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Magnesium in PDB 7dl5: Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution

Enzymatic activity of Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution

All present enzymatic activity of Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution:
1.16.3.2;

Protein crystallography data

The structure of Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution, PDB code: 7dl5 was solved by Y.Liu, X.Leng, J.Zang, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.61 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 107.093, 107.093, 110.589, 90, 90, 120
R / Rfree (%) 17.8 / 22.7

Other elements in 7dl5:

The structure of Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution (pdb code 7dl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution, PDB code: 7dl5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7dl5

Go back to Magnesium Binding Sites List in 7dl5
Magnesium binding site 1 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:48.5
occ:0.33
 O H:HOH345 2.5 50.6 0.3
NE2 H:HIS116 2.6 67.1 1.0
O H:HOH375 2.6 57.6 0.3
CE1 H:HIS116 3.3 69.2 1.0
CD2 H:HIS116 3.7 68.1 1.0
ND1 H:HIS116 4.5 68.9 1.0
CB H:LYS114 4.6 48.3 1.0
CG H:HIS116 4.7 65.6 1.0
O H:LYS114 4.8 46.0 1.0
CG H:LYS114 4.8 55.1 1.0
CD H:LYS114 4.8 63.8 1.0

Magnesium binding site 2 out of 6 in 7dl5

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Magnesium binding site 2 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg203

b:51.5
occ:1.00
 OE1 H:GLN48 2.2 35.3 1.0
OE1 H:GLN135 2.3 51.3 1.0
O H:HOH340 2.3 49.9 1.0
O H:HOH330 2.7 42.6 1.0
OE1 H:GLU132 3.0 51.9 1.0
CD H:GLN135 3.3 55.6 1.0
CD H:GLN48 3.4 44.2 1.0
O H:HOH363 3.4 53.9 1.0
NZ H:LYS47 3.7 48.7 1.0
CZ2 H:TRP44 3.9 38.5 1.0
CB H:GLN135 4.0 45.9 1.0
NE2 H:GLN135 4.0 63.6 1.0
CD H:GLU132 4.0 54.7 1.0
NE2 H:GLN48 4.1 37.8 1.0
CG H:GLN135 4.2 53.6 1.0
CH2 H:TRP44 4.3 35.6 1.0
OE2 H:GLU132 4.4 57.4 1.0
CE2 H:TRP44 4.5 35.9 1.0
CG H:GLN48 4.5 40.7 1.0
CB H:GLN48 4.7 30.5 1.0
CE H:LYS47 4.8 64.7 1.0
O H:HOH350 4.9 46.4 1.0
NE1 H:TRP44 4.9 33.9 1.0

Magnesium binding site 3 out of 6 in 7dl5

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Magnesium binding site 3 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:45.1
occ:1.00
 O A:HOH356 1.9 40.6 1.0
OD1 A:ASP87 2.4 37.8 1.0
O A:HOH335 2.5 37.1 1.0
O A:HOH354 2.7 47.3 1.0
CG A:ASP87 3.5 33.0 1.0
OD2 A:ASP87 3.8 36.9 1.0
CB A:ASP87 4.8 33.1 1.0
O A:ASP87 4.8 36.1 1.0

Magnesium binding site 4 out of 6 in 7dl5

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Magnesium binding site 4 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:55.3
occ:0.33
 O A:HOH350 2.1 57.6 0.3
O A:HOH369 2.5 54.5 0.3
NE2 A:HIS116 2.7 59.8 1.0
CE1 A:HIS116 3.7 60.8 1.0
CD2 A:HIS116 3.7 59.5 1.0
CB A:LYS114 4.6 49.9 1.0
CD A:LYS114 4.8 60.6 1.0
ND1 A:HIS116 4.8 59.8 1.0
CG A:HIS116 4.9 58.6 1.0
O A:LYS114 4.9 44.7 1.0
CG A:LYS114 4.9 52.0 1.0

Magnesium binding site 5 out of 6 in 7dl5

Go back to Magnesium Binding Sites List in 7dl5
Magnesium binding site 5 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:56.4
occ:1.00
 OE1 A:GLN135 2.0 56.5 1.0
OE1 A:GLN48 2.2 36.1 1.0
O A:HOH332 2.3 50.9 1.0
O A:HOH334 2.8 46.2 1.0
OE1 A:GLU132 3.0 53.4 1.0
CD A:GLN135 3.1 56.0 1.0
CD A:GLN48 3.4 37.1 1.0
O A:HOH357 3.5 42.1 1.0
O A:HOH362 3.7 51.2 1.0
CZ2 A:TRP44 3.8 35.4 1.0
NE2 A:GLN135 3.9 65.2 1.0
CB A:GLN135 3.9 48.2 1.0
CD A:GLU132 4.0 54.3 1.0
CG A:GLN135 4.0 53.8 1.0
NE2 A:GLN48 4.1 34.7 1.0
CH2 A:TRP44 4.2 34.9 1.0
OE2 A:GLU132 4.3 55.0 1.0
CG A:GLN48 4.5 32.7 1.0
CE2 A:TRP44 4.5 35.8 1.0
CB A:GLN48 4.7 30.8 1.0
NE1 A:TRP44 5.0 33.2 1.0

Magnesium binding site 6 out of 6 in 7dl5

Go back to Magnesium Binding Sites List in 7dl5
Magnesium binding site 6 out of 6 in the Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution


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 Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:67.6
occ:1.00
 OE1 A:GLU128 2.3 68.7 1.0
O A:HOH307 2.4 55.1 1.0
O A:HOH306 2.4 54.2 1.0
O A:HOH305 2.5 54.6 1.0
OE2 A:GLU51 2.8 66.0 1.0
CD A:GLU128 3.1 67.7 1.0
CG A:GLU128 3.7 60.8 1.0
CD A:GLU51 3.8 61.6 1.0
OE2 A:GLU128 3.9 72.1 1.0
OE1 A:GLU51 4.0 64.8 1.0
NZ A:LYS58 4.1 56.1 1.0
OE2 A:GLU132 4.5 55.0 1.0
CE1 A:HIS55 4.6 41.1 1.0

Reference:

Y.Liu, X.Leng, J.Zang, G.Zhao. Crystal Structure of Thermotoga Maritima Ferritin Mutant at 2.3 Angstrom Resolution To Be Published.
Page generated: Wed Oct 2 15:55:00 2024

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