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Magnesium in PDB 3se1: Frog M-Ferritin with Magnesium, R72D Mutant

Enzymatic activity of Frog M-Ferritin with Magnesium, R72D Mutant

All present enzymatic activity of Frog M-Ferritin with Magnesium, R72D Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, R72D Mutant, PDB code: 3se1 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) 91.67 / 1.65
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.560, 183.560, 183.560, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.3

Other elements in 3se1:

The structure of Frog M-Ferritin with Magnesium, R72D Mutant also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Magnesium, R72D Mutant (pdb code 3se1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Frog M-Ferritin with Magnesium, R72D Mutant, PDB code: 3se1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3se1

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Magnesium binding site 1 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg176

b:39.7
occ:1.00
 O A:HOH267 1.9 32.8 1.0
O A:HOH382 2.2 24.7 1.0
OD1 A:ASP140 2.5 23.8 1.0
OD2 A:ASP140 2.7 29.7 1.0
CG A:ASP140 2.8 21.3 1.0
OE1 A:GLU57 3.5 47.2 1.0
O A:GLU136 3.8 13.8 1.0
O A:HOH405 4.1 31.5 1.0
CB A:GLU136 4.1 17.3 1.0
OE1 A:GLU136 4.1 45.1 1.0
CB A:ASP140 4.3 11.8 1.0
C A:GLU136 4.4 14.1 1.0
MG A:MG182 4.5 31.4 1.0
CA A:GLU136 4.5 14.5 1.0
CD A:GLU57 4.5 36.7 1.0
O A:HOH351 4.7 28.9 1.0
CE1 A:HIS61 4.8 35.2 1.0
CG A:GLU136 4.9 26.8 1.0
CD A:GLU136 4.9 34.2 1.0
CE1 A:HIS54 5.0 31.6 1.0

Magnesium binding site 2 out of 9 in 3se1

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Magnesium binding site 2 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg177

b:23.0
occ:0.33
 O A:HOH215 2.4 25.3 1.0
CG2 A:THR118 3.7 7.0 1.0
O A:HOH288 4.2 14.7 1.0
O A:HOH342 4.6 18.5 1.0
CB A:THR118 5.0 7.6 1.0

Magnesium binding site 3 out of 9 in 3se1

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Magnesium binding site 3 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg178

b:23.2
occ:1.00
 O A:HOH432 2.0 28.5 1.0
O A:HOH209 2.2 28.4 1.0
O A:HOH338 2.5 25.0 1.0
OD2 A:ASP127 3.9 13.7 1.0
OG A:SER131 4.6 21.3 1.0
OD1 A:ASP127 4.7 7.1 1.0
CG A:ASP127 4.7 5.8 1.0
O A:HOH265 4.7 33.9 1.0
CB A:SER131 4.9 12.9 1.0

Magnesium binding site 4 out of 9 in 3se1

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Magnesium binding site 4 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg179

b:22.3
occ:1.00
 OD1 A:ASP72 1.9 15.9 1.0
O A:HOH370 1.9 30.2 1.0
O A:HOH378 2.0 21.0 1.0
O A:HOH303 2.2 13.5 1.0
O A:HOH245 2.5 38.5 1.0
O A:HOH366 2.9 23.5 1.0
CG A:ASP72 3.0 20.9 1.0
OD2 A:ASP72 3.6 22.9 1.0
OH A:TYR68 3.9 18.9 1.0
OD2 A:ASP122 4.0 11.1 1.0
OD1 A:ASP122 4.0 8.1 1.0
O A:HOH420 4.1 24.6 1.0
O A:HOH279 4.2 12.4 1.0
CB A:ASP72 4.2 13.1 1.0
CG A:ASP122 4.3 7.0 1.0
ND1 A:HIS124 4.6 6.6 1.0
CA A:ASP72 4.7 13.4 1.0
O A:HOH230 4.7 9.1 1.0
CZ A:TYR68 4.8 13.8 1.0
O A:ASP72 4.9 19.3 1.0
O A:HOH374 4.9 23.2 1.0

Magnesium binding site 5 out of 9 in 3se1

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Magnesium binding site 5 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg181

b:25.7
occ:1.00
 OE1 A:GLU58 1.7 17.7 0.5
O A:HOH291 1.9 22.2 1.0
OE1 A:GLU23 2.1 24.3 1.0
OE1 A:GLU58 2.4 18.2 0.5
CD A:GLU58 2.5 12.5 0.5
CD A:GLU23 2.7 18.0 1.0
OE2 A:GLU23 2.7 27.4 1.0
ND1 A:HIS61 2.8 34.9 1.0
OE2 A:GLU58 2.8 19.1 0.5
O A:HOH330 3.1 26.3 1.0
O A:HOH405 3.1 31.5 1.0
CG A:HIS61 3.4 20.0 1.0
CD A:GLU58 3.4 14.1 0.5
CB A:HIS61 3.5 13.3 1.0
CE1 A:HIS61 3.8 35.2 1.0
CG A:GLU58 3.9 14.6 0.5
O A:HOH418 3.9 31.0 1.0
OE2 A:GLU58 4.0 20.5 0.5
CG A:GLU23 4.1 11.5 1.0
CG1 A:VAL106 4.2 13.2 1.0
OE1 A:GLN137 4.4 22.9 1.0
CA A:GLU58 4.4 10.3 0.5
CA A:GLU58 4.4 11.6 0.5
CG A:GLU58 4.5 6.1 0.5
CB A:GLU58 4.5 11.6 0.5
CB A:GLU58 4.6 13.3 0.5
CD2 A:HIS61 4.6 29.8 1.0
MG A:MG182 4.6 31.4 1.0
CB A:GLU23 4.7 8.9 1.0
NE2 A:HIS61 4.7 37.5 1.0
CD2 A:TYR133 4.8 7.3 1.0
O A:HOH351 4.9 28.9 1.0
O A:GLU58 4.9 10.4 1.0
CE2 A:TYR133 4.9 12.0 1.0
CA A:HIS61 4.9 11.1 1.0

Magnesium binding site 6 out of 9 in 3se1

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Magnesium binding site 6 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg182

b:31.4
occ:1.00
 O A:HOH351 1.9 28.9 1.0
OE1 A:GLU103 2.0 17.4 1.0
OD2 A:ASP140 2.2 29.7 1.0
O A:HOH405 2.2 31.5 1.0
O A:HOH330 2.2 26.3 1.0
OE1 A:GLN137 2.6 22.9 1.0
CD A:GLU103 2.8 18.4 1.0
OE2 A:GLU103 2.9 26.5 1.0
OE2 A:GLU58 3.2 20.5 0.5
CD A:GLN137 3.3 20.0 1.0
CG A:ASP140 3.3 21.3 1.0
NE2 A:GLN137 3.4 13.7 1.0
CB A:ASP140 3.7 11.8 1.0
OE2 A:GLU58 3.7 19.1 0.5
CD A:GLU58 4.1 14.1 0.5
CG A:GLU103 4.2 13.0 1.0
OE1 A:GLU58 4.2 17.7 0.5
CD A:GLU58 4.2 12.5 0.5
OE1 A:GLU58 4.4 18.2 0.5
OD1 A:ASP140 4.5 23.8 1.0
MG A:MG176 4.5 39.7 1.0
O A:HOH291 4.5 22.2 1.0
CA A:GLN137 4.6 11.3 1.0
O A:HOH418 4.6 31.0 1.0
MG A:MG181 4.6 25.7 1.0
CG A:GLN137 4.6 17.7 1.0
CB A:GLU103 4.8 11.1 1.0
O A:GLU136 4.8 13.8 1.0

Magnesium binding site 7 out of 9 in 3se1

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Magnesium binding site 7 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg183

b:42.4
occ:1.00
 O A:HOH411 1.9 30.8 1.0
O A:HOH371 2.7 33.8 1.0
O A:HOH229 2.7 31.8 1.0
OD2 A:ASP112 2.9 19.9 1.0
O A:HOH284 3.1 36.3 1.0
O A:HOH437 3.4 41.1 1.0
O A:HOH332 3.4 22.6 1.0
CA A:ALA109 3.6 7.5 1.0
CB A:ALA109 3.8 9.2 1.0
CG A:ASP112 3.8 15.4 1.0
CB A:ASP112 3.8 8.9 1.0
O A:HOH207 4.1 14.6 1.0
O A:HOH376 4.2 30.4 1.0
N A:ALA109 4.4 7.4 1.0
O A:HOH246 4.4 39.9 1.0
O A:ALA109 4.5 7.0 1.0
O A:GLN108 4.5 7.4 1.0
C A:ALA109 4.5 7.9 1.0
O A:HOH406 4.6 34.7 1.0
O A:HOH264 4.7 28.6 1.0
C A:GLN108 4.8 6.5 1.0
O A:HOH380 4.9 31.9 1.0
OD1 A:ASP112 5.0 13.9 1.0

Magnesium binding site 8 out of 9 in 3se1

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Magnesium binding site 8 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg184

b:2.0
occ:0.33
 O A:HOH299 2.0 11.5 1.0
O A:HOH286 2.0 6.1 1.0
OE2 A:GLU130 3.9 7.5 1.0
OE1 A:GLU130 4.1 11.3 1.0
O A:HOH288 4.2 14.7 1.0
O A:HOH324 4.3 12.6 1.0
CD A:GLU130 4.5 6.8 1.0

Magnesium binding site 9 out of 9 in 3se1

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Magnesium binding site 9 out of 9 in the Frog M-Ferritin with Magnesium, R72D 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, R72D Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg193

b:2.8
occ:0.50
 O A:HOH383 1.8 10.0 1.0
O A:HOH248 2.0 2.3 0.5
O A:HOH212 2.0 6.6 1.0
O A:HOH386 2.1 5.9 0.5
OD2 A:ASP80 3.9 7.0 1.0
OD1 A:ASP80 3.9 3.9 1.0
O A:HOH196 4.4 2.0 1.0
CG A:ASP80 4.4 5.9 1.0

Reference:

T.Tosha, H.L.Ng, T.Alber, E.C.Theil. Frog M-Ferritin with Magnesium, R72D Mutant To Be Published.
Page generated: Thu Aug 15 10:53:17 2024

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