Magnesium in PDB 4pkn: Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco

The structure of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco, PDB code: 4pkn was solved by X.Fei, X.Ye, N.Laronde-Leblanc, G.H.Lorimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	122.19 / 3.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	171.952, 173.653, 411.270, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.1

The structure of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco also contains other interesting chemical elements:

Fluorine	(F)	42 atoms
Potassium	(K)	14 atoms

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco (pdb code 4pkn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco, PDB code: 4pkn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg603 b:41.0 occ:1.00 F2 G:BEF602 2.0 42.6 1.0 OD1 G:ASP87 2.2 59.2 1.0 O1B G:ADP601 2.2 24.9 1.0 OD2 G:ASP87 2.4 56.8 1.0 CG G:ASP87 2.6 58.0 1.0 O1A G:ADP601 2.8 37.2 1.0 BE G:BEF602 3.2 19.7 1.0 PB G:ADP601 3.3 25.6 1.0 PA G:ADP601 3.6 33.2 1.0 O3A G:ADP601 3.6 50.1 1.0 O5' G:ADP601 3.6 35.0 1.0 O3B G:ADP601 3.7 20.5 1.0 F1 G:BEF602 3.8 0.8 1.0 CB G:ASP87 4.1 56.6 1.0 O G:SER151 4.2 68.6 1.0 N G:GLY88 4.2 73.9 1.0 OG G:SER151 4.2 78.0 1.0 CA G:SER151 4.2 70.9 1.0 C5' G:ADP601 4.4 37.8 1.0 F3 G:BEF602 4.5 29.4 1.0 C G:SER151 4.6 64.6 1.0 O2B G:ADP601 4.6 20.6 1.0 CB G:SER151 4.7 74.9 1.0 CA G:ASP87 4.7 52.4 1.0 CA G:GLY88 4.9 73.8 1.0 C G:ASP87 4.9 54.6 1.0

Magnesium binding site 2 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:27.0 occ:1.00 O1B A:ADP601 2.0 32.6 1.0 OD1 A:ASP87 2.4 51.6 1.0 O3A A:ADP601 2.4 75.9 1.0 O1A A:ADP601 2.6 70.6 1.0 PB A:ADP601 2.7 33.0 1.0 F3 A:BEF602 2.8 52.2 1.0 OD2 A:ASP87 2.9 52.9 1.0 PA A:ADP601 2.9 65.8 1.0 CG A:ASP87 3.0 52.3 1.0 O5' A:ADP601 3.2 63.6 1.0 BE A:BEF602 3.3 62.8 1.0 O3B A:ADP601 3.5 31.7 1.0 F2 A:BEF602 3.9 41.9 1.0 O2B A:ADP601 4.0 31.1 1.0 O A:SER151 4.0 71.9 1.0 N A:GLY88 4.2 65.8 1.0 OG A:SER151 4.4 81.2 1.0 O2A A:ADP601 4.4 60.9 1.0 CA A:SER151 4.4 74.4 1.0 CB A:ASP87 4.4 52.9 1.0 C5' A:ADP601 4.4 61.9 1.0 F1 A:BEF602 4.4 46.1 1.0 C A:SER151 4.6 71.3 1.0 CA A:GLY88 4.9 63.7 1.0 CB A:SER151 4.9 78.5 1.0 CA A:ASP87 5.0 52.2 1.0

Magnesium binding site 3 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:32.1 occ:1.00 F3 B:BEF602 2.2 12.8 1.0 O1A B:ADP601 2.3 33.8 1.0 O1B B:ADP601 2.6 39.7 1.0 OD1 B:ASP87 2.7 83.9 1.0 O3A B:ADP601 2.8 36.6 1.0 OD2 B:ASP87 2.9 85.3 1.0 PA B:ADP601 2.9 32.2 1.0 CG B:ASP87 3.1 83.4 1.0 O5' B:ADP601 3.1 66.3 1.0 PB B:ADP601 3.4 36.4 1.0 O B:SER151 3.6 65.6 1.0 BE B:BEF602 3.7 66.0 1.0 OG B:SER151 3.9 74.4 1.0 K B:K604 3.9 0.9 1.0 C5' B:ADP601 4.1 66.8 1.0 O3B B:ADP601 4.1 33.8 1.0 CA B:SER151 4.2 72.2 1.0 C B:SER151 4.3 65.9 1.0 O2A B:ADP601 4.4 26.4 1.0 F1 B:BEF602 4.4 7.1 1.0 CB B:SER151 4.5 72.9 1.0 O2B B:ADP601 4.6 42.0 1.0 CB B:ASP87 4.6 81.2 1.0 N B:GLY88 4.6 70.0 1.0 OD2 B:ASP398 4.9 0.6 1.0

Magnesium binding site 4 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg603 b:33.2 occ:1.00 F3 F:BEF602 1.9 44.2 1.0 O1B F:ADP601 2.1 37.6 1.0 OD1 F:ASP87 2.3 80.1 1.0 OD2 F:ASP87 2.5 77.6 1.0 O1A F:ADP601 2.6 53.8 1.0 CG F:ASP87 2.8 79.8 1.0 PB F:ADP601 3.3 35.9 1.0 BE F:BEF602 3.5 58.2 1.0 PA F:ADP601 3.6 47.7 1.0 O3A F:ADP601 3.6 71.6 1.0 O F:SER151 3.8 76.2 1.0 O3B F:ADP601 3.9 34.5 1.0 O5' F:ADP601 3.9 51.1 1.0 OG F:SER151 4.1 93.3 1.0 CA F:SER151 4.2 82.7 1.0 CB F:ASP87 4.3 70.3 1.0 C5' F:ADP601 4.3 56.5 1.0 F1 F:BEF602 4.4 65.6 1.0 C F:SER151 4.4 77.7 1.0 N F:GLY88 4.5 56.0 1.0 O2B F:ADP601 4.6 30.5 1.0 CB F:SER151 4.6 89.0 1.0 OD2 F:ASP398 4.7 73.8 1.0 F2 F:BEF602 4.7 60.3 1.0 O2A F:ADP601 5.0 41.4 1.0

Magnesium binding site 5 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg603 b:11.7 occ:1.00 F3 E:BEF602 2.0 27.4 1.0 O3A E:ADP601 2.2 49.5 1.0 OD1 E:ASP87 2.8 59.9 1.0 O3B E:ADP601 2.8 47.8 1.0 OD2 E:ASP87 2.8 61.6 1.0 CG E:ASP87 3.2 60.8 1.0 O1A E:ADP601 3.2 69.0 1.0 PB E:ADP601 3.2 36.7 1.0 PA E:ADP601 3.2 63.5 1.0 BE E:BEF602 3.5 13.1 1.0 C5' E:ADP601 3.5 45.4 1.0 O5' E:ADP601 3.8 40.8 1.0 O E:SER151 3.8 79.0 1.0 OG E:SER151 3.9 79.2 1.0 CA E:SER151 4.0 84.3 1.0 O2B E:ADP601 4.0 29.2 1.0 C E:SER151 4.3 81.8 1.0 O1B E:ADP601 4.4 32.3 1.0 CB E:SER151 4.4 81.8 1.0 O2A E:ADP601 4.5 59.8 1.0 F1 E:BEF602 4.5 65.9 1.0 F2 E:BEF602 4.7 53.2 1.0 CB E:ASP87 4.7 61.7 1.0 N E:GLY88 4.8 65.9 1.0 O E:ILE150 4.9 64.0 1.0 OD2 E:ASP398 4.9 77.5 1.0 C4' E:ADP601 5.0 50.7 1.0 K E:K604 5.0 87.6 1.0

Magnesium binding site 6 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg603 b:21.4 occ:1.00 OD1 C:ASP87 2.0 69.0 1.0 F3 C:BEF602 2.0 45.0 1.0 O1B C:ADP601 2.3 56.4 1.0 O2A C:ADP601 2.3 58.9 1.0 OD2 C:ASP87 2.5 69.2 1.0 CG C:ASP87 2.6 68.8 1.0 BE C:BEF602 3.1 9.6 1.0 PB C:ADP601 3.4 52.8 1.0 F2 C:BEF602 3.4 68.6 1.0 PA C:ADP601 3.4 56.6 1.0 O3A C:ADP601 3.5 29.6 1.0 OG C:SER151 3.9 85.5 1.0 O3B C:ADP601 3.9 53.9 1.0 CB C:ASP87 4.0 68.6 1.0 O C:SER151 4.0 73.1 1.0 N C:GLY88 4.1 57.5 1.0 O5' C:ADP601 4.1 71.9 1.0 CA C:SER151 4.4 75.5 1.0 CB C:SER151 4.6 81.9 1.0 CA C:ASP87 4.6 66.9 1.0 OD2 C:ASP398 4.6 83.1 1.0 O2B C:ADP601 4.7 52.7 1.0 O1A C:ADP601 4.7 55.6 1.0 C C:SER151 4.7 73.6 1.0 F1 C:BEF602 4.7 69.4 1.0 C C:ASP87 4.9 65.7 1.0 CA C:GLY88 4.9 56.9 1.0 C5' C:ADP601 5.0 72.5 1.0

Magnesium binding site 7 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


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 the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg603 b:16.3 occ:1.00 F2 D:BEF602 1.9 35.4 1.0 OD1 D:ASP87 2.2 61.8 1.0 O1B D:ADP601 2.4 42.7 1.0 O1A D:ADP601 2.6 43.6 1.0 O3A D:ADP601 2.7 59.2 1.0 OD2 D:ASP87 2.9 63.0 1.0 CG D:ASP87 2.9 63.1 1.0 PA D:ADP601 3.1 38.0 1.0 PB D:ADP601 3.1 38.4 1.0 BE D:BEF602 3.4 30.1 1.0 O5' D:ADP601 3.5 54.8 1.0 O3B D:ADP601 3.8 33.3 1.0 O D:SER151 3.9 64.8 1.0 OG D:SER151 4.1 73.9 1.0 CB D:ASP87 4.4 65.9 1.0 CA D:SER151 4.4 70.2 1.0 O2B D:ADP601 4.4 36.8 1.0 F3 D:BEF602 4.4 30.3 1.0 C5' D:ADP601 4.5 58.4 1.0 N D:GLY88 4.5 67.6 1.0 O2A D:ADP601 4.5 38.1 1.0 C D:SER151 4.6 67.4 1.0 F1 D:BEF602 4.6 51.9 1.0 OD2 D:ASP398 4.6 0.8 1.0 K D:K604 4.7 63.3 1.0 CB D:SER151 4.8 71.7 1.0 CA D:ASP87 5.0 69.3 1.0

Magnesium binding site 8 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ K:Mg603 b:44.5 occ:1.00 F2 K:BEF602 2.0 19.7 1.0 O3B K:ADP601 2.2 51.1 1.0 OD1 K:ASP87 2.5 59.3 1.0 O3A K:ADP601 2.5 29.5 1.0 OD2 K:ASP87 2.8 62.7 1.0 CG K:ASP87 3.0 60.4 1.0 O5' K:ADP601 3.0 50.7 1.0 PB K:ADP601 3.0 46.7 1.0 PA K:ADP601 3.0 50.5 1.0 O1A K:ADP601 3.0 51.2 1.0 BE K:BEF602 3.3 82.7 1.0 O2B K:ADP601 4.0 40.5 1.0 O1B K:ADP601 4.0 48.2 1.0 C5' K:ADP601 4.2 50.9 1.0 N K:GLY88 4.2 75.8 1.0 F3 K:BEF602 4.3 25.5 1.0 OG K:SER151 4.3 84.3 1.0 O K:SER151 4.4 69.4 1.0 F1 K:BEF602 4.4 1.0 1.0 CB K:ASP87 4.4 57.5 1.0 CA K:SER151 4.5 77.5 1.0 O2A K:ADP601 4.5 50.6 1.0 CB K:SER151 4.8 82.0 1.0 CA K:GLY88 4.9 77.9 1.0 C K:SER151 4.9 71.0 1.0 C3' K:ADP601 4.9 43.4 1.0

Magnesium binding site 9 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg603 b:51.2 occ:1.00 F3 J:BEF602 1.9 18.6 1.0 O1B J:ADP601 2.4 31.6 1.0 OD2 J:ASP87 2.4 64.1 1.0 OD1 J:ASP87 2.6 58.3 1.0 CG J:ASP87 2.8 63.7 1.0 O1A J:ADP601 2.8 80.9 1.0 O3A J:ADP601 3.4 11.7 1.0 BE J:BEF602 3.4 90.8 1.0 PB J:ADP601 3.5 34.7 1.0 PA J:ADP601 3.5 77.7 1.0 O5' J:ADP601 3.6 61.0 1.0 O J:SER151 3.9 69.5 1.0 OG J:SER151 3.9 86.1 1.0 CA J:SER151 3.9 73.1 1.0 O3B J:ADP601 4.2 33.9 1.0 F2 J:BEF602 4.2 31.1 1.0 N J:GLY88 4.3 71.2 1.0 CB J:ASP87 4.3 70.0 1.0 CB J:SER151 4.4 80.4 1.0 C J:SER151 4.4 69.8 1.0 O2B J:ADP601 4.7 33.2 1.0 F1 J:BEF602 4.8 49.2 1.0 O J:ILE150 4.9 80.5 1.0 C3' J:ADP601 4.9 41.9 1.0 CA J:GLY88 5.0 66.8 1.0 C5' J:ADP601 5.0 62.5 1.0 O2A J:ADP601 5.0 74.6 1.0

Magnesium binding site 10 out of 14 in the Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of the Football-Shaped Groel-GROES2-(Adpbefx)14 Complex Containing Substrate Rubisco within 5.0Å range: probe atom residue distance (Å) B Occ I:Mg603 b:17.2 occ:1.00 O1A I:ADP601 2.0 75.5 1.0 F3 I:BEF602 2.1 77.0 1.0 O1B I:ADP601 2.2 62.1 1.0 OD1 I:ASP87 2.6 81.9 1.0 PA I:ADP601 3.1 73.7 1.0 OD2 I:ASP87 3.1 80.3 1.0 CG I:ASP87 3.2 82.6 1.0 BE I:BEF602 3.3 92.1 1.0 PB I:ADP601 3.4 61.6 1.0 O3A I:ADP601 3.4 2.6 1.0 O5' I:ADP601 3.5 64.1 1.0 O I:SER151 3.8 92.3 1.0 F1 I:BEF602 4.1 39.2 1.0 OG I:SER151 4.1 94.6 1.0 O3B I:ADP601 4.1 59.7 1.0 CA I:SER151 4.2 94.5 1.0 C I:SER151 4.4 93.9 1.0 O2A I:ADP601 4.5 75.3 1.0 O2B I:ADP601 4.5 61.4 1.0 C5' I:ADP601 4.6 64.0 1.0 K I:K604 4.6 67.9 1.0 F2 I:BEF602 4.6 0.3 1.0 CB I:SER151 4.7 94.6 1.0 CB I:ASP87 4.7 85.9 1.0 N I:GLY88 4.8 71.4 1.0 OD2 I:ASP398 4.9 0.0 1.0 O I:ILE150 5.0 71.5 1.0

X.Fei, X.Ye, N.A.Laronde, G.H.Lorimer. Formation and Structures of Groel:GROES2 Chaperonin Footballs, the Protein-Folding Functional Form. Proc.Natl.Acad.Sci.Usa V. 111 12775 2014.
ISSN: ESSN 1091-6490
PubMed: 25136110
DOI: 10.1073/PNAS.1412922111