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Magnesium in PDB 3ka3: Frog M-Ferritin with Magnesium

Enzymatic activity of Frog M-Ferritin with Magnesium

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

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, PDB code: 3ka3 was solved by T.Tosha, H.L.Ng, E.Theil, T.Alber, O.Bhattasali, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.40
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.886, 183.886, 183.886, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 15.9

Other elements in 3ka3:

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

Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Magnesium (pdb code 3ka3). 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, PDB code: 3ka3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3ka3

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Magnesium binding site 1 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg176

b:29.2
occ:1.00
 OE2 A:GLU57 1.9 27.0 1.0
O A:HOH446 1.9 30.1 1.0
OE1 A:GLU136 2.1 16.1 0.5
O A:HOH453 2.1 30.1 1.0
O A:HOH379 2.1 20.2 1.0
OD2 A:ASP140 2.4 28.1 1.0
CD A:GLU57 2.9 27.2 1.0
OD1 A:ASP140 2.9 25.1 1.0
CG A:ASP140 3.0 19.1 1.0
OE1 A:GLU57 3.3 32.1 1.0
CD A:GLU136 3.3 21.3 0.5
CB A:GLU136 3.8 18.6 0.5
CB A:GLU136 3.8 21.2 0.5
O A:GLU136 3.8 15.9 1.0
O A:HOH338 3.9 28.2 1.0
CG A:GLU136 4.1 16.3 0.5
OE1 A:GLU136 4.2 31.1 0.5
CG A:GLU57 4.2 22.1 0.5
CG A:GLU57 4.3 20.4 0.5
OE2 A:GLU136 4.3 22.2 0.5
C A:GLU136 4.3 15.7 1.0
CG A:GLU136 4.4 24.9 0.5
CB A:ASP140 4.5 14.7 1.0
CA A:GLU136 4.5 16.9 0.5
CA A:GLU136 4.5 15.3 0.5
MG A:MG180 4.5 31.2 1.0
NH2 A:ARG143 4.6 33.7 0.5
MG A:MG192 4.7 30.4 1.0
O A:HOH478 4.7 30.0 1.0
O A:HOH317 4.8 58.3 1.0
CE1 A:HIS61 4.8 33.4 1.0
CD A:GLU136 4.8 30.7 0.5

Magnesium binding site 2 out of 10 in 3ka3

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Magnesium binding site 2 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg177

b:21.3
occ:1.00
 O A:HOH428 2.0 25.4 1.0
O A:HOH394 2.0 19.8 1.0
O A:HOH381 2.0 21.8 1.0
OG A:SER10 2.1 16.6 1.0
O A:HOH345 2.1 15.7 1.0
O A:HOH413 2.1 22.2 1.0
CB A:SER10 3.2 14.3 1.0
CA A:SER10 3.9 11.6 1.0
O A:SER10 4.1 11.9 1.0
OE1 A:GLU13 4.1 13.7 1.0
O A:HOH352 4.3 19.1 1.0
O A:HOH452 4.3 34.9 1.0
C A:SER10 4.3 11.1 1.0
O A:HOH247 4.4 35.9 1.0
O A:HOH285 4.4 44.2 1.0
O A:HOH355 4.4 17.1 1.0
O A:HOH236 4.6 39.7 1.0
CD A:GLU13 4.6 11.6 1.0

Magnesium binding site 3 out of 10 in 3ka3

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Magnesium binding site 3 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg178

b:21.3
occ:1.00
 O A:HOH435 2.0 25.6 1.0
O A:HOH445 2.0 28.1 1.0
O A:HOH416 2.1 24.0 1.0
OD2 A:ASP127 4.0 20.9 1.0
OD1 A:ASP127 4.4 21.0 1.0
O A:HOH212 4.6 34.0 1.0
CG A:ASP127 4.7 17.7 1.0
OG A:SER131 4.8 15.8 0.5
O A:HOH282 4.9 45.0 1.0
OG A:SER131 5.0 23.7 0.5

Magnesium binding site 4 out of 10 in 3ka3

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Magnesium binding site 4 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg179

b:14.2
occ:0.33
 O A:HOH349 2.2 15.9 1.0
O A:HOH310 2.2 15.2 1.0
OE2 A:GLU130 4.0 15.9 1.0
O A:HOH398 4.3 22.6 1.0
OE1 A:GLU130 4.3 20.9 1.0
O A:HOH386 4.4 16.5 1.0
CD A:GLU130 4.6 16.6 1.0
MG A:MG190 4.7 36.6 0.3

Magnesium binding site 5 out of 10 in 3ka3

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Magnesium binding site 5 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg180

b:31.2
occ:1.00
 OE1 A:GLU103 1.9 19.4 1.0
O A:HOH411 2.2 26.7 1.0
O A:HOH338 2.3 28.2 1.0
MG A:MG192 2.4 30.4 1.0
O A:HOH478 2.5 30.0 1.0
OD2 A:ASP140 2.6 28.1 1.0
OE1 A:GLN137 2.7 31.5 1.0
CD A:GLU103 2.9 16.8 1.0
OE2 A:GLU103 3.2 30.3 1.0
CD A:GLN137 3.4 18.5 1.0
NE2 A:GLN137 3.5 17.0 1.0
CG A:ASP140 3.5 19.1 1.0
OE2 A:GLU58 3.6 30.4 1.0
CB A:ASP140 3.7 14.7 1.0
OE1 A:GLU136 4.0 16.1 0.5
OE2 A:GLU136 4.0 22.2 0.5
CD A:GLU58 4.2 22.0 1.0
OE1 A:GLU58 4.3 21.7 1.0
O A:HOH423 4.3 27.9 1.0
OE2 A:GLU57 4.3 27.0 1.0
CG A:GLU103 4.3 13.1 1.0
CD A:GLU136 4.3 21.3 0.5
MG A:MG176 4.5 29.2 1.0
CA A:GLN137 4.5 13.6 1.0
OD1 A:ASP140 4.6 25.1 1.0
CG A:GLN137 4.6 18.8 1.0
CE1 A:HIS54 4.8 22.6 0.5
CB A:GLU103 4.9 12.5 1.0
O A:GLU136 4.9 15.9 1.0
CB A:GLN137 5.0 16.6 1.0
ND1 A:HIS54 5.0 20.8 0.5

Magnesium binding site 6 out of 10 in 3ka3

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Magnesium binding site 6 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg183

b:28.1
occ:1.00
 O A:HOH483 2.1 29.6 1.0
O A:HOH250 2.1 31.6 1.0
O A:HOH239 2.4 36.4 1.0
O A:HOH291 4.0 12.7 1.0
O A:HOH364 4.2 21.4 1.0
O A:HOH481 4.3 34.0 1.0
O A:VAL1 4.7 21.2 1.0
O A:HOH330 4.8 50.6 1.0

Magnesium binding site 7 out of 10 in 3ka3

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Magnesium binding site 7 out of 10 in the Frog M-Ferritin 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 with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:21.2
occ:0.33
 O A:HOH333 1.7 29.3 1.0
O A:HOH361 1.8 30.7 1.0
OE1 A:GLU130 3.8 20.9 1.0
OD1 A:ASP127 3.8 21.0 1.0
OG A:SER131 4.0 15.8 0.5
CB A:GLU130 4.4 15.2 1.0
O A:HOH212 4.5 34.0 1.0
CD A:GLU130 4.6 16.6 1.0
CG A:ASP127 4.8 17.7 1.0

Magnesium binding site 8 out of 10 in 3ka3

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg186

b:14.7
occ:0.50
 O A:HOH360 2.1 16.9 1.0
O A:HOH363 2.1 13.3 0.5
O A:HOH297 4.2 15.5 1.0
CD A:LYS82 4.4 14.2 0.5
O A:HOH391 4.5 22.9 1.0
CE A:LYS83 4.6 12.5 0.5
NZ A:LYS82 4.6 16.1 0.5
CE A:LYS82 4.7 13.6 0.5
O A:HOH430 4.8 32.8 1.0
CE A:LYS83 4.9 14.0 0.5

Magnesium binding site 9 out of 10 in 3ka3

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:36.6
occ:0.33
 O A:HOH432 2.1 28.6 1.0
O A:HOH342 2.4 22.7 0.3
O A:HOH398 3.1 22.6 1.0
O A:HOH349 4.0 15.9 1.0
CG2 A:THR118 4.5 15.3 1.0
MG A:MG179 4.7 14.2 0.3
O A:HOH386 4.9 16.5 1.0
O A:HOH253 4.9 42.3 1.0
O A:HOH407 5.0 24.4 1.0

Magnesium binding site 10 out of 10 in 3ka3

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg192

b:30.4
occ:1.00
 O A:HOH338 1.7 28.2 1.0
OE1 A:GLN137 1.9 31.5 1.0
OE2 A:GLU136 2.0 22.2 0.5
O A:HOH423 2.2 27.9 1.0
MG A:MG180 2.4 31.2 1.0
O A:HOH411 2.6 26.7 1.0
CD A:GLU136 2.9 21.3 0.5
CD A:GLN137 3.1 18.5 1.0
OE1 A:GLU136 3.2 16.1 0.5
ND1 A:HIS61 3.8 34.0 1.0
NE2 A:GLN137 3.8 17.0 1.0
OE2 A:GLU58 3.8 30.4 1.0
OD2 A:ASP140 3.9 28.1 1.0
CE1 A:HIS61 3.9 33.4 1.0
OE1 A:GLU58 4.0 21.7 1.0
OE1 A:GLU103 4.0 19.4 1.0
CG A:GLU136 4.2 16.3 0.5
O A:HOH478 4.3 30.0 1.0
CA A:GLN137 4.3 13.6 1.0
CB A:GLN137 4.3 16.6 1.0
CG A:GLN137 4.3 18.8 1.0
OE2 A:GLU57 4.3 27.0 1.0
CD A:GLU58 4.3 22.0 1.0
N A:GLN137 4.4 14.3 1.0
MG A:MG176 4.7 29.2 1.0
C A:GLU136 4.8 15.7 1.0
O A:TYR133 4.8 14.6 1.0
OE2 A:GLU23 4.8 26.8 1.0
CG1 A:VAL106 4.9 13.3 1.0

Reference:

T.Tosha, H.L.Ng, O.Bhattasali, T.Alber, E.C.Theil. Moving Metal Ions Through Ferritin-Protein Nanocages From Three-Fold Pores to Catalytic Sites. J.Am.Chem.Soc. V. 132 14562 2010.
ISSN: ISSN 0002-7863
PubMed: 20866049
DOI: 10.1021/JA105583D
Page generated: Wed Aug 14 17:58:46 2024

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