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Magnesium in PDB 3ka8: Frog M-Ferritin, Eqh Mutant, with Cobalt

Enzymatic activity of Frog M-Ferritin, Eqh Mutant, with Cobalt

All present enzymatic activity of Frog M-Ferritin, Eqh Mutant, with Cobalt:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin, Eqh Mutant, with Cobalt, PDB code: 3ka8 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 / 1.35
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.490, 183.490, 183.490, 90.00, 90.00, 90.00
R / Rfree (%) 13 / 15.3

Other elements in 3ka8:

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

Cobalt (Co) 5 atoms
Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin, Eqh Mutant, with Cobalt (pdb code 3ka8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Frog M-Ferritin, Eqh Mutant, with Cobalt, PDB code: 3ka8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ka8

Go back to Magnesium Binding Sites List in 3ka8
Magnesium binding site 1 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg181

b:11.2
occ:0.50
 O A:HOH391 2.1 10.8 0.5
O A:HOH385 2.1 15.2 1.0
O A:HOH361 4.2 14.0 1.0
CD A:LYS82 4.4 11.3 0.5
O A:HOH436 4.5 23.1 1.0
CE A:LYS83 4.6 15.8 1.0
NZ A:LYS82 4.6 13.9 0.5
O A:HOH226 4.7 30.5 1.0
CE A:LYS82 4.8 13.0 0.5

Magnesium binding site 2 out of 6 in 3ka8

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Magnesium binding site 2 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg182

b:12.6
occ:0.33
 O A:HOH499 1.9 27.2 1.0
O A:HOH210 2.0 28.9 1.0
OD1 A:ASP127 3.9 15.3 1.0
OG A:SER131 4.2 17.5 1.0
OE1 A:GLU130 4.2 14.5 1.0
O A:HOH498 4.3 32.7 1.0
CG A:ASP127 4.9 12.5 1.0
O A:HOH409 4.9 17.3 1.0
CB A:GLU130 5.0 10.7 1.0

Magnesium binding site 3 out of 6 in 3ka8

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Magnesium binding site 3 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg183

b:22.0
occ:1.00
 O A:HOH435 2.0 21.1 1.0
O A:HOH468 2.0 26.4 1.0
O A:HOH487 2.1 28.8 1.0
OG A:SER10 2.1 17.4 1.0
O A:HOH400 2.1 16.7 1.0
O A:HOH434 2.2 25.7 1.0
CB A:SER10 3.2 12.6 1.0
CA A:SER10 3.9 10.8 1.0
O A:SER10 4.1 10.3 1.0
OE1 A:GLU13 4.1 13.4 1.0
O A:HOH317 4.2 39.8 1.0
O A:HOH224 4.2 35.9 1.0
O A:HOH386 4.3 21.3 1.0
C A:SER10 4.3 9.7 1.0
O A:HOH251 4.3 41.8 1.0
O A:HOH394 4.5 19.3 1.0
CD A:GLU13 4.7 10.0 1.0
O A:HOH215 5.0 31.7 1.0

Magnesium binding site 4 out of 6 in 3ka8

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Magnesium binding site 4 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:29.8
occ:1.00
 O A:HOH283 1.9 28.8 1.0
O A:HOH319 2.2 39.4 1.0
O A:HOH407 4.1 22.2 1.0
O A:HOH258 4.4 36.5 1.0
O A:HOH410 4.4 20.5 1.0

Magnesium binding site 5 out of 6 in 3ka8

Go back to Magnesium Binding Sites List in 3ka8
Magnesium binding site 5 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg189

b:18.1
occ:0.50
 O A:HOH339 1.9 38.5 1.0
O A:HOH327 2.0 34.9 1.0
O A:HOH337 2.2 35.3 1.0
O A:HOH338 2.4 53.1 1.0
O A:HOH326 3.0 38.4 1.0
NE2 A:HIS45 3.4 16.2 0.5
CD2 A:HIS45 3.6 16.4 0.5
CE1 A:HIS45 3.8 17.5 0.5
CG A:HIS45 4.0 13.3 0.5
O A:HOH197 4.0 33.6 1.0
ND1 A:HIS45 4.1 15.6 0.5
ND1 A:HIS45 4.8 20.8 0.5
CG A:HIS45 4.9 16.3 0.5

Magnesium binding site 6 out of 6 in 3ka8

Go back to Magnesium Binding Sites List in 3ka8
Magnesium binding site 6 out of 6 in the Frog M-Ferritin, Eqh Mutant, with Cobalt


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, Eqh Mutant, with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg193

b:14.2
occ:1.00
 O A:HOH314 2.0 18.9 1.0
O A:HOH334 2.1 19.8 1.0
O A:HOH281 2.1 18.0 1.0
O A:HOH335 2.1 22.1 1.0
O A:SER131 4.2 13.3 1.0
O A:HOH253 4.2 31.9 1.0
O A:GLU130 4.3 13.9 1.0
CA A:SER131 4.5 12.1 1.0
O A:HOH463 4.7 35.7 1.0
C A:SER131 4.7 13.1 1.0
CB A:GLU135 4.8 12.8 1.0
O A:HOH498 4.8 32.7 1.0
CL A:CL190 5.0 18.4 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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