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Magnesium in PDB 3sh6: Frog M-Ferritin, D122R Mutant, with Magnesium

Enzymatic activity of Frog M-Ferritin, D122R Mutant, with Magnesium

All present enzymatic activity of Frog M-Ferritin, D122R Mutant, with Magnesium:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin, D122R Mutant, with Magnesium, PDB code: 3sh6 was solved by T.Tosha, H.L.Ng, T.Alber, E.C.Theil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 52.93 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.374, 183.374, 183.374, 90.00, 90.00, 90.00
R / Rfree (%) 16.6 / 19.2

Other elements in 3sh6:

The structure of Frog M-Ferritin, D122R Mutant, with Magnesium also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin, D122R Mutant, with Magnesium (pdb code 3sh6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Frog M-Ferritin, D122R Mutant, with Magnesium, PDB code: 3sh6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3sh6

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Magnesium binding site 1 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg176

b:28.2
occ:1.00
 OE1 A:GLU103 1.9 23.9 1.0
O A:HOH249 2.0 33.4 1.0
O A:HOH282 2.1 31.3 1.0
O A:HOH291 2.1 36.2 1.0
OE1 A:GLN137 2.3 35.0 1.0
OD2 A:ASP140 2.4 32.9 1.0
CD A:GLU103 2.8 19.2 1.0
OE2 A:GLU103 3.0 29.6 1.0
CD A:GLN137 3.3 30.6 1.0
CG A:ASP140 3.5 23.8 1.0
NE2 A:GLN137 3.5 22.8 1.0
CB A:ASP140 3.7 18.0 1.0
OE2 A:GLU58 3.7 30.1 1.0
OE1 A:GLU58 4.0 25.3 1.0
CD A:GLU58 4.1 22.0 1.0
O A:HOH319 4.2 37.9 1.0
CG A:GLU103 4.2 14.4 1.0
MG A:MG184 4.2 46.7 1.0
O A:HOH267 4.3 37.1 1.0
OD1 A:ASP140 4.6 27.8 1.0
CE1 A:HIS54 4.7 18.5 0.5
CG A:GLN137 4.7 27.8 1.0
CA A:GLN137 4.7 20.7 1.0
ND1 A:HIS54 4.7 21.4 0.5
MG A:MG180 4.8 46.9 1.0
CB A:GLU103 4.8 13.2 1.0

Magnesium binding site 2 out of 7 in 3sh6

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Magnesium binding site 2 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg177

b:15.2
occ:0.50
 O A:HOH317 2.0 16.6 0.5
O A:HOH316 2.1 15.5 0.5
O A:HOH224 4.2 17.4 1.0
NZ A:LYS82 4.6 22.9 1.0
CE A:LYS83 4.7 13.8 0.5
O A:HOH277 4.7 29.9 1.0
CD A:LYS82 4.7 16.5 1.0
CE A:LYS83 4.9 10.8 0.5

Magnesium binding site 3 out of 7 in 3sh6

Go back to Magnesium Binding Sites List in 3sh6
Magnesium binding site 3 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg178

b:20.6
occ:0.50
 O A:HOH199 3.0 16.6 1.0

Magnesium binding site 4 out of 7 in 3sh6

Go back to Magnesium Binding Sites List in 3sh6
Magnesium binding site 4 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg179

b:25.2
occ:1.00
 O A:HOH315 2.1 29.9 1.0
O A:VAL1 4.6 29.5 1.0
N A:GLN3 5.0 15.6 1.0
CB A:GLN3 5.0 15.2 1.0

Magnesium binding site 5 out of 7 in 3sh6

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Magnesium binding site 5 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg180

b:46.9
occ:1.00
 O A:HOH281 2.0 33.6 1.0
O A:HOH319 2.1 37.9 1.0
O A:HOH318 2.1 31.2 1.0
OE2 A:GLU136 2.6 47.9 1.0
OD1 A:ASP140 2.6 27.8 1.0
OD2 A:ASP140 2.8 32.9 1.0
CG A:GLU136 2.9 36.6 1.0
CG A:ASP140 2.9 23.8 1.0
OE2 A:GLU57 3.0 34.7 0.5
CD A:GLU136 3.1 42.9 1.0
CD A:GLU57 3.2 23.6 0.5
OE1 A:GLU57 3.3 26.6 0.5
OE1 A:GLU57 3.8 31.3 0.5
O A:GLU136 4.0 22.9 1.0
CB A:GLU136 4.2 30.1 1.0
OE1 A:GLU136 4.4 49.1 1.0
O A:HOH291 4.4 36.2 1.0
CG A:GLU57 4.4 18.7 0.5
CB A:ASP140 4.4 18.0 1.0
C A:GLU136 4.5 24.4 1.0
NH2 A:ARG143 4.6 24.6 0.2
NE2 A:HIS54 4.6 26.6 0.5
CA A:GLU136 4.7 26.6 1.0
MG A:MG176 4.8 28.2 1.0
O A:HOH282 4.8 31.3 1.0
O A:HOH267 4.9 37.1 1.0
CD2 A:HIS54 4.9 17.1 0.5

Magnesium binding site 6 out of 7 in 3sh6

Go back to Magnesium Binding Sites List in 3sh6
Magnesium binding site 6 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg184

b:46.7
occ:1.00
 O A:HOH291 2.7 36.2 1.0
OE2 A:GLU23 2.7 30.4 1.0
O A:HOH267 2.8 37.1 1.0
ND1 A:HIS61 3.2 31.3 1.0
O A:HOH249 3.3 33.4 1.0
OE1 A:GLU58 3.4 25.3 1.0
O A:HOH313 3.4 54.0 1.0
OE1 A:GLN137 3.6 35.0 1.0
CD A:GLU23 3.6 19.6 1.0
CE1 A:HIS61 3.8 32.2 1.0
OE1 A:GLU23 3.8 23.8 1.0
OE2 A:GLU58 3.8 30.1 1.0
CD2 A:TYR133 3.8 24.7 1.0
CD A:GLU58 4.0 22.0 1.0
CG1 A:VAL106 4.1 19.6 1.0
CG A:HIS61 4.1 20.6 1.0
CD A:GLN137 4.1 30.6 1.0
MG A:MG176 4.2 28.2 1.0
CD1 A:LEU110 4.4 24.6 1.0
CB A:HIS61 4.5 16.9 1.0
CE2 A:TYR133 4.5 23.7 1.0
NE2 A:GLN137 4.6 22.8 1.0
NE2 A:HIS61 4.7 31.1 1.0
CG A:TYR133 4.8 23.5 1.0
CB A:TYR133 4.9 23.3 1.0
CD2 A:HIS61 4.9 30.6 1.0
O A:TYR133 5.0 25.1 1.0
CG A:GLU23 5.0 17.7 1.0

Magnesium binding site 7 out of 7 in 3sh6

Go back to Magnesium Binding Sites List in 3sh6
Magnesium binding site 7 out of 7 in the Frog M-Ferritin, D122R Mutant, with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Frog M-Ferritin, D122R Mutant, with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:33.1
occ:0.33
 O A:HOH300 1.9 34.0 1.0
O A:HOH273 2.2 43.9 1.0
OE2 A:GLU130 3.8 31.5 1.0
OE1 A:GLU130 4.5 37.5 1.0
CD A:GLU130 4.6 33.3 1.0

Reference:

T.Tosha, H.L.Ng, T.Alber, E.C.Theil. Frog M-Ferritin, D122R Mutant, with Magnesium To Be Published.
Page generated: Mon Dec 14 08:50:57 2020

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