Atomistry » Magnesium » PDB 5j2n-5jc8 » 5j8w
Atomistry »
  Magnesium »
    PDB 5j2n-5jc8 »
      5j8w »

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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Go back to Magnesium Binding Sites List in 5j8w
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy