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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

Go back to Magnesium Binding Sites List in 3ka3
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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