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Magnesium in PDB 3e76: Crystal Structure of Wild-Type Groel with Bound Thallium Ions

Enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions

All present enzymatic activity of Crystal Structure of Wild-Type Groel with Bound Thallium Ions:
3.6.4.9;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76 was solved by P.D.Kiser, G.H.Lorimer, K.Palczewski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.39 / 3.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.676, 260.954, 287.872, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 29.3

Other elements in 3e76:

The structure of Crystal Structure of Wild-Type Groel with Bound Thallium Ions also contains other interesting chemical elements:

Thallium (Tl) 46 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions (pdb code 3e76). 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 Wild-Type Groel with Bound Thallium Ions, PDB code: 3e76:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 3e76

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Magnesium binding site 1 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg553

b:0.2
occ:1.00
 OD1 A:ASP87 2.1 0.2 1.0
O2A A:AGS549 2.2 0.2 1.0
O2G A:AGS549 2.2 0.2 1.0
O1B A:AGS549 2.3 0.2 1.0
CG A:ASP87 3.3 0.2 1.0
PB A:AGS549 3.4 0.2 1.0
PG A:AGS549 3.5 0.2 1.0
PA A:AGS549 3.5 0.2 1.0
O3B A:AGS549 3.8 0.2 1.0
O3A A:AGS549 3.9 0.2 1.0
CB A:ASP87 4.0 0.2 1.0
N A:GLY88 4.0 0.2 1.0
C5' A:AGS549 4.2 0.2 1.0
CA A:ASP87 4.2 0.2 1.0
OD2 A:ASP87 4.3 0.2 1.0
O5' A:AGS549 4.4 0.2 1.0
O3G A:AGS549 4.6 0.2 1.0
C A:ASP87 4.6 0.2 1.0
O1A A:AGS549 4.7 0.2 1.0
S1G A:AGS549 4.7 0.2 1.0
O2B A:AGS549 4.7 0.2 1.0
CA A:GLY88 5.0 0.2 1.0

Magnesium binding site 2 out of 14 in 3e76

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Magnesium binding site 2 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg553

b:0.2
occ:1.00
 O2A B:AGS549 2.1 0.2 1.0
O1B B:AGS549 2.2 0.2 1.0
O2G B:AGS549 2.2 0.2 1.0
OD1 B:ASP87 2.2 0.2 1.0
PB B:AGS549 3.3 0.2 1.0
CG B:ASP87 3.4 0.2 1.0
PA B:AGS549 3.4 0.2 1.0
PG B:AGS549 3.5 0.2 1.0
O3B B:AGS549 3.7 0.2 1.0
O3A B:AGS549 3.8 0.2 1.0
OD2 B:ASP87 4.0 0.2 1.0
C5' B:AGS549 4.1 0.2 1.0
O5' B:AGS549 4.3 0.2 1.0
N B:GLY88 4.5 0.2 1.0
O3G B:AGS549 4.5 0.2 1.0
CB B:ASP87 4.6 0.2 1.0
O1A B:AGS549 4.6 0.2 1.0
S1G B:AGS549 4.6 0.2 1.0
O2B B:AGS549 4.7 0.2 1.0
CA B:ASP87 4.8 0.2 1.0

Magnesium binding site 3 out of 14 in 3e76

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Magnesium binding site 3 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg553

b:0.2
occ:1.00
 OD1 C:ASP87 2.0 0.2 1.0
O2A C:AGS549 2.0 0.2 1.0
O2G C:AGS549 2.1 0.2 1.0
O1B C:AGS549 2.3 0.2 1.0
CG C:ASP87 3.3 0.2 1.0
PA C:AGS549 3.4 0.2 1.0
PB C:AGS549 3.4 0.2 1.0
PG C:AGS549 3.4 0.2 1.0
O3A C:AGS549 3.8 0.2 1.0
O3B C:AGS549 3.8 0.2 1.0
CB C:ASP87 4.1 0.2 1.0
C5' C:AGS549 4.1 0.2 1.0
N C:GLY88 4.1 0.2 1.0
OD2 C:ASP87 4.1 0.2 1.0
O5' C:AGS549 4.3 0.2 1.0
CA C:ASP87 4.4 0.2 1.0
O1A C:AGS549 4.5 0.2 1.0
O3G C:AGS549 4.5 0.2 1.0
S1G C:AGS549 4.7 0.2 1.0
O2B C:AGS549 4.7 0.2 1.0
C C:ASP87 4.8 0.2 1.0

Magnesium binding site 4 out of 14 in 3e76

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Magnesium binding site 4 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg553

b:0.2
occ:1.00
 O2A D:AGS549 2.0 0.2 1.0
OD1 D:ASP87 2.1 0.2 1.0
O2G D:AGS549 2.1 0.2 1.0
O1B D:AGS549 2.2 0.2 1.0
CG D:ASP87 3.2 0.2 1.0
PB D:AGS549 3.3 0.2 1.0
PA D:AGS549 3.3 0.2 1.0
PG D:AGS549 3.3 0.2 1.0
O3B D:AGS549 3.6 0.2 1.0
O3A D:AGS549 3.7 0.2 1.0
OD2 D:ASP87 3.8 0.2 1.0
C5' D:AGS549 4.1 0.2 1.0
O5' D:AGS549 4.2 0.2 1.0
N D:GLY88 4.3 0.2 1.0
O3G D:AGS549 4.4 0.2 1.0
O1A D:AGS549 4.4 0.2 1.0
CB D:ASP87 4.5 0.2 1.0
S1G D:AGS549 4.6 0.2 1.0
O2B D:AGS549 4.6 0.2 1.0
CA D:ASP87 4.7 0.2 1.0

Magnesium binding site 5 out of 14 in 3e76

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Magnesium binding site 5 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg553

b:0.2
occ:1.00
 OD1 E:ASP87 2.1 0.2 1.0
O2A E:AGS549 2.1 0.2 1.0
O2G E:AGS549 2.2 0.2 1.0
O1B E:AGS549 2.2 0.2 1.0
CG E:ASP87 3.2 0.2 1.0
PB E:AGS549 3.4 0.2 1.0
PA E:AGS549 3.4 0.2 1.0
PG E:AGS549 3.5 0.2 1.0
O3B E:AGS549 3.8 0.2 1.0
O3A E:AGS549 3.8 0.2 1.0
OD2 E:ASP87 3.8 0.2 1.0
C5' E:AGS549 4.1 0.2 1.0
O5' E:AGS549 4.3 0.2 1.0
N E:GLY88 4.4 0.2 1.0
CB E:ASP87 4.5 0.2 1.0
O1A E:AGS549 4.5 0.2 1.0
O3G E:AGS549 4.5 0.2 1.0
S1G E:AGS549 4.7 0.2 1.0
O2B E:AGS549 4.7 0.2 1.0
CA E:ASP87 4.7 0.2 1.0

Magnesium binding site 6 out of 14 in 3e76

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Magnesium binding site 6 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg553

b:0.2
occ:1.00
 OD1 F:ASP87 2.0 0.2 1.0
O2G F:AGS549 2.1 0.2 1.0
O2A F:AGS549 2.1 0.2 1.0
O1B F:AGS549 2.2 0.2 1.0
CG F:ASP87 3.2 0.2 1.0
PB F:AGS549 3.3 0.2 1.0
PG F:AGS549 3.3 0.2 1.0
PA F:AGS549 3.4 0.2 1.0
O3B F:AGS549 3.6 0.2 1.0
O3A F:AGS549 3.7 0.2 1.0
OD2 F:ASP87 3.8 0.2 1.0
C5' F:AGS549 4.1 0.2 1.0
N F:GLY88 4.3 0.2 1.0
O5' F:AGS549 4.3 0.2 1.0
CB F:ASP87 4.4 0.2 1.0
O3G F:AGS549 4.4 0.2 1.0
O1A F:AGS549 4.5 0.2 1.0
S1G F:AGS549 4.5 0.2 1.0
O2B F:AGS549 4.6 0.2 1.0
CA F:ASP87 4.6 0.2 1.0

Magnesium binding site 7 out of 14 in 3e76

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Magnesium binding site 7 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg553

b:0.2
occ:1.00
 OD1 G:ASP87 2.1 0.2 1.0
O2G G:AGS549 2.1 0.2 1.0
O2A G:AGS549 2.2 0.2 1.0
O1B G:AGS549 2.3 0.2 1.0
CG G:ASP87 3.3 0.2 1.0
PB G:AGS549 3.4 0.2 1.0
PG G:AGS549 3.5 0.2 1.0
PA G:AGS549 3.5 0.2 1.0
O3B G:AGS549 3.8 0.2 1.0
O3A G:AGS549 3.9 0.2 1.0
OD2 G:ASP87 4.1 0.2 1.0
C5' G:AGS549 4.2 0.2 1.0
CB G:ASP87 4.3 0.2 1.0
N G:GLY88 4.3 0.2 1.0
O5' G:AGS549 4.4 0.2 1.0
O3G G:AGS549 4.5 0.2 1.0
O1A G:AGS549 4.6 0.2 1.0
CA G:ASP87 4.6 0.2 1.0
S1G G:AGS549 4.7 0.2 1.0
O2B G:AGS549 4.8 0.2 1.0

Magnesium binding site 8 out of 14 in 3e76

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Magnesium binding site 8 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg553

b:0.2
occ:1.00
 O2A H:AGS549 2.1 0.2 1.0
O2G H:AGS549 2.1 0.2 1.0
O1B H:AGS549 2.2 0.2 1.0
OD1 H:ASP87 2.3 0.2 1.0
PB H:AGS549 3.3 0.2 1.0
PG H:AGS549 3.4 0.2 1.0
PA H:AGS549 3.4 0.2 1.0
CG H:ASP87 3.5 0.2 1.0
O3B H:AGS549 3.7 0.2 1.0
O3A H:AGS549 3.8 0.2 1.0
OD2 H:ASP87 4.1 0.2 1.0
C5' H:AGS549 4.2 0.2 1.0
O5' H:AGS549 4.3 0.2 1.0
O3G H:AGS549 4.5 0.2 1.0
N H:GLY88 4.5 0.2 1.0
O1A H:AGS549 4.5 0.2 1.0
S1G H:AGS549 4.6 0.2 1.0
CB H:ASP87 4.7 0.2 1.0
O2B H:AGS549 4.7 0.2 1.0
CA H:ASP87 4.8 0.2 1.0

Magnesium binding site 9 out of 14 in 3e76

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Magnesium binding site 9 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg553

b:0.2
occ:1.00
 O2A I:AGS549 2.0 0.2 1.0
OD1 I:ASP87 2.1 0.2 1.0
O1B I:AGS549 2.2 0.2 1.0
O2G I:AGS549 2.2 0.2 1.0
CG I:ASP87 3.2 0.2 1.0
PB I:AGS549 3.4 0.2 1.0
PA I:AGS549 3.4 0.2 1.0
PG I:AGS549 3.5 0.2 1.0
O3A I:AGS549 3.8 0.2 1.0
O3B I:AGS549 3.8 0.2 1.0
C5' I:AGS549 4.0 0.2 1.0
N I:GLY88 4.0 0.2 1.0
OD2 I:ASP87 4.0 0.2 1.0
CB I:ASP87 4.1 0.2 1.0
O5' I:AGS549 4.2 0.2 1.0
CA I:ASP87 4.4 0.2 1.0
O1A I:AGS549 4.5 0.2 1.0
O3G I:AGS549 4.6 0.2 1.0
O2B I:AGS549 4.7 0.2 1.0
C I:ASP87 4.7 0.2 1.0
S1G I:AGS549 4.7 0.2 1.0
CA I:GLY88 4.9 0.2 1.0

Magnesium binding site 10 out of 14 in 3e76

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Magnesium binding site 10 out of 14 in the Crystal Structure of Wild-Type Groel with Bound Thallium Ions


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 Wild-Type Groel with Bound Thallium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg553

b:0.2
occ:1.00
 O2G J:AGS549 2.1 0.2 1.0
OD1 J:ASP87 2.1 0.2 1.0
O1B J:AGS549 2.2 0.2 1.0
O2A J:AGS549 2.3 0.2 1.0
CG J:ASP87 3.3 0.2 1.0
PG J:AGS549 3.4 0.2 1.0
PB J:AGS549 3.4 0.2 1.0
PA J:AGS549 3.6 0.2 1.0
O3B J:AGS549 3.7 0.2 1.0
O3A J:AGS549 3.9 0.2 1.0
OD2 J:ASP87 3.9 0.2 1.0
C5' J:AGS549 4.3 0.2 1.0
N J:GLY88 4.4 0.2 1.0
CB J:ASP87 4.5 0.2 1.0
O3G J:AGS549 4.5 0.2 1.0
S1G J:AGS549 4.5 0.2 1.0
O5' J:AGS549 4.5 0.2 1.0
O2B J:AGS549 4.7 0.2 1.0
CA J:ASP87 4.7 0.2 1.0
O1A J:AGS549 4.7 0.2 1.0

Reference:

P.D.Kiser, G.H.Lorimer, K.Palczewski. Use of Thallium to Identify Monovalent Cation Binding Sites in Groel. Acta Crystallogr.,Sect.F V. 65 967 2009.
ISSN: ESSN 1744-3091
PubMed: 19851000
DOI: 10.1107/S1744309109032928
Page generated: Sun Aug 10 20:24:12 2025

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