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Magnesium in PDB 3shx: Frog M-Ferritin with Magnesium, L134P Mutant

Enzymatic activity of Frog M-Ferritin with Magnesium, L134P Mutant

All present enzymatic activity of Frog M-Ferritin with Magnesium, L134P Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, L134P Mutant, PDB code: 3shx 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) 55.38 / 1.35
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.775, 183.775, 183.775, 90.00, 90.00, 90.00
R / Rfree (%) 13.7 / 16.3

Other elements in 3shx:

The structure of Frog M-Ferritin with Magnesium, L134P Mutant also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Magnesium, L134P Mutant (pdb code 3shx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Frog M-Ferritin with Magnesium, L134P Mutant, PDB code: 3shx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3shx

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Magnesium binding site 1 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg176

b:13.7
occ:0.50
 O A:HOH218 1.9 14.0 1.0
O A:HOH319 2.1 14.2 0.5
OD1 A:ASP80 4.0 9.3 1.0
OD2 A:ASP80 4.0 11.1 1.0
CG A:ASP80 4.4 9.5 1.0

Magnesium binding site 2 out of 10 in 3shx

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Magnesium binding site 2 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg177

b:26.3
occ:0.50
 OE2 A:GLU57 1.8 21.4 0.5
OE1 A:GLU136 1.9 35.6 1.0
O A:HOH267 2.0 43.0 1.0
O A:HOH425 2.1 35.0 1.0
O A:HOH222 2.2 34.3 1.0
OD2 A:ASP140 2.4 31.6 1.0
OD1 A:ASP140 2.8 32.4 1.0
CG A:ASP140 2.9 21.3 1.0
CD A:GLU57 2.9 19.0 0.5
CD A:GLU136 3.2 35.8 1.0
OE1 A:GLU57 3.4 24.2 0.5
CB A:GLU136 3.9 26.2 1.0
O A:GLU136 3.9 22.4 1.0
CG A:GLU136 4.1 30.5 1.0
OE2 A:GLU136 4.2 38.5 1.0
O A:HOH375 4.2 41.9 1.0
CG A:GLU57 4.2 18.1 0.5
MG A:MG190 4.3 38.5 1.0
C A:GLU136 4.4 20.7 1.0
CB A:ASP140 4.4 18.4 1.0
O A:HOH348 4.5 42.2 1.0
O A:HOH346 4.5 59.5 1.0
CA A:GLU136 4.5 24.2 1.0
O A:HOH371 4.8 30.7 1.0
CE1 A:HIS54 4.9 21.2 0.5

Magnesium binding site 3 out of 10 in 3shx

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Magnesium binding site 3 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg178

b:15.6
occ:0.25
 CE1 A:HIS169 3.6 15.7 1.0
NE2 A:HIS169 4.4 13.4 1.0
ND1 A:HIS169 4.5 15.0 1.0
O A:HOH352 4.9 25.5 1.0
CL A:CL187 5.0 12.3 0.2

Magnesium binding site 4 out of 10 in 3shx

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Magnesium binding site 4 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg179

b:21.2
occ:1.00
 O A:HOH240 2.0 23.3 1.0
O A:HOH239 2.0 24.3 1.0
O A:HOH340 2.0 27.5 1.0
O A:HOH248 2.1 19.6 1.0
O A:HOH297 2.1 16.3 1.0
OG A:SER10 2.1 17.0 1.0
CB A:SER10 3.3 13.9 1.0
CA A:SER10 3.9 12.2 1.0
O A:SER10 4.1 12.0 1.0
OE1 A:GLU13 4.2 13.4 1.0
O A:HOH285 4.3 21.3 1.0
O A:HOH288 4.3 39.3 1.0
C A:SER10 4.3 11.4 1.0
O A:HOH427 4.4 37.2 1.0
O A:HOH270 4.5 17.5 1.0
O A:HOH244 4.5 38.4 1.0
CD A:GLU13 4.6 10.0 1.0

Magnesium binding site 5 out of 10 in 3shx

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Magnesium binding site 5 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg180

b:25.2
occ:1.00
 O A:HOH306 2.0 19.3 1.0
O A:HOH436 2.1 28.1 1.0
O A:HOH447 2.2 29.8 1.0
O A:HOH446 2.2 32.2 1.0
O A:HOH313 4.2 20.7 1.0
O A:HOH450 4.4 31.3 1.0
O A:VAL1 4.7 20.6 1.0
N A:GLN3 4.9 11.3 1.0
CB A:GLN3 5.0 11.4 1.0

Magnesium binding site 6 out of 10 in 3shx

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Magnesium binding site 6 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg184

b:22.7
occ:0.33
 O A:HOH350 2.1 25.5 1.0
O A:HOH451 2.2 25.6 1.0
NA A:NA193 2.8 24.5 0.2
OE2 A:GLU130 4.0 25.4 1.0
O A:HOH387 4.3 24.7 1.0
O A:HOH410 4.3 22.2 1.0
O A:HOH393 4.3 27.9 1.0
OE1 A:GLU130 4.4 38.5 1.0
CD A:GLU130 4.7 26.1 1.0

Magnesium binding site 7 out of 10 in 3shx

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Magnesium binding site 7 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


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 with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg186

b:17.4
occ:0.16
 O A:HOH368 2.1 37.5 1.0
O A:HOH416 2.3 28.3 1.0
CG2 A:THR118 4.4 18.9 1.0
O A:HOH387 4.6 24.7 1.0
O A:HOH409 4.7 27.1 1.0
O A:HOH412 4.7 29.3 1.0

Magnesium binding site 8 out of 10 in 3shx

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Magnesium binding site 8 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Frog M-Ferritin with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg189

b:47.0
occ:1.00
 O A:HOH421 2.3 34.1 1.0
O A:HOH370 2.3 55.3 1.0
O A:HOH343 2.5 21.8 1.0
O A:HOH440 3.2 31.2 1.0
CA A:GLY155 4.1 13.6 1.0
O A:HOH291 4.3 40.5 1.0
OE1 A:GLU158 4.3 20.4 1.0
O A:GLY155 4.3 13.9 1.0
C A:GLY155 4.4 12.9 1.0
O A:LEU156 4.4 15.9 1.0
O A:HOH259 4.4 49.1 1.0
O A:LYS152 4.6 14.1 1.0
O A:HOH216 4.8 35.2 1.0

Magnesium binding site 9 out of 10 in 3shx

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Magnesium binding site 9 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Frog M-Ferritin with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:38.5
occ:1.00
 O A:HOH375 2.0 41.9 1.0
OE1 A:GLU103 2.1 27.2 1.0
O A:HOH372 2.2 32.4 1.0
O A:HOH371 2.4 30.7 1.0
OD2 A:ASP140 2.5 31.6 1.0
CD A:GLU103 2.9 18.4 1.0
OE2 A:GLU103 3.0 25.2 1.0
OE1 A:GLN137 3.4 29.1 1.0
CG A:ASP140 3.5 21.3 1.0
OE2 A:GLU58 3.5 25.0 1.0
NE2 A:GLN137 3.7 21.7 1.0
CD A:GLN137 3.7 29.6 1.0
CB A:ASP140 3.8 18.4 1.0
OE1 A:GLU136 3.8 35.6 1.0
OE2 A:GLU136 4.0 38.5 1.0
OE2 A:GLU57 4.0 21.4 0.5
OE1 A:GLU58 4.1 21.1 1.0
CD A:GLU58 4.1 20.3 1.0
O A:HOH369 4.2 33.9 1.0
CD A:GLU136 4.3 35.8 1.0
CG A:GLU103 4.3 13.3 1.0
MG A:MG177 4.3 26.3 0.5
ND1 A:HIS54 4.5 17.3 0.5
CE1 A:HIS54 4.6 17.6 0.5
OD1 A:ASP140 4.6 32.4 1.0
CA A:GLN137 4.8 19.1 1.0
CG A:GLN137 4.9 27.1 1.0
CD A:GLU57 4.9 19.0 0.5
CB A:GLU103 5.0 12.1 1.0

Magnesium binding site 10 out of 10 in 3shx

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Magnesium binding site 10 out of 10 in the Frog M-Ferritin with Magnesium, L134P Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Frog M-Ferritin with Magnesium, L134P Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg192

b:23.0
occ:0.16
 O A:HOH373 2.1 30.2 1.0
O A:HOH374 2.4 64.5 1.0
OD1 A:ASP127 3.9 24.6 1.0
OE1 A:GLU130 4.5 38.5 1.0
NA A:NA193 4.6 24.5 0.2
OG A:SER131 4.8 34.6 1.0

Reference:

T.Tosha, H.L.Ng, T.Alber, E.C.Theil. Frog M-Ferritin with Magnesium, L134P Mutant To Be Published.
Page generated: Thu Aug 15 10:58:46 2024

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