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Magnesium in PDB 1pf9: Groel-Groes-Adp

Protein crystallography data

The structure of Groel-Groes-Adp, PDB code: 1pf9 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) 40.16 / 2.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 255.260, 265.250, 184.400, 90.00, 90.00, 90.00
R / Rfree (%) 26.9 / 28.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Groel-Groes-Adp (pdb code 1pf9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Groel-Groes-Adp, PDB code: 1pf9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1pf9

Go back to Magnesium Binding Sites List in 1pf9
Magnesium binding site 1 out of 7 in the Groel-Groes-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:2.0
occ:1.00
 O2A A:ADP700 1.9 7.6 1.0
O1B A:ADP700 2.0 8.3 1.0
OD1 A:ASP87 2.2 9.4 1.0
PB A:ADP700 3.0 11.1 1.0
PA A:ADP700 3.1 7.9 1.0
CG A:ASP87 3.2 8.3 1.0
O3B A:ADP700 3.3 10.2 1.0
OD2 A:ASP87 3.4 8.4 1.0
O5' A:ADP700 3.5 7.9 1.0
O3A A:ADP700 3.6 8.9 1.0
O A:HOH800 3.7 64.0 1.0
OD2 A:ASP398 4.1 12.9 1.0
N A:GLY88 4.2 6.5 1.0
O1A A:ADP700 4.4 6.0 1.0
O2B A:ADP700 4.4 7.7 1.0
O A:SER151 4.5 7.0 1.0
CB A:ASP87 4.6 7.4 1.0
CA A:GLY88 4.8 6.7 1.0
C5' A:ADP700 4.8 8.2 1.0
CA A:SER151 4.9 6.2 1.0
CA A:ASP87 4.9 7.4 1.0
OG A:SER151 5.0 7.4 1.0

Magnesium binding site 2 out of 7 in 1pf9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg602

b:2.0
occ:1.00
 O2A B:ADP701 1.9 7.7 1.0
O1B B:ADP701 2.0 8.0 1.0
OD1 B:ASP87 2.2 9.5 1.0
PB B:ADP701 3.0 10.4 1.0
PA B:ADP701 3.1 8.3 1.0
CG B:ASP87 3.2 8.2 1.0
OD2 B:ASP87 3.4 8.4 1.0
O5' B:ADP701 3.4 8.0 1.0
O3B B:ADP701 3.4 10.2 1.0
O3A B:ADP701 3.5 8.8 1.0
O B:HOH801 3.9 63.9 1.0
OD2 B:ASP398 4.0 12.7 1.0
N B:GLY88 4.2 6.7 1.0
O1A B:ADP701 4.4 6.4 1.0
O B:SER151 4.4 7.0 1.0
O2B B:ADP701 4.4 7.6 1.0
CB B:ASP87 4.6 7.3 1.0
C5' B:ADP701 4.8 8.3 1.0
OG B:SER151 4.8 7.2 1.0
CA B:SER151 4.9 6.4 1.0
CA B:GLY88 4.9 6.7 1.0
CA B:ASP87 5.0 7.2 1.0

Magnesium binding site 3 out of 7 in 1pf9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg603

b:2.0
occ:1.00
 O2A C:ADP702 1.9 7.3 1.0
O1B C:ADP702 2.0 8.3 1.0
OD1 C:ASP87 2.2 9.7 1.0
PB C:ADP702 3.0 10.8 1.0
PA C:ADP702 3.0 8.0 1.0
CG C:ASP87 3.3 8.3 1.0
O3B C:ADP702 3.3 10.2 1.0
O5' C:ADP702 3.4 7.9 1.0
OD2 C:ASP87 3.5 8.2 1.0
O3A C:ADP702 3.5 8.8 1.0
O C:HOH802 3.7 64.1 1.0
OD2 C:ASP398 4.0 12.8 1.0
N C:GLY88 4.2 6.6 1.0
O1A C:ADP702 4.4 6.2 1.0
O2B C:ADP702 4.4 7.7 1.0
O C:SER151 4.5 7.0 1.0
CB C:ASP87 4.6 7.4 1.0
C5' C:ADP702 4.8 8.2 1.0
OG C:SER151 4.8 7.2 1.0
CA C:GLY88 4.9 6.7 1.0
CA C:ASP87 4.9 7.4 1.0
CA C:SER151 5.0 6.4 1.0

Magnesium binding site 4 out of 7 in 1pf9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg604

b:2.0
occ:1.00
 O2A D:ADP703 1.8 7.4 1.0
O1B D:ADP703 2.0 8.1 1.0
OD1 D:ASP87 2.1 9.5 1.0
PB D:ADP703 3.0 10.4 1.0
PA D:ADP703 3.0 8.1 1.0
CG D:ASP87 3.2 8.3 1.0
O3B D:ADP703 3.2 10.2 1.0
OD2 D:ASP87 3.4 8.4 1.0
O5' D:ADP703 3.4 8.0 1.0
O3A D:ADP703 3.5 8.7 1.0
O D:HOH803 3.8 63.9 1.0
OD2 D:ASP398 4.2 12.9 1.0
N D:GLY88 4.2 6.6 1.0
O1A D:ADP703 4.3 6.2 1.0
O2B D:ADP703 4.4 7.4 1.0
O D:SER151 4.5 7.0 1.0
CB D:ASP87 4.6 7.5 1.0
C5' D:ADP703 4.8 8.2 1.0
CA D:GLY88 4.8 6.5 1.0
OG D:SER151 4.9 7.2 1.0
CA D:ASP87 4.9 7.3 1.0
CA D:SER151 5.0 6.3 1.0

Magnesium binding site 5 out of 7 in 1pf9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg605

b:2.0
occ:1.00
 O1B E:ADP704 1.9 8.0 1.0
O2A E:ADP704 1.9 7.6 1.0
OD1 E:ASP87 2.2 9.6 1.0
PB E:ADP704 3.0 10.4 1.0
PA E:ADP704 3.0 8.5 1.0
CG E:ASP87 3.2 8.3 1.0
O5' E:ADP704 3.3 7.9 1.0
O3B E:ADP704 3.3 10.1 1.0
OD2 E:ASP87 3.4 8.3 1.0
O3A E:ADP704 3.5 8.8 1.0
O E:HOH804 3.8 64.0 1.0
OD2 E:ASP398 4.0 12.7 1.0
N E:GLY88 4.2 6.5 1.0
O1A E:ADP704 4.3 6.4 1.0
O2B E:ADP704 4.3 7.8 1.0
O E:SER151 4.5 7.0 1.0
CB E:ASP87 4.6 7.4 1.0
C5' E:ADP704 4.7 8.1 1.0
CA E:GLY88 4.8 6.5 1.0
OG E:SER151 4.9 7.0 1.0
CA E:ASP87 4.9 7.3 1.0
CA E:SER151 5.0 6.4 1.0

Magnesium binding site 6 out of 7 in 1pf9

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg606

b:2.0
occ:1.00
 O2A F:ADP705 1.7 7.3 1.0
O1B F:ADP705 1.9 8.2 1.0
OD1 F:ASP87 2.3 9.4 1.0
PA F:ADP705 2.8 7.8 1.0
PB F:ADP705 2.9 10.5 1.0
O5' F:ADP705 3.2 7.9 1.0
O3B F:ADP705 3.3 10.2 1.0
O3A F:ADP705 3.3 8.8 1.0
CG F:ASP87 3.4 8.2 1.0
OD2 F:ASP87 3.5 8.3 1.0
O F:HOH805 3.8 64.1 1.0
O1A F:ADP705 4.1 6.3 1.0
OD2 F:ASP398 4.2 12.8 1.0
N F:GLY88 4.3 6.7 1.0
O2B F:ADP705 4.3 7.7 1.0
O F:SER151 4.5 7.0 1.0
C5' F:ADP705 4.6 8.3 1.0
CB F:ASP87 4.7 7.4 1.0
CA F:GLY88 4.9 6.7 1.0
OG F:SER151 5.0 7.2 1.0

Magnesium binding site 7 out of 7 in 1pf9

Go back to Magnesium Binding Sites List in 1pf9
Magnesium binding site 7 out of 7 in the Groel-Groes-Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Groel-Groes-Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg607

b:2.0
occ:1.00
 O2A G:ADP706 1.8 7.3 1.0
O1B G:ADP706 2.1 8.3 1.0
OD1 G:ASP87 2.2 9.4 1.0
PA G:ADP706 3.0 7.8 1.0
PB G:ADP706 3.1 10.3 1.0
CG G:ASP87 3.2 8.3 1.0
O3B G:ADP706 3.3 10.2 1.0
OD2 G:ASP87 3.4 8.5 1.0
O5' G:ADP706 3.4 8.2 1.0
O3A G:ADP706 3.6 8.6 1.0
O G:HOH806 3.9 63.9 1.0
OD2 G:ASP398 4.0 12.8 1.0
N G:GLY88 4.3 6.5 1.0
O1A G:ADP706 4.3 6.2 1.0
O2B G:ADP706 4.5 7.5 1.0
O G:SER151 4.5 7.1 1.0
CB G:ASP87 4.7 7.5 1.0
C5' G:ADP706 4.8 8.1 1.0
OG G:SER151 4.8 7.2 1.0
CA G:SER151 4.9 6.3 1.0
CA G:GLY88 5.0 6.6 1.0

Reference:

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
Page generated: Tue Aug 13 10:51:23 2024

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