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Magnesium in PDB 4lpn: Frog M-Ferritin with Cobalt, D127E Mutant

Enzymatic activity of Frog M-Ferritin with Cobalt, D127E Mutant

All present enzymatic activity of Frog M-Ferritin with Cobalt, D127E Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Cobalt, D127E Mutant, PDB code: 4lpn was solved by R.Torres, R.Behera, C.W.Goulding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.00 / 1.66
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.003, 184.003, 184.003, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.7

Other elements in 4lpn:

The structure of Frog M-Ferritin with Cobalt, D127E Mutant also contains other interesting chemical elements:

Cobalt (Co) 11 atoms
Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M-Ferritin with Cobalt, D127E Mutant (pdb code 4lpn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Frog M-Ferritin with Cobalt, D127E Mutant, PDB code: 4lpn:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4lpn

Go back to Magnesium Binding Sites List in 4lpn
Magnesium binding site 1 out of 3 in the Frog M-Ferritin with Cobalt, D127E 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg220

b:21.5
occ:1.00
O A:HOH441 2.0 26.0 1.0
OG A:SER10 2.1 19.3 1.0
O A:HOH367 2.1 26.1 1.0
O A:HOH377 2.1 21.7 1.0
O A:HOH443 2.1 28.5 1.0
O A:HOH348 2.1 17.7 1.0
CB A:SER10 3.1 16.9 1.0
HB2 A:SER10 3.2 20.3 1.0
HA A:SER10 3.5 15.5 1.0
CA A:SER10 3.8 12.9 1.0
HB3 A:SER10 3.9 20.3 1.0
O A:SER10 4.1 14.3 1.0
OE1 A:GLU13 4.1 16.2 1.0
O A:HOH335 4.2 22.5 1.0
O A:HOH437 4.3 31.2 1.0
C A:SER10 4.3 13.8 1.0
HB3 A:GLU13 4.5 17.0 1.0
O A:HOH331 4.5 21.0 1.0
CD A:GLU13 4.6 15.9 1.0
HB2 A:ALA14 4.9 16.3 1.0
HH22 A:ARG5 4.9 18.7 1.0

Magnesium binding site 2 out of 3 in 4lpn

Go back to Magnesium Binding Sites List in 4lpn
Magnesium binding site 2 out of 3 in the Frog M-Ferritin with Cobalt, D127E 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg221

b:18.8
occ:0.33
O A:HOH472 2.1 33.4 1.0
O A:HOH420 2.1 29.1 1.0
HG23 A:THR118 3.9 23.6 1.0
O A:HOH427 4.2 33.6 1.0
HG21 A:THR118 4.4 23.6 1.0
O A:HOH344 4.4 24.9 1.0
O A:HOH405 4.5 26.0 1.0
CG2 A:THR118 4.6 19.6 1.0
O A:HOH404 4.7 26.1 1.0
HG22 A:THR118 4.9 23.6 1.0

Magnesium binding site 3 out of 3 in 4lpn

Go back to Magnesium Binding Sites List in 4lpn
Magnesium binding site 3 out of 3 in the Frog M-Ferritin with Cobalt, D127E 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 Cobalt, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:35.3
occ:1.00
O A:HOH492 2.1 39.6 1.0
O A:HOH491 2.1 43.1 1.0
CE1 A:HIS45 3.7 18.9 0.5
NE2 A:HIS45 3.8 26.5 0.5
ND1 A:HIS45 3.9 35.8 0.5
HE1 A:HIS45 3.9 22.6 0.5
HE2 A:HIS45 4.1 31.8 0.5
CD2 A:HIS45 4.1 30.9 0.5
CG A:HIS45 4.2 19.6 0.5
O A:HOH493 4.2 39.8 1.0
HD1 A:HIS45 4.2 43.0 0.5
HB2 A:HIS45 4.4 18.5 0.5
HD2 A:HIS45 4.6 37.1 0.5
HD1 A:HIS45 4.7 29.0 0.5
ND1 A:HIS45 4.8 24.1 0.5
HB3 A:HIS45 5.0 20.2 0.5
HB2 A:HIS45 5.0 20.2 0.5

Reference:

R.Torres, R.Behera, T.Takehiko, J.Bradley, C.W.Goulding, E.C.Theil. D127E Ion Channel Exit Modification in Ferritin Nanocages Entraps Fe(II) and Impairs Its Distribution to Diiron Catalytic Centers To Be Published.
Page generated: Mon Dec 14 19:10:18 2020

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