Magnesium in PDB 5da8: Crystal Structure of Chaperonin Groel From

Protein crystallography data

The structure of Crystal Structure of Chaperonin Groel From, PDB code: 5da8 was solved by C.Chang, N.Marshall, B.Feldmann, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 3.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 138.996, 159.781, 228.823, 75.46, 90.51, 91.22
R / Rfree (%) 23 / 26.3

Other elements in 5da8:

The structure of Crystal Structure of Chaperonin Groel From also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Chaperonin Groel From (pdb code 5da8). 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 Chaperonin Groel From, PDB code: 5da8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 5da8

Go back to Magnesium Binding Sites List in 5da8
Magnesium binding site 1 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg601

b:51.2
occ:1.00
 O H:THR30 2.1 36.7 1.0
O H:LYS51 3.0 28.3 1.0
O H:GLY32 3.0 44.4 1.0
C H:THR30 3.3 31.8 1.0
CA H:GLY35 3.9 32.4 1.0
CA H:THR30 4.0 27.4 1.0
CB H:THR30 4.1 31.9 1.0
C H:LYS51 4.1 25.7 1.0
C H:GLY32 4.2 41.0 1.0
N H:GLY32 4.2 43.3 1.0
N H:LEU31 4.3 32.2 1.0
N H:GLY35 4.3 31.7 1.0
C H:LEU31 4.4 37.1 1.0
CB H:LYS51 4.4 28.2 1.0
CA H:LEU31 4.5 29.5 1.0
OG1 H:THR30 4.6 34.0 1.0
OD2 H:ASP87 4.6 35.6 1.0
C H:GLY35 4.7 33.6 1.0
CA H:GLY32 4.8 35.1 1.0
CA H:LYS51 4.8 29.6 1.0
O H:LEU31 4.9 40.8 1.0
O H:GLY35 4.9 37.0 1.0

Magnesium binding site 2 out of 7 in 5da8

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Magnesium binding site 2 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Mg601

b:53.0
occ:1.00
 O M:THR30 2.1 51.5 1.0
O M:LYS51 2.3 45.4 1.0
C M:THR30 3.2 39.1 1.0
C M:LYS51 3.5 36.5 1.0
CB M:THR30 3.5 39.8 1.0
CA M:THR30 3.8 35.5 1.0
O M:GLY32 4.0 46.4 1.0
OG1 M:THR30 4.2 39.7 1.0
CB M:LYS51 4.3 26.1 1.0
N M:LEU31 4.4 34.5 1.0
CA M:LYS51 4.4 33.5 1.0
N M:ASP52 4.4 32.4 1.0
CA M:ASP52 4.5 36.3 1.0
N M:GLY53 4.5 39.1 1.0
N M:GLY32 4.6 44.6 1.0
CG2 M:THR30 4.7 37.0 1.0
CA M:LEU31 4.7 30.8 1.0
CA M:GLY35 4.7 39.0 1.0
O4 M:SO4602 4.7 55.0 0.7
C M:LEU31 4.8 33.7 1.0
C M:ASP52 4.9 32.4 1.0

Magnesium binding site 3 out of 7 in 5da8

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Magnesium binding site 3 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Mg601

b:67.1
occ:1.00
 O Q:LYS51 2.0 22.6 1.0
O Q:THR30 2.1 31.0 1.0
CB Q:THR30 2.1 21.2 1.0
C Q:THR30 2.6 22.6 1.0
CA Q:THR30 2.7 16.8 1.0
OG1 Q:THR30 2.8 17.2 1.0
C Q:LYS51 3.2 18.1 1.0
CG2 Q:THR30 3.3 18.7 1.0
N Q:GLY53 3.8 18.5 1.0
N Q:LEU31 3.9 22.1 1.0
N Q:THR30 4.1 19.1 1.0
N Q:ASP52 4.1 16.9 1.0
CA Q:LYS51 4.1 18.8 1.0
OD1 Q:ASP87 4.2 58.4 1.0
C Q:ASP52 4.2 20.0 1.0
CA Q:ASP52 4.2 13.2 1.0
CB Q:LYS51 4.3 13.9 1.0
CA Q:GLY53 4.5 16.7 1.0
CA Q:LEU31 4.6 20.4 1.0
CA Q:GLY35 4.7 24.9 1.0
O Q:GLY32 4.9 30.8 1.0
O Q:ARG36 5.0 27.1 1.0

Magnesium binding site 4 out of 7 in 5da8

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Magnesium binding site 4 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Mg601

b:34.5
occ:1.00
 O R:THR30 2.1 23.7 1.0
O R:GLY32 3.0 26.7 1.0
O R:LYS51 3.0 17.6 1.0
C R:THR30 3.3 22.0 1.0
CA R:THR30 4.1 22.6 1.0
N R:GLY32 4.1 20.4 1.0
C R:GLY32 4.1 22.1 1.0
C R:LYS51 4.2 15.7 1.0
CB R:THR30 4.2 24.3 1.0
CA R:GLY35 4.2 22.1 1.0
C R:LEU31 4.3 19.5 1.0
N R:LEU31 4.3 19.7 1.0
CB R:LYS51 4.4 15.6 1.0
CA R:LEU31 4.5 13.8 1.0
N R:GLY35 4.5 19.9 1.0
CA R:GLY32 4.7 18.6 1.0
O R:LEU31 4.8 26.2 1.0
OG1 R:THR30 4.9 21.1 1.0
CA R:LYS51 4.9 14.4 1.0
C R:GLY35 4.9 23.0 1.0

Magnesium binding site 5 out of 7 in 5da8

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Magnesium binding site 5 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
S:Mg601

b:54.4
occ:1.00
 O S:THR30 2.1 37.4 1.0
O S:GLY32 2.9 50.8 1.0
O S:LYS51 2.9 30.6 1.0
C S:THR30 3.3 32.3 1.0
C S:GLY32 4.0 46.6 1.0
C S:LYS51 4.1 25.9 1.0
CA S:THR30 4.1 35.9 1.0
N S:GLY32 4.1 37.8 1.0
CA S:GLY35 4.2 46.9 1.0
CB S:THR30 4.2 31.5 1.0
C S:LEU31 4.2 40.4 1.0
N S:LEU31 4.3 30.4 1.0
CB S:LYS51 4.3 26.1 1.0
CA S:LEU31 4.4 32.6 1.0
N S:GLY35 4.5 43.5 1.0
CA S:GLY32 4.7 38.3 1.0
O S:LEU31 4.7 51.3 1.0
CA S:LYS51 4.7 26.1 1.0
O S:GLY35 4.7 48.4 1.0
OG1 S:THR30 4.8 28.6 1.0
C S:GLY35 4.8 42.6 1.0

Magnesium binding site 6 out of 7 in 5da8

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Magnesium binding site 6 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mg601

b:58.1
occ:1.00
 O T:GLY32 3.7 57.9 1.0
O T:THR30 3.7 47.1 1.0
O T:LYS51 4.0 42.3 1.0
C T:GLY32 4.4 54.9 1.0
N T:GLY32 4.6 53.2 1.0
CA T:GLY32 4.9 53.6 1.0
C T:THR30 5.0 45.9 1.0
C T:LYS51 5.0 39.6 1.0

Magnesium binding site 7 out of 7 in 5da8

Go back to Magnesium Binding Sites List in 5da8
Magnesium binding site 7 out of 7 in the Crystal Structure of Chaperonin Groel From


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 Chaperonin Groel From within 5.0Å range:
probe atom residue distance (Å) B Occ
V:Mg601

b:61.6
occ:1.00
 O V:LYS51 2.0 26.7 1.0
O V:THR30 2.1 31.2 1.0
CB V:THR30 2.1 26.4 1.0
C V:THR30 2.6 28.8 1.0
CA V:THR30 2.7 27.4 1.0
OG1 V:THR30 2.8 20.5 1.0
C V:LYS51 3.3 23.2 1.0
CG2 V:THR30 3.3 25.4 1.0
N V:GLY53 3.7 24.5 1.0
N V:LEU31 3.9 21.8 1.0
N V:THR30 4.1 25.4 1.0
N V:ASP52 4.1 24.4 1.0
CA V:ASP52 4.1 25.0 1.0
C V:ASP52 4.2 28.0 1.0
CA V:LYS51 4.2 26.2 1.0
CB V:LYS51 4.4 24.5 1.0
CA V:GLY53 4.4 22.0 1.0
CA V:LEU31 4.6 18.1 1.0
CA V:GLY35 4.8 25.7 1.0
O V:GLY32 5.0 26.0 1.0

Reference:

C.Chang, N.Marshall, B.Feldmann, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). Crystal Structure of Chaperonin Groel From To Be Published.
Page generated: Mon Dec 14 20:10:57 2020

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