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Magnesium in PDB 5j8s: Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8s was solved by C.Pozzi, F.Di Pisa, S.Mangani, C.Bernacchioni, P.Turano, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.77 / 1.50
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 185.010, 185.010, 185.010, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 17.9

Other elements in 5j8s:

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Chlorine (Cl) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j8s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8s:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5j8s

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Magnesium binding site 1 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:12.3
occ:0.80
 OE1 A:GLU23 2.0 13.8 0.8
OE1 A:GLU58 2.0 16.1 0.8
O A:HOH340 2.0 13.2 0.8
O A:HOH342 2.0 16.8 0.8
ND1 A:HIS61 2.2 14.0 0.8
CD A:GLU23 3.0 15.1 1.0
CD A:GLU58 3.0 16.6 1.0
CE1 A:HIS61 3.1 15.6 1.0
CG A:HIS61 3.2 14.0 1.0
OE2 A:GLU23 3.3 16.6 1.0
OE2 A:GLU58 3.5 17.4 1.0
CB A:HIS61 3.6 13.4 1.0
CG1 A:VAL106 4.0 12.6 1.0
OE1 A:GLN137 4.2 16.4 1.0
NE2 A:HIS61 4.2 16.1 1.0
O A:HOH362 4.2 17.4 1.0
CG A:GLU23 4.3 14.5 1.0
CD2 A:HIS61 4.3 15.7 1.0
CG A:GLU58 4.3 14.5 1.0
CA A:GLU58 4.4 13.4 1.0
CB A:GLU58 4.6 13.1 1.0
CB A:GLU23 4.7 12.7 1.0
O A:HOH490 4.8 29.6 1.0
CA A:GLU23 4.9 11.6 1.0
O A:HOH403 4.9 24.1 0.6
CD A:GLN137 4.9 15.8 1.0
O A:GLU58 5.0 12.5 1.0

Magnesium binding site 2 out of 8 in 5j8s

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Magnesium binding site 2 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:13.2
occ:0.45
 O A:HOH313 2.0 13.3 0.5
O A:HOH319 2.0 14.1 0.9
OD2 A:ASP80 4.0 10.9 1.0
OD1 A:ASP80 4.1 9.9 1.0
CG A:ASP80 4.5 10.2 1.0
O A:HOH463 4.7 9.9 1.0

Magnesium binding site 3 out of 8 in 5j8s

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Magnesium binding site 3 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:19.2
occ:0.50
 O A:HOH434 1.9 19.1 0.5
O A:HOH583 2.1 13.8 0.7
O A:HOH634 2.1 21.5 0.5
O A:HOH562 2.1 25.1 0.5
O A:VAL1 4.3 21.6 1.0
O A:HOH588 4.3 35.5 1.0
O A:HOH601 4.9 52.8 1.0
N A:GLN3 4.9 12.2 1.0
CB A:GLN3 4.9 12.4 1.0

Magnesium binding site 4 out of 8 in 5j8s

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Magnesium binding site 4 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:18.3
occ:0.50
 O A:HOH610 2.0 20.6 0.5
O A:HOH309 2.1 24.7 1.0
O A:HOH626 2.1 30.2 0.5
OD2 A:ASP146 4.0 14.2 1.0
O A:HOH374 4.1 22.9 1.0
O A:HOH495 4.3 31.6 1.0
O A:HOH450 4.3 20.8 1.0
O A:HOH411 4.8 17.6 1.0

Magnesium binding site 5 out of 8 in 5j8s

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Magnesium binding site 5 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:20.2
occ:0.75
 O A:HOH427 2.0 22.9 0.8
O A:HOH599 2.1 23.8 0.8
O A:HOH388 2.2 23.1 0.8
O A:HOH308 3.9 45.9 1.0
OD2 A:ASP127 4.0 18.3 1.0
OD1 A:ASP127 4.5 19.6 1.0
CG A:ASP127 4.7 16.1 1.0
O A:HOH489 4.7 40.3 1.0
O A:HOH576 4.8 41.4 1.0
OG A:SER131 4.9 14.7 0.5
OG A:SER131 5.0 15.0 0.5
O A:HOH611 5.0 42.3 1.0

Magnesium binding site 6 out of 8 in 5j8s

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Magnesium binding site 6 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:24.3
occ:0.80
 O A:HOH345 2.0 18.5 0.8
O A:HOH481 2.1 23.2 0.8
O A:HOH421 2.1 17.9 1.0
O A:HOH604 2.1 26.2 0.8
OG A:SER10 2.2 14.5 0.8
O A:HOH469 2.2 22.4 0.8
CB A:SER10 3.3 13.9 1.0
CA A:SER10 3.9 12.7 1.0
O A:SER10 4.1 12.2 1.0
OE1 A:GLU13 4.1 14.1 1.0
O A:HOH556 4.2 35.4 1.0
O A:HOH312 4.3 19.1 1.0
C A:SER10 4.4 12.9 1.0
O A:HOH534 4.4 42.5 1.0
O A:HOH529 4.4 18.1 1.0
O A:HOH656 4.5 42.0 1.0
CD A:GLU13 4.6 12.3 1.0
OE2 A:GLU13 4.9 12.6 1.0

Magnesium binding site 7 out of 8 in 5j8s

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Magnesium binding site 7 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:12.1
occ:0.33
 O A:HOH522 2.0 13.8 1.0
O A:HOH335 2.1 12.4 1.0
OE2 A:GLU130 3.9 15.4 1.0
OE1 A:GLU130 4.2 19.1 1.0
O A:HOH590 4.3 15.3 1.0
O A:HOH412 4.3 20.1 1.0
CD A:GLU130 4.5 16.2 1.0

Magnesium binding site 8 out of 8 in 5j8s

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Magnesium binding site 8 out of 8 in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Iron-Free State of Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:37.6
occ:0.25
 O A:HOH305 2.0 29.9 1.0
O A:HOH304 2.1 21.6 1.0
OD1 A:ASP127 3.6 19.6 1.0
O A:HOH489 4.0 40.3 1.0
OG A:SER131 4.2 14.7 0.5
OE1 A:GLU130 4.4 19.1 1.0
O A:HOH388 4.7 23.1 0.8
CG A:ASP127 4.7 16.1 1.0
CB A:GLU130 5.0 13.4 1.0

Reference:

C.Bernacchioni, C.Pozzi, F.Di Pisa, S.Mangani, P.Turano. Ferroxidase Activity in Eukaryotic Ferritin Is Controlled By Accessory-Iron-Binding Sites in the Catalytic Cavity. Chemistry V. 22 16213 2016.
ISSN: ISSN 0947-6539
PubMed: 27650996
DOI: 10.1002/CHEM.201602842
Page generated: Sun Sep 29 17:38:31 2024

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