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Magnesium in PDB 3ka4: Frog M-Ferritin with Cobalt

Enzymatic activity of Frog M-Ferritin with Cobalt

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

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, PDB code: 3ka4 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 (°) 183.765, 183.765, 183.765, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 17.4

Other elements in 3ka4:

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

Cobalt (Co) 8 atoms
Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Cobalt (pdb code 3ka4). 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 with Cobalt, PDB code: 3ka4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 1 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg185

b:13.7
occ:0.50
 O A:HOH255 2.1 16.8 1.0
O A:HOH282 2.1 12.2 0.5
O A:HOH236 4.3 15.1 1.0
O A:HOH315 4.5 25.9 1.0
CE A:LYS83 4.6 16.7 1.0
NZ A:LYS82 4.6 24.8 0.0
CD A:LYS82 4.7 15.8 1.0
O A:HOH329 4.7 28.3 1.0
CD A:LYS82 4.7 16.6 0.0
CE A:LYS82 4.9 18.9 1.0

Magnesium binding site 2 out of 6 in 3ka4

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Magnesium binding site 2 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg186

b:17.1
occ:0.33
 O A:HOH322 1.8 27.4 1.0
O A:HOH323 2.0 28.2 1.0
OD1 A:ASP127 3.8 17.2 1.0
OG A:SER131 4.2 20.0 1.0
OE1 A:GLU130 4.3 17.4 1.0
O A:HOH409 4.4 29.9 1.0
O A:HOH309 4.9 21.2 1.0
CG A:ASP127 4.9 13.5 1.0
CB A:GLU130 4.9 12.9 1.0

Magnesium binding site 3 out of 6 in 3ka4

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Magnesium binding site 3 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg187

b:22.4
occ:1.00
 O A:HOH340 2.0 24.8 1.0
O A:HOH360 2.0 27.5 1.0
O A:HOH337 2.0 20.4 1.0
OG A:SER10 2.1 18.4 1.0
O A:HOH242 2.1 17.3 1.0
O A:HOH382 2.2 27.2 1.0
CB A:SER10 3.2 13.6 1.0
CA A:SER10 3.9 12.4 1.0
O A:SER10 4.1 12.0 1.0
OE1 A:GLU13 4.2 14.2 1.0
O A:HOH264 4.2 22.3 1.0
C A:SER10 4.3 10.5 1.0
O A:HOH239 4.3 37.7 1.0
O A:HOH252 4.5 20.6 1.0
CD A:GLU13 4.7 12.5 1.0
O A:HOH207 4.9 32.0 1.0

Magnesium binding site 4 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 4 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg188

b:19.8
occ:0.50
 O A:HOH276 2.1 22.8 1.0
OD2 A:ASP146 4.0 15.0 1.0
O A:HOH418 4.2 30.1 1.0
O A:HOH302 4.3 20.5 1.0
O A:HOH280 4.3 27.1 1.0
O A:HOH311 4.6 23.5 1.0

Magnesium binding site 5 out of 6 in 3ka4

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Magnesium binding site 5 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg196

b:31.3
occ:1.00
 O A:HOH334 1.9 31.0 1.0
O A:HOH362 2.0 40.2 1.0
O A:HOH365 2.1 38.5 1.0
O A:HOH364 2.1 42.0 1.0
O A:HOH363 2.2 44.1 1.0
O A:HOH301 2.4 21.9 1.0
OD1 A:ASN21 4.2 10.5 1.0
O A:HOH310 4.4 21.3 1.0
O A:HOH295 4.4 20.4 1.0
O A:HOH314 4.4 24.8 1.0
O A:ARG18 4.4 10.8 1.0
O A:HOH343 4.5 25.0 1.0
CB A:LEU22 5.0 11.1 1.0

Magnesium binding site 6 out of 6 in 3ka4

Go back to Magnesium Binding Sites List in 3ka4
Magnesium binding site 6 out of 6 in the Frog M-Ferritin 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 with Cobalt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg197

b:30.0
occ:1.00
 O A:HOH339 2.0 19.0 1.0
O A:HOH338 2.1 19.9 1.0
O A:HOH332 2.1 22.6 1.0
O A:SER131 4.2 15.3 1.0
O A:HOH414 4.3 32.6 1.0
O A:GLU130 4.3 14.9 1.0
CA A:SER131 4.5 13.8 1.0
O A:HOH227 4.5 37.6 1.0
O A:HOH409 4.6 29.9 1.0
C A:SER131 4.7 13.6 1.0
CB A:GLU135 4.7 14.8 1.0
CG A:GLU135 4.9 15.0 1.0
CL A:CL194 5.0 20.3 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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