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Magnesium in PDB 5j9v: Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

All present enzymatic activity of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A:
1.16.3.1;

Protein crystallography data

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v 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) 42.15 / 1.16
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.744, 183.744, 183.744, 90.00, 90.00, 90.00
R / Rfree (%) 12.8 / 13.8

Other elements in 5j9v:

The structure of Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A also contains other interesting chemical elements:

Iron (Fe) 7 atoms
Chlorine (Cl) 17 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j9v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5j9v

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Magnesium binding site 1 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:11.9
occ:0.80
 O A:HOH623 2.0 16.7 0.8
O A:HOH616 2.0 17.4 0.8
O A:HOH394 2.1 12.6 0.8
O A:HOH425 2.1 14.3 0.8
O A:HOH540 2.1 14.5 0.8
O A:HOH636 2.1 16.2 0.8
O A:SER131 4.2 12.1 1.0
O A:HOH583 4.2 27.3 1.0
O A:HOH517 4.3 28.9 1.0
O A:GLU130 4.4 12.9 1.0
CA A:SER131 4.5 12.7 0.4
CA A:SER131 4.5 10.5 0.6
O A:HOH402 4.5 30.9 1.0
O A:HOH586 4.6 31.1 1.0
CB A:GLU135 4.7 11.7 1.0
C A:SER131 4.7 9.8 1.0
CL A:CL216 4.9 13.1 0.7
CG A:GLU135 4.9 11.1 0.8

Magnesium binding site 2 out of 6 in 5j9v

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Magnesium binding site 2 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:17.8
occ:0.60
 O A:HOH609 2.0 20.1 0.6
O A:HOH423 2.0 20.9 0.6
O A:HOH614 2.1 23.0 0.6
O A:HOH640 2.1 23.9 0.6
O A:HOH560 2.1 16.3 0.8
O A:HOH561 2.3 24.8 0.6
O A:HOH554 4.3 29.6 1.0
O A:VAL1 4.5 19.1 1.0
O A:HOH521 4.8 49.5 1.0
N A:GLN3 5.0 8.7 1.0

Magnesium binding site 3 out of 6 in 5j9v

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Magnesium binding site 3 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:15.0
occ:0.20
 O A:HOH645 1.9 31.1 1.0
O A:HOH606 2.8 22.1 1.0
O A:HOH643 3.8 30.7 1.0
O A:HOH404 4.1 18.0 1.0
CG2 A:THR118 4.3 12.1 1.0
O A:HOH369 4.6 20.5 1.0
O A:HOH604 4.8 21.5 1.0

Magnesium binding site 4 out of 6 in 5j9v

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Magnesium binding site 4 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:15.3
occ:0.50
 O A:HOH585 1.9 21.7 0.5
O A:HOH522 2.0 23.6 0.5
O A:HOH581 2.0 25.5 0.5
O A:HOH591 2.0 21.3 0.5
O A:HOH638 2.1 23.2 0.5
O A:HOH312 2.1 13.4 0.5
OD2 A:ASP146 4.0 13.3 1.0
O A:HOH641 4.1 38.3 1.0
O A:HOH453 4.2 33.1 1.0
O A:HOH447 4.2 24.1 1.0
O A:HOH457 4.3 15.7 1.0
O A:HOH542 4.6 42.6 1.0
O A:HOH417 4.7 15.1 1.0

Magnesium binding site 5 out of 6 in 5j9v

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Magnesium binding site 5 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:14.5
occ:0.80
 O A:HOH449 2.1 18.9 0.8
O A:HOH431 2.1 19.6 0.8
O A:HOH364 2.1 15.5 0.8
O A:HOH569 2.1 20.6 0.8
OG A:SER10 2.1 11.0 0.8
O A:HOH416 2.1 13.4 1.0
CB A:SER10 3.2 10.9 0.2
CB A:SER10 3.2 10.4 0.8
CA A:SER10 3.9 10.6 0.2
CA A:SER10 3.9 9.7 0.8
O A:SER10 4.1 8.9 1.0
OE1 A:GLU13 4.2 10.5 1.0
O A:HOH337 4.3 17.9 1.0
OG A:SER10 4.3 11.1 0.2
C A:SER10 4.4 8.3 1.0
O A:HOH559 4.4 59.4 1.0
O A:HOH531 4.4 15.0 1.0
O A:HOH527 4.5 34.5 1.0
O A:HOH631 4.6 41.6 1.0
CD A:GLU13 4.6 8.7 1.0

Magnesium binding site 6 out of 6 in 5j9v

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Magnesium binding site 6 out of 6 in the Ten Minutes Iron Loaded 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 Ten Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:25.8
occ:0.50
 O A:HOH356 1.7 27.2 0.5
O A:HOH461 1.8 28.2 0.5
O A:HOH507 2.0 40.7 0.5
O A:HOH570 2.1 35.2 0.5
O A:HOH452 2.1 26.4 0.5
O A:GLU158 2.2 15.2 1.0
C A:GLU158 3.3 12.7 1.0
O A:HOH432 4.0 37.0 1.0
CA A:GLU158 4.1 13.7 1.0
N A:GLY160 4.2 9.5 1.0
N A:ASN159 4.3 10.6 1.0
CA A:ASN159 4.4 10.3 0.5
CA A:ASN159 4.4 11.9 0.5
CB A:GLU158 4.4 14.6 1.0
CL A:CL226 4.5 24.7 0.6
C A:ASN159 4.9 9.1 1.0
O A:HOH582 5.0 26.7 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 17:39:37 2024

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