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

Protein crystallography data

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

Other elements in 1svt:

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

Magnesium Binding Sites:

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 1svt

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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 1svt

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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 1svt

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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 1svt

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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 1svt

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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 1svt

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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 1svt

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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

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 14:20:39 2024

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