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Magnesium in PDB 1sx4: Groel-Groes-ADP7

Protein crystallography data

The structure of Groel-Groes-ADP7, PDB code: 1sx4 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) 40.00 / 3.00
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 (%) 25.8 / 28.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Groel-Groes-ADP7 (pdb code 1sx4). 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-ADP7, PDB code: 1sx4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 1sx4

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Magnesium binding site 1 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:2.0
occ:1.00
 O2A A:ADP600 1.8 2.5 1.0
O1B A:ADP600 1.9 2.2 1.0
OD1 A:ASP87 2.2 5.0 1.0
PB A:ADP600 2.9 6.3 1.0
O3B A:ADP600 3.0 5.2 1.0
CG A:ASP87 3.2 3.1 1.0
PA A:ADP600 3.2 2.0 1.0
OD2 A:ASP87 3.4 3.1 1.0
O3A A:ADP600 3.6 2.7 1.0
O5' A:ADP600 3.9 2.0 1.0
O A:HOH610 3.9 43.3 1.0
OD2 A:ASP398 4.0 5.6 1.0
N A:GLY88 4.2 2.0 1.0
C5' A:ADP600 4.3 2.5 1.0
O1A A:ADP600 4.4 2.0 1.0
O2B A:ADP600 4.5 2.0 1.0
O A:SER151 4.5 2.3 1.0
CB A:ASP87 4.7 2.0 1.0
CA A:SER151 4.8 2.0 1.0
CA A:GLY88 4.9 2.0 1.0
OG A:SER151 4.9 2.8 1.0

Magnesium binding site 2 out of 7 in 1sx4

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Magnesium binding site 2 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg601

b:2.0
occ:1.00
 O2A B:ADP600 1.8 2.4 1.0
O1B B:ADP600 1.9 2.1 1.0
OD1 B:ASP87 2.3 5.1 1.0
PB B:ADP600 3.0 5.2 1.0
PA B:ADP600 3.1 2.6 1.0
CG B:ASP87 3.2 3.0 1.0
OD2 B:ASP87 3.3 3.1 1.0
O3B B:ADP600 3.4 5.0 1.0
O3A B:ADP600 3.5 2.5 1.0
O5' B:ADP600 3.6 2.1 1.0
OD2 B:ASP398 3.8 5.3 1.0
C5' B:ADP600 4.2 2.0 1.0
O B:SER151 4.3 2.5 1.0
O B:HOH605 4.3 36.5 1.0
N B:GLY88 4.3 2.1 1.0
O1A B:ADP600 4.4 2.7 1.0
O2B B:ADP600 4.4 2.1 1.0
CB B:ASP87 4.7 2.0 1.0
CA B:SER151 4.8 2.0 1.0
OG B:SER151 4.8 2.6 1.0

Magnesium binding site 3 out of 7 in 1sx4

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Magnesium binding site 3 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg601

b:2.0
occ:1.00
 O1B C:ADP600 1.9 2.6 1.0
O2A C:ADP600 2.0 2.0 1.0
OD1 C:ASP87 2.1 5.3 1.0
PB C:ADP600 3.1 5.8 1.0
CG C:ASP87 3.1 3.2 1.0
PA C:ADP600 3.2 2.0 1.0
O3B C:ADP600 3.3 5.1 1.0
OD2 C:ASP87 3.4 2.8 1.0
O3A C:ADP600 3.7 2.6 1.0
O5' C:ADP600 3.8 2.0 1.0
OD2 C:ASP398 3.8 5.5 1.0
O C:HOH607 4.2 53.0 1.0
N C:GLY88 4.3 2.0 1.0
C5' C:ADP600 4.4 2.4 1.0
O C:SER151 4.4 2.2 1.0
O1A C:ADP600 4.5 2.6 1.0
CB C:ASP87 4.5 2.0 1.0
O2B C:ADP600 4.6 2.0 1.0
OG C:SER151 4.7 2.5 1.0
CA C:SER151 4.8 2.1 1.0
CA C:ASP87 4.9 2.0 1.0
CA C:GLY88 5.0 2.0 1.0

Magnesium binding site 4 out of 7 in 1sx4

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Magnesium binding site 4 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg601

b:2.0
occ:1.00
 O2A D:ADP600 1.7 2.1 1.0
O1B D:ADP600 1.9 2.1 1.0
OD1 D:ASP87 2.1 5.0 1.0
PB D:ADP600 3.0 5.1 1.0
O3B D:ADP600 3.1 4.9 1.0
PA D:ADP600 3.1 2.2 1.0
CG D:ASP87 3.2 3.2 1.0
OD2 D:ASP87 3.4 3.3 1.0
O3A D:ADP600 3.5 2.6 1.0
O5' D:ADP600 3.7 2.0 1.0
OD2 D:ASP398 4.1 5.9 1.0
O D:HOH604 4.2 22.6 1.0
N D:GLY88 4.2 2.0 1.0
C5' D:ADP600 4.2 2.3 1.0
O1A D:ADP600 4.4 2.0 1.0
O D:SER151 4.4 2.4 1.0
O2B D:ADP600 4.4 2.0 1.0
CB D:ASP87 4.6 2.1 1.0
OG D:SER151 4.7 2.5 1.0
CA D:GLY88 4.8 2.0 1.0
CA D:SER151 4.9 2.0 1.0

Magnesium binding site 5 out of 7 in 1sx4

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Magnesium binding site 5 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg601

b:2.0
occ:1.00
 O1B E:ADP600 1.8 2.0 1.0
O2A E:ADP600 1.8 2.3 1.0
OD1 E:ASP87 2.2 5.0 1.0
PB E:ADP600 2.8 5.3 1.0
PA E:ADP600 3.0 2.7 1.0
O3B E:ADP600 3.1 4.9 1.0
CG E:ASP87 3.3 3.2 1.0
O3A E:ADP600 3.4 2.5 1.0
OD2 E:ASP87 3.5 3.0 1.0
O5' E:ADP600 3.6 2.1 1.0
O E:HOH608 3.9 38.7 1.0
OD2 E:ASP398 3.9 5.4 1.0
C5' E:ADP600 4.2 2.3 1.0
N E:GLY88 4.2 2.0 1.0
O2B E:ADP600 4.3 2.1 1.0
O1A E:ADP600 4.3 2.5 1.0
O E:SER151 4.5 2.4 1.0
CB E:ASP87 4.7 2.1 1.0
CA E:GLY88 4.7 2.0 1.0
OG E:SER151 5.0 2.1 1.0

Magnesium binding site 6 out of 7 in 1sx4

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Magnesium binding site 6 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg601

b:2.0
occ:1.00
 O2A F:ADP600 1.6 2.0 1.0
O1B F:ADP600 1.7 2.3 1.0
OD1 F:ASP87 2.3 4.9 1.0
PB F:ADP600 2.8 5.6 1.0
PA F:ADP600 2.8 2.0 1.0
O3B F:ADP600 3.2 5.0 1.0
O3A F:ADP600 3.3 2.7 1.0
CG F:ASP87 3.4 2.9 1.0
O5' F:ADP600 3.4 2.1 1.0
OD2 F:ASP87 3.5 3.0 1.0
C5' F:ADP600 4.1 2.2 1.0
O1A F:ADP600 4.1 2.2 1.0
OD2 F:ASP398 4.1 5.6 1.0
O2B F:ADP600 4.2 2.2 1.0
N F:GLY88 4.3 2.0 1.0
O F:SER151 4.5 2.5 1.0
CB F:ASP87 4.8 2.0 1.0
O F:HOH609 4.8 36.8 1.0
CA F:GLY88 4.9 2.0 1.0
OG F:SER151 4.9 2.3 1.0
CA F:SER151 5.0 2.0 1.0

Magnesium binding site 7 out of 7 in 1sx4

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Magnesium binding site 7 out of 7 in the Groel-Groes-ADP7


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Groel-Groes-ADP7 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg601

b:2.0
occ:1.00
 O2A G:ADP600 1.8 2.0 1.0
O1B G:ADP600 2.0 2.6 1.0
OD1 G:ASP87 2.2 4.9 1.0
PA G:ADP600 3.1 2.2 1.0
PB G:ADP600 3.1 5.0 1.0
CG G:ASP87 3.2 3.2 1.0
OD2 G:ASP87 3.3 3.2 1.0
O3B G:ADP600 3.3 4.8 1.0
O3A G:ADP600 3.6 2.5 1.0
O5' G:ADP600 3.7 2.3 1.0
OD2 G:ASP398 3.9 5.4 1.0
O G:HOH607 4.2 40.2 1.0
C5' G:ADP600 4.3 2.2 1.0
N G:GLY88 4.4 2.0 1.0
O G:SER151 4.4 2.7 1.0
O1A G:ADP600 4.4 2.5 1.0
O2B G:ADP600 4.5 2.0 1.0
OG G:SER151 4.6 2.5 1.0
CB G:ASP87 4.7 2.0 1.0
CA G:SER151 4.7 2.0 1.0
O G:HOH608 4.9 45.7 1.0
CA G:GLY88 5.0 2.0 1.0

Reference:

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
Page generated: Tue Aug 13 14:22:20 2024

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