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Magnesium in PDB 1sx3: GROEL14-(Atpgammas)14

Protein crystallography data

The structure of GROEL14-(Atpgammas)14, PDB code: 1sx3 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) 39.84 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.571, 260.112, 150.200, 90.00, 101.14, 90.00
R / Rfree (%) 24.6 / 26.5

Other elements in 1sx3:

The structure of GROEL14-(Atpgammas)14 also contains other interesting chemical elements:

Potassium (K) 16 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the GROEL14-(Atpgammas)14 (pdb code 1sx3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the GROEL14-(Atpgammas)14, PDB code: 1sx3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 1sx3

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Magnesium binding site 1 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg550

b:7.7
occ:1.00
O A:HOH562 1.5 17.0 1.0
O3G A:AGS1 2.1 13.6 1.0
OD1 A:ASP87 2.1 17.9 1.0
O2A A:AGS1 2.2 4.3 1.0
O1B A:AGS1 2.2 10.4 1.0
O A:HOH561 2.2 15.2 1.0
CG A:ASP87 3.2 15.9 1.0
PB A:AGS1 3.3 11.8 1.0
PG A:AGS1 3.4 16.7 1.0
OD2 A:ASP87 3.5 18.6 1.0
PA A:AGS1 3.5 14.1 1.0
O3A A:AGS1 3.7 18.3 1.0
O3B A:AGS1 3.7 14.0 1.0
O2G A:AGS1 3.9 14.6 1.0
O A:HOH580 4.2 18.8 1.0
N A:GLY88 4.3 12.6 1.0
O A:HOH566 4.4 14.2 1.0
C5' A:AGS1 4.5 13.3 1.0
O5' A:AGS1 4.5 13.7 1.0
CB A:ASP87 4.5 13.1 1.0
S1G A:AGS1 4.6 20.5 1.0
O1A A:AGS1 4.6 9.4 1.0
O2B A:AGS1 4.7 13.0 1.0
CA A:ASP87 4.8 12.5 1.0

Magnesium binding site 2 out of 14 in 1sx3

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Magnesium binding site 2 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg550

b:8.6
occ:1.00
O B:HOH562 1.7 17.3 1.0
O2A B:AGS1 2.1 9.9 1.0
O1B B:AGS1 2.1 14.3 1.0
OD1 B:ASP87 2.2 18.4 1.0
O3G B:AGS1 2.3 21.9 1.0
O B:HOH561 2.3 16.8 1.0
PB B:AGS1 3.0 16.1 1.0
CG B:ASP87 3.3 16.7 1.0
PA B:AGS1 3.4 13.3 1.0
O3A B:AGS1 3.4 16.3 1.0
PG B:AGS1 3.4 24.8 1.0
OD2 B:ASP87 3.5 20.0 1.0
O3B B:AGS1 3.6 17.7 1.0
O B:HOH589 3.9 10.2 1.0
O2G B:AGS1 4.0 24.1 1.0
C5' B:AGS1 4.1 17.1 1.0
O5' B:AGS1 4.2 18.1 1.0
N B:GLY88 4.3 13.4 1.0
O B:HOH566 4.3 14.6 1.0
O2B B:AGS1 4.4 12.1 1.0
O1A B:AGS1 4.5 12.2 1.0
CB B:ASP87 4.7 12.5 1.0
S1G B:AGS1 4.7 19.6 1.0
CA B:ASP87 4.9 12.7 1.0

Magnesium binding site 3 out of 14 in 1sx3

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Magnesium binding site 3 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg550

b:9.7
occ:1.00
O C:HOH562 1.6 17.2 1.0
O2A C:AGS1 2.0 9.3 1.0
O3G C:AGS1 2.2 14.4 1.0
O C:HOH561 2.2 15.2 1.0
O1B C:AGS1 2.3 20.1 1.0
OD1 C:ASP87 2.4 17.7 1.0
PA C:AGS1 3.3 10.2 1.0
PB C:AGS1 3.3 16.2 1.0
CG C:ASP87 3.4 16.0 1.0
PG C:AGS1 3.4 20.7 1.0
O3A C:AGS1 3.6 12.3 1.0
OD2 C:ASP87 3.6 18.8 1.0
O3B C:AGS1 3.7 19.4 1.0
O2G C:AGS1 4.0 18.0 1.0
O C:HOH567 4.1 17.0 1.0
C5' C:AGS1 4.2 15.8 1.0
O5' C:AGS1 4.3 13.0 1.0
O C:HOH580 4.3 19.0 1.0
O1A C:AGS1 4.3 9.4 1.0
N C:GLY88 4.5 12.6 1.0
S1G C:AGS1 4.6 15.9 1.0
O2B C:AGS1 4.7 19.4 1.0
CB C:ASP87 4.7 12.5 1.0
CA C:ASP87 4.9 12.8 1.0

Magnesium binding site 4 out of 14 in 1sx3

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Magnesium binding site 4 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg550

b:10.3
occ:1.00
O D:HOH563 1.6 17.6 1.0
O2A D:AGS561 2.0 7.7 1.0
O1B D:AGS561 2.1 9.6 1.0
O3G D:AGS561 2.2 18.5 1.0
OD1 D:ASP87 2.2 17.1 1.0
O D:HOH562 2.3 16.8 1.0
PB D:AGS561 3.3 14.2 1.0
CG D:ASP87 3.3 16.3 1.0
PA D:AGS561 3.3 11.9 1.0
PG D:AGS561 3.4 17.5 1.0
OD2 D:ASP87 3.5 19.3 1.0
O3A D:AGS561 3.7 10.8 1.0
O3B D:AGS561 3.8 15.8 1.0
O2G D:AGS561 4.1 17.4 1.0
O D:HOH567 4.2 14.8 1.0
C5' D:AGS561 4.3 14.8 1.0
O D:HOH579 4.3 16.5 1.0
O5' D:AGS561 4.3 11.0 1.0
N D:GLY88 4.3 13.2 1.0
O1A D:AGS561 4.5 11.1 1.0
S1G D:AGS561 4.5 19.0 1.0
O2B D:AGS561 4.6 12.9 1.0
CB D:ASP87 4.7 12.7 1.0
CA D:ASP87 5.0 12.9 1.0

Magnesium binding site 5 out of 14 in 1sx3

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Magnesium binding site 5 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg550

b:6.1
occ:1.00
O E:HOH562 1.6 19.1 1.0
OD1 E:ASP87 2.1 18.6 1.0
O E:HOH561 2.1 15.9 1.0
O2A E:AGS1 2.2 2.0 1.0
O3G E:AGS1 2.3 11.3 1.0
O1B E:AGS1 2.3 9.4 1.0
CG E:ASP87 3.2 16.9 1.0
PB E:AGS1 3.2 15.7 1.0
OD2 E:ASP87 3.4 20.0 1.0
PG E:AGS1 3.5 19.7 1.0
PA E:AGS1 3.6 19.4 1.0
O3A E:AGS1 3.7 19.2 1.0
O3B E:AGS1 3.8 11.4 1.0
O2G E:AGS1 4.0 7.4 1.0
O E:HOH568 4.1 5.6 1.0
O E:HOH566 4.3 2.0 1.0
N E:GLY88 4.3 11.8 1.0
C5' E:AGS1 4.4 15.2 1.0
CB E:ASP87 4.5 11.2 1.0
O5' E:AGS1 4.5 13.8 1.0
O1A E:AGS1 4.6 8.7 1.0
O2B E:AGS1 4.6 14.3 1.0
S1G E:AGS1 4.7 20.6 1.0
CA E:ASP87 4.8 11.8 1.0

Magnesium binding site 6 out of 14 in 1sx3

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Magnesium binding site 6 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg550

b:7.2
occ:1.00
O F:HOH562 1.9 18.2 1.0
O2A F:AGS1 2.2 2.0 1.0
O F:HOH561 2.2 16.6 1.0
O3G F:AGS1 2.3 22.4 1.0
OD1 F:ASP87 2.3 17.7 1.0
O1B F:AGS1 2.3 23.8 1.0
CG F:ASP87 3.3 16.4 1.0
PB F:AGS1 3.4 13.8 1.0
PG F:AGS1 3.5 22.1 1.0
PA F:AGS1 3.5 11.0 1.0
OD2 F:ASP87 3.5 19.6 1.0
O3B F:AGS1 3.7 10.8 1.0
O3A F:AGS1 3.8 15.5 1.0
O2G F:AGS1 4.0 12.3 1.0
O F:HOH566 4.3 8.0 1.0
O F:HOH581 4.3 6.9 1.0
C5' F:AGS1 4.4 15.5 1.0
O5' F:AGS1 4.4 13.9 1.0
O1A F:AGS1 4.5 12.5 1.0
N F:GLY88 4.5 12.2 1.0
S1G F:AGS1 4.7 23.7 1.0
CB F:ASP87 4.7 12.3 1.0
O2B F:AGS1 4.7 19.6 1.0

Magnesium binding site 7 out of 14 in 1sx3

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Magnesium binding site 7 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg550

b:9.4
occ:1.00
O G:HOH562 1.7 17.9 1.0
O2A G:AGS1 1.9 11.8 1.0
O3G G:AGS1 2.1 16.8 1.0
O G:HOH561 2.2 16.8 1.0
OD1 G:ASP87 2.2 17.5 1.0
O1B G:AGS1 2.5 16.4 1.0
CG G:ASP87 3.2 16.4 1.0
OD2 G:ASP87 3.4 19.7 1.0
PA G:AGS1 3.4 9.0 1.0
PB G:AGS1 3.4 10.3 1.0
PG G:AGS1 3.5 14.4 1.0
O3A G:AGS1 3.5 10.7 1.0
O3B G:AGS1 3.9 13.0 1.0
O2G G:AGS1 4.1 16.5 1.0
O G:HOH575 4.1 4.6 1.0
O G:HOH566 4.2 9.2 1.0
C5' G:AGS1 4.4 6.1 1.0
O5' G:AGS1 4.4 8.7 1.0
O1A G:AGS1 4.5 14.9 1.0
N G:GLY88 4.5 12.5 1.0
S1G G:AGS1 4.6 15.0 1.0
CB G:ASP87 4.6 13.1 1.0
O2B G:AGS1 4.8 12.1 1.0
CA G:ASP87 5.0 12.8 1.0

Magnesium binding site 8 out of 14 in 1sx3

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Magnesium binding site 8 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg550

b:4.6
occ:1.00
O H:HOH562 2.0 16.4 1.0
O H:HOH561 2.0 15.2 1.0
O2A H:AGS1 2.0 10.8 1.0
O3G H:AGS1 2.2 8.0 1.0
OD1 H:ASP87 2.2 17.9 1.0
O1B H:AGS1 2.2 10.6 1.0
PA H:AGS1 3.2 11.4 1.0
PB H:AGS1 3.2 6.7 1.0
CG H:ASP87 3.3 16.7 1.0
O3A H:AGS1 3.3 8.6 1.0
PG H:AGS1 3.4 15.0 1.0
OD2 H:ASP87 3.5 19.2 1.0
O3B H:AGS1 3.8 7.8 1.0
O H:HOH566 4.0 10.6 1.0
O2G H:AGS1 4.0 7.0 1.0
O H:HOH577 4.0 8.3 1.0
O5' H:AGS1 4.2 14.5 1.0
C5' H:AGS1 4.3 16.3 1.0
O1A H:AGS1 4.4 11.3 1.0
N H:GLY88 4.4 12.5 1.0
S1G H:AGS1 4.5 17.6 1.0
O2B H:AGS1 4.6 11.8 1.0
CB H:ASP87 4.7 12.4 1.0
CA H:ASP87 5.0 12.4 1.0

Magnesium binding site 9 out of 14 in 1sx3

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Magnesium binding site 9 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg550

b:9.7
occ:1.00
O I:HOH562 1.7 17.1 1.0
O I:HOH561 2.0 16.1 1.0
O2A I:AGS1 2.1 7.5 1.0
O3G I:AGS1 2.2 20.4 1.0
OD1 I:ASP87 2.2 17.6 1.0
O1B I:AGS1 2.3 13.1 1.0
CG I:ASP87 3.3 16.4 1.0
PB I:AGS1 3.4 13.9 1.0
OD2 I:ASP87 3.5 19.0 1.0
PG I:AGS1 3.5 19.8 1.0
PA I:AGS1 3.5 10.9 1.0
O3A I:AGS1 3.7 13.2 1.0
O3B I:AGS1 3.8 15.6 1.0
O2G I:AGS1 4.2 16.6 1.0
O I:HOH566 4.2 19.3 1.0
N I:GLY88 4.5 12.4 1.0
C5' I:AGS1 4.5 13.8 1.0
O5' I:AGS1 4.5 14.0 1.0
O1A I:AGS1 4.6 5.0 1.0
CB I:ASP87 4.6 12.9 1.0
S1G I:AGS1 4.7 16.2 1.0
O2B I:AGS1 4.7 9.8 1.0
CA I:ASP87 5.0 13.2 1.0

Magnesium binding site 10 out of 14 in 1sx3

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Magnesium binding site 10 out of 14 in the GROEL14-(Atpgammas)14


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of GROEL14-(Atpgammas)14 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg550

b:8.8
occ:1.00
O J:HOH562 1.6 17.9 1.0
O2A J:AGS1 2.1 3.5 1.0
O3G J:AGS1 2.1 14.1 1.0
O J:HOH561 2.2 15.6 1.0
OD1 J:ASP87 2.3 18.6 1.0
O1B J:AGS1 2.3 12.6 1.0
CG J:ASP87 3.3 15.7 1.0
PG J:AGS1 3.3 15.4 1.0
PB J:AGS1 3.4 10.1 1.0
OD2 J:ASP87 3.5 18.5 1.0
PA J:AGS1 3.6 5.6 1.0
O3B J:AGS1 3.7 10.1 1.0
O3A J:AGS1 3.7 8.6 1.0
O2G J:AGS1 3.9 13.2 1.0
O J:HOH566 4.1 11.9 1.0
N J:GLY88 4.4 12.4 1.0
C5' J:AGS1 4.4 6.7 1.0
O5' J:AGS1 4.5 4.8 1.0
O1A J:AGS1 4.6 2.3 1.0
CB J:ASP87 4.6 12.3 1.0
S1G J:AGS1 4.6 12.8 1.0
O2B J:AGS1 4.8 10.0 1.0
CA J:ASP87 4.9 12.6 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 14:22:13 2024

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