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Magnesium in PDB 5j8w: One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

Enzymatic activity of One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A

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

Protein crystallography data

The structure of One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8w 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) 18.53 / 1.11
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.340, 184.340, 184.340, 90.00, 90.00, 90.00
R / Rfree (%) 13.1 / 14.1

Other elements in 5j8w:

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

Iron (Fe) 1 atom
Chlorine (Cl) 20 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A (pdb code 5j8w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A, PDB code: 5j8w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 5j8w

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Magnesium binding site 1 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg222

b:12.0
occ:0.80
 O A:HOH575 2.0 17.6 0.8
O A:HOH361 2.0 12.1 0.8
O A:HOH470 2.0 15.9 0.8
O A:HOH451 2.1 16.3 0.8
O A:HOH429 2.1 10.9 1.0
OG A:SER10 2.1 8.1 0.8
CB A:SER10 3.1 7.7 0.2
CB A:SER10 3.3 7.8 0.8
CA A:SER10 3.9 7.6 0.2
CA A:SER10 3.9 7.4 0.8
OG A:SER10 4.1 7.8 0.2
O A:SER10 4.1 6.9 1.0
OE1 A:GLU13 4.2 7.7 1.0
O A:HOH545 4.2 28.4 1.0
O A:HOH332 4.3 13.4 1.0
C A:SER10 4.4 6.6 1.0
O A:HOH639 4.4 39.5 1.0
O A:HOH512 4.4 32.4 1.0
O A:HOH528 4.4 12.8 1.0
O A:HOH655 4.5 32.5 1.0
CD A:GLU13 4.6 6.4 1.0
OE2 A:GLU13 5.0 6.7 1.0

Magnesium binding site 2 out of 9 in 5j8w

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Magnesium binding site 2 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg223

b:14.4
occ:0.25
 O A:HOH662 1.9 25.8 0.9
O A:HOH619 2.6 14.2 1.0
O A:HOH391 4.1 13.8 1.0
O A:HOH672 4.2 41.0 1.0
CG2 A:THR118 4.4 7.8 1.0
O A:HOH625 4.6 14.4 1.0
O A:HOH412 4.7 10.8 1.0

Magnesium binding site 3 out of 9 in 5j8w

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Magnesium binding site 3 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg224

b:11.4
occ:0.80
 O A:HOH628 2.0 13.9 0.8
O A:HOH641 2.0 15.3 0.8
O A:HOH383 2.1 12.0 0.8
O A:HOH436 2.1 12.4 0.8
O A:HOH660 2.1 14.7 0.8
O A:HOH544 2.1 12.8 0.8
O A:HOH577 4.2 27.4 1.0
O A:SER131 4.2 10.0 1.0
O A:HOH563 4.3 27.4 1.0
O A:GLU130 4.4 9.8 1.0
CA A:SER131 4.5 10.0 0.5
CA A:SER131 4.5 8.5 0.5
O A:HOH601 4.6 29.9 1.0
O A:HOH465 4.7 23.6 1.0
C A:SER131 4.7 7.8 1.0
CB A:GLU135 4.7 10.0 1.0
CG A:GLU135 4.9 9.7 1.0
CL A:CL212 4.9 13.3 0.8

Magnesium binding site 4 out of 9 in 5j8w

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Magnesium binding site 4 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg225

b:9.6
occ:0.20
 O A:HOH306 1.8 7.5 0.6
O A:HOH485 2.0 14.8 0.6
OD1 A:ASP127 3.2 11.9 0.5
OE1 A:GLU130 3.4 8.6 0.3
OD1 A:ASP127 3.9 6.8 0.5
OG A:SER131 4.2 8.7 0.5
OE1 A:GLU130 4.3 7.7 0.7
O A:HOH465 4.3 23.6 1.0
CG A:ASP127 4.4 11.1 0.5
CD A:GLU130 4.6 8.3 0.3
CB A:GLU130 4.8 8.2 0.3
CG A:ASP127 4.9 6.7 0.5
O A:HOH544 4.9 12.8 0.8
CB A:GLU130 5.0 7.5 0.7

Magnesium binding site 5 out of 9 in 5j8w

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Magnesium binding site 5 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg226

b:6.2
occ:0.33
 O A:HOH650 2.0 8.8 1.0
O A:HOH644 2.0 7.8 1.0
OE2 A:GLU130 3.8 8.4 0.3
OE2 A:GLU130 4.0 7.6 0.7
O A:HOH322 4.2 12.4 0.5
O A:HOH574 4.3 9.8 1.0
OE1 A:GLU130 4.3 7.7 0.7
O A:HOH391 4.4 13.8 1.0
CD A:GLU130 4.6 7.5 0.7
CD A:GLU130 4.6 8.3 0.3
OE1 A:GLU130 4.7 8.6 0.3

Magnesium binding site 6 out of 9 in 5j8w

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Magnesium binding site 6 out of 9 in the One Minute 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 One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg227

b:13.2
occ:0.60
 O A:HOH524 1.9 18.1 0.6
O A:HOH610 2.0 19.6 0.6
O A:HOH312 2.1 11.4 0.7
O A:HOH598 2.1 15.4 0.6
O A:HOH622 2.1 20.8 0.6
O A:HOH661 2.1 16.3 0.6
OD2 A:ASP146 3.9 9.6 1.0
O A:HOH381 4.1 16.4 1.0
O A:HOH668 4.2 29.1 1.0
O A:HOH492 4.2 22.4 1.0
O A:HOH469 4.3 12.0 1.0
O A:HOH413 4.6 11.5 1.0
O A:HOH546 4.7 35.5 1.0

Magnesium binding site 7 out of 9 in 5j8w

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Magnesium binding site 7 out of 9 in the One Minute 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 7 of One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg228

b:12.1
occ:0.50
 O A:HOH630 1.9 15.3 0.5
O A:HOH444 2.0 12.8 0.5
O A:HOH634 2.1 15.4 0.5
O A:HOH664 2.1 16.1 0.5
O A:HOH564 2.1 14.2 1.0
O A:HOH570 2.2 19.1 0.5
O A:HOH559 4.3 22.9 1.0
O A:HOH568 4.5 39.7 1.0
O A:VAL1 4.5 13.6 0.8
N A:GLN3 5.0 6.3 1.0

Magnesium binding site 8 out of 9 in 5j8w

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Magnesium binding site 8 out of 9 in the One Minute 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 8 of One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg229

b:13.9
occ:0.50
 O A:HOH401 1.7 11.8 0.5
O A:HOH567 2.0 17.7 0.5
O A:HOH651 2.1 21.6 0.5
O A:HOH658 2.2 23.4 0.5
O A:HOH392 2.3 13.2 1.0
O A:HOH615 2.3 17.2 0.5
O A:HOH646 3.7 15.9 0.5
O A:HOH640 4.1 18.1 1.0
OD1 A:ASN21 4.3 6.4 1.0
O A:ARG18 4.4 6.2 1.0
O A:HOH553 4.4 19.3 1.0
CL A:CL208 4.5 19.1 0.7
O A:HOH663 4.6 36.4 1.0
O A:HOH534 4.8 27.6 1.0
CB A:LEU22 4.8 6.0 1.0
O A:HOH618 5.0 13.7 1.0

Magnesium binding site 9 out of 9 in 5j8w

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Magnesium binding site 9 out of 9 in the One Minute 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 9 of One Minute Iron Loaded Rana Catesbeiana H' Ferritin Variant E57A/E136A/D140A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg230

b:12.1
occ:0.50
 O A:HOH656 2.0 11.1 1.0
O A:HOH511 2.1 10.1 0.5
O A:HOH573 2.1 13.7 1.0
O A:HOH596 2.2 12.9 0.5
O A:HOH351 4.2 11.2 1.0
CD A:LYS82 4.4 8.0 0.5
O A:HOH582 4.4 11.7 1.0
CE A:LYS82 4.6 8.3 0.5
CE A:LYS83 4.6 6.5 0.5
NZ A:LYS82 4.6 7.7 0.5
O A:HOH500 4.7 24.1 1.0
CE A:LYS83 4.8 7.2 0.5
CD A:LYS82 4.9 7.3 0.5

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 17:38:40 2024

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