.0 O5' B:ADP700 3.3 3.5 1.0 O3A B:ADP700 3.6 3.5 1.0 AL B:AF3702 3.6 12.2 1.0 O3B B:ADP700 4.0 2.7 1.0 O B:SER151 4.2 2.4 1.0 O1A B:ADP700 4.3 2.0 1.0 OD2 B:ASP398 4.5 9.0 1.0 O2B B:ADP700 4.5 2.0 1.0 N B:GLY88 4.6 2.0 1.0 CA B:SER151 4.7 2.1 1.0 CB B:ASP87 4.7 2.6 1.0 C5' B:ADP700 4.7 4.4 1.0 F2 B:AF3702 4.7 8.5 1.0 C B:SER151 4.9 2.0 1.0 F3 B:AF3702 4.9 5.3 1.0 OG B:SER151 4.9 3.0 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg801 b:2.0 occ:1.00 O2A C:ADP800 1.7 2.0 1.0 F1 C:AF3802 1.8 7.3 1.0 O1B C:ADP800 2.1 2.1 1.0 OD1 C:ASP87 2.5 2.5 1.0 PA C:ADP800 2.9 2.5 1.0 OD2 C:ASP87 3.2 2.6 1.0 O5' C:ADP800 3.2 3.4 1.0 PB C:ADP800 3.3 2.1 1.0 CG C:ASP87 3.3 3.1 1.0 O3A C:ADP800 3.5 3.7 1.0 AL C:AF3802 3.6 12.4 1.0 O3B C:ADP800 4.0 2.7 1.0 O C:SER151 4.2 2.1 1.0 O1A C:ADP800 4.3 2.0 1.0 O2B C:ADP800 4.5 2.0 1.0 OD2 C:ASP398 4.5 9.4 1.0 C5' C:ADP800 4.6 4.2 1.0 CA C:SER151 4.7 2.0 1.0 N C:GLY88 4.7 2.0 1.0 F2 C:AF3802 4.7 8.8 1.0 CB C:ASP87 4.8 2.8 1.0 F3 C:AF3802 4.9 5.2 1.0 C C:SER151 4.9 2.0 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg901 b:2.0 occ:1.00 O2A D:ADP900 1.8 2.0 1.0 F1 D:AF3902 1.8 7.7 1.0 O1B D:ADP900 1.9 2.0 1.0 OD1 D:ASP87 2.5 2.3 1.0 PA D:ADP900 2.9 2.3 1.0 PB D:ADP900 3.1 2.0 1.0 OD2 D:ASP87 3.1 2.6 1.0 O5' D:ADP900 3.1 3.7 1.0 CG D:ASP87 3.2 3.0 1.0 O3A D:ADP900 3.4 3.4 1.0 AL D:AF3902 3.6 12.3 1.0 O3B D:ADP900 3.8 2.6 1.0 O1A D:ADP900 4.2 2.0 1.0 O2B D:ADP900 4.3 2.0 1.0 O D:SER151 4.4 2.5 1.0 C5' D:ADP900 4.6 4.3 1.0 N D:GLY88 4.6 2.0 1.0 CB D:ASP87 4.8 2.8 1.0 F2 D:AF3902 4.8 8.9 1.0 CA D:SER151 4.8 2.0 1.0 OD2 D:ASP398 4.9 9.0 1.0 F3 D:AF3902 4.9 5.6 1.0 C3' D:ADP900 4.9 6.0 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg1001 b:2.0 occ:1.00 O2A E:ADP1000 1.8 2.3 1.0 F1 E:AF31002 1.9 7.5 1.0 O1B E:ADP1000 2.0 2.0 1.0 OD1 E:ASP87 2.5 2.4 1.0 PA E:ADP1000 3.0 2.8 1.0 OD2 E:ASP87 3.1 2.8 1.0 CG E:ASP87 3.2 3.0 1.0 PB E:ADP1000 3.2 2.1 1.0 O5' E:ADP1000 3.3 3.5 1.0 O3A E:ADP1000 3.5 3.4 1.0 AL E:AF31002 3.6 12.1 1.0 O3B E:ADP1000 3.9 2.8 1.0 O E:SER151 4.2 2.4 1.0 O1A E:ADP1000 4.3 2.0 1.0 O2B E:ADP1000 4.5 2.0 1.0 N E:GLY88 4.6 2.0 1.0 OD2 E:ASP398 4.6 9.1 1.0 C5' E:ADP1000 4.7 4.4 1.0 CA E:SER151 4.7 2.0 1.0 CB E:ASP87 4.7 2.6 1.0 F2 E:AF31002 4.7 8.5 1.0 F3 E:AF31002 4.9 5.4 1.0 C E:SER151 4.9 2.0 1.0 OG E:SER151 5.0 2.9 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg1101 b:2.0 occ:1.00 O2A F:ADP1100 1.7 2.1 1.0 F1 F:AF31102 1.8 7.6 1.0 O1B F:ADP1100 2.0 2.0 1.0 OD1 F:ASP87 2.5 2.5 1.0 PA F:ADP1100 2.9 2.6 1.0 OD2 F:ASP87 3.2 2.8 1.0 PB F:ADP1100 3.2 2.0 1.0 CG F:ASP87 3.2 3.0 1.0 O5' F:ADP1100 3.3 3.3 1.0 O3A F:ADP1100 3.4 3.4 1.0 AL F:AF31102 3.6 12.1 1.0 O3B F:ADP1100 3.9 2.7 1.0 O1A F:ADP1100 4.2 2.0 1.0 O F:SER151 4.3 2.2 1.0 O2B F:ADP1100 4.5 2.0 1.0 N F:GLY88 4.6 2.0 1.0 OD2 F:ASP398 4.6 9.2 1.0 C5' F:ADP1100 4.7 4.2 1.0 F2 F:AF31102 4.7 8.7 1.0 CB F:ASP87 4.7 2.7 1.0 CA F:SER151 4.8 2.0 1.0 F3 F:AF31102 4.8 5.7 1.0 K F:K1103 5.0 24.0 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of Groel-Groes


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 Groel-Groes within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg1201 b:2.0 occ:1.00 F1 G:AF31202 1.7 7.4 1.0 O2A G:ADP1200 1.8 2.0 1.0 O1B G:ADP1200 2.0 2.0 1.0 OD1 G:ASP87 2.4 2.6 1.0 PA G:ADP1200 3.0 2.4 1.0 OD2 G:ASP87 3.2 2.4 1.0 PB G:ADP1200 3.2 2.3 1.0 CG G:ASP87 3.2 2.9 1.0 O5' G:ADP1200 3.3 3.6 1.0 O3A G:ADP1200 3.5 3.5 1.0 AL G:AF31202 3.6 12.2 1.0 O3B G:ADP1200 3.9 2.7 1.0 O1A G:ADP1200 4.3 2.0 1.0 O G:SER151 4.3 2.3 1.0 O2B G:ADP1200 4.5 2.1 1.0 OD2 G:ASP398 4.6 9.1 1.0 N G:GLY88 4.6 2.0 1.0 F2 G:AF31202 4.6 8.8 1.0 C5' G:ADP1200 4.7 4.2 1.0 CB G:ASP87 4.7 2.7 1.0 CA G:SER151 4.8 2.0 1.0 F3 G:AF31202 4.8 5.3 1.0 C G:SER151 5.0 2.0 1.0

C.Chaudhry, G.W.Farr, M.J.Todd, H.S.Rye, A.T.Brunger, P.D.Adams, A.L.Horwich, P.B.Sigler. Role of the Gamma-Phosphate of Atp in Triggering Protein Folding By Groel-Groes: Function, Structure and Energetics. Embo J. V. 22 4877 2003.
ISSN: ISSN 0261-4189
PubMed: 14517228
DOI: 10.1093/EMBOJ/CDG477