Magnesium in PDB 6i9t: Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N

Enzymatic activity of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N

All present enzymatic activity of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N:
1.16.3.1;

Protein crystallography data

The structure of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6i9t was solved by C.Pozzi, F.Di Pisa, S.Mangani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.30 / 1.20
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.830, 183.830, 183.830, 90.00, 90.00, 90.00
R / Rfree (%) 12.1 / 13.7

Other elements in 6i9t:

The structure of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N (pdb code 6i9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6i9t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 6i9t

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Magnesium binding site 1 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:11.1
occ:0.50
MG A:MG202 0.0 11.1 0.5
O A:HOH371 1.9 14.1 0.5
OD2 A:ASP140 1.9 10.9 0.5
OD2 A:ASP140 2.0 14.8 0.5
O A:HOH445 2.0 17.6 0.5
O A:HOH456 2.1 16.5 0.6
O A:HOH324 2.2 13.6 0.5
OE2 A:GLU57 2.3 14.1 0.5
CG A:ASP140 2.6 13.9 0.5
O A:HOH321 2.8 14.0 0.5
OD1 A:ASN54 3.0 10.1 0.4
OD1 A:ASP140 3.0 15.4 0.5
CG A:ASP140 3.0 10.1 0.5
MG A:MG202 3.1 14.6 0.4
CD A:GLU57 3.3 13.5 0.5
O A:HOH303 3.3 19.6 0.5
CB A:ASP140 3.5 10.2 0.5
O A:HOH351 3.6 13.0 0.5
OE1 A:GLU57 3.6 13.0 0.5
CB A:ASP140 3.6 13.2 0.5
O A:HOH324 3.7 14.3 0.5
OE2 A:GLU103 3.8 14.1 1.0
OE2 A:GLU58 3.8 12.7 0.6
OE1 A:GLU57 3.9 15.3 0.5
O A:HOH303 3.9 18.3 0.3
OE1 A:GLU136 4.0 14.2 0.5
OD1 A:ASP140 4.1 10.7 0.5
OE2 A:GLU58 4.1 7.7 0.4
OE2 A:GLU136 4.2 16.6 0.5
CG A:ASN54 4.2 9.0 0.4
OE1 A:GLU103 4.2 11.2 1.0
NH1 A:ARG143 4.3 17.5 0.6
OD1 A:ASN54 4.3 12.9 0.6
CD A:GLU103 4.4 10.3 1.0
CG A:GLU57 4.4 12.4 0.5
O A:HOH400 4.5 19.2 1.0
O A:HOH446 4.6 16.0 0.5
CG A:ASN54 4.6 11.6 0.6
MG A:MG211 4.8 13.1 0.5
O A:HOH498 4.8 20.1 0.5
CD A:GLU57 4.9 11.7 0.5
CA A:ASP140 4.9 12.2 0.5
CD A:GLU58 4.9 10.7 0.6
O A:HOH348 4.9 12.1 0.5
CA A:ASP140 4.9 9.9 0.5
CG A:GLU136 4.9 14.4 0.5
CE1 A:HIS61 4.9 6.4 0.4
O A:HOH348 4.9 10.2 0.5
CB A:ASN54 5.0 8.2 0.4
CD A:GLU136 5.0 15.7 0.5

Magnesium binding site 2 out of 13 in 6i9t

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Magnesium binding site 2 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:14.6
occ:0.40
MG A:MG202 0.0 14.6 0.4
O A:HOH321 1.7 14.0 0.5
O A:HOH303 1.9 19.6 0.5
O A:HOH498 2.0 20.1 0.5
OD2 A:ASP140 2.0 10.9 0.5
OE2 A:GLU136 2.1 16.6 0.5
OE1 A:GLU136 2.1 14.2 0.5
O A:HOH446 2.2 16.0 0.5
OD2 A:ASP140 2.2 14.8 0.5
OE2 A:GLU57 2.3 14.1 0.5
CD A:GLU136 2.4 15.7 0.5
CG A:GLU136 2.4 14.4 0.5
O A:HOH303 2.7 18.3 0.3
CG A:ASP140 2.8 10.1 0.5
CG A:ASP140 2.9 13.9 0.5
CD A:GLU57 3.0 13.5 0.5
OD1 A:ASP140 3.1 15.4 0.5
MG A:MG202 3.1 11.1 0.5
OD1 A:ASP140 3.1 10.7 0.5
OE1 A:GLU57 3.1 15.3 0.5
CD A:GLU136 3.3 14.2 0.5
O A:HOH467 3.3 20.6 0.3
OE1 A:GLU136 3.4 17.7 0.5
MG A:MG212 3.6 20.0 0.3
O A:HOH511 3.7 21.9 0.3
O A:HOH324 3.7 13.6 0.5
OE1 A:GLU57 3.7 13.0 0.5
O A:HOH445 3.8 17.6 0.5
O A:HOH351 3.8 13.0 0.5
CB A:GLU136 3.8 12.6 0.5
O A:GLU136 3.9 10.1 0.5
CB A:GLU136 3.9 13.2 0.5
O A:HOH313 4.0 18.1 0.4
CG A:GLU136 4.0 13.6 0.5
O A:GLU136 4.0 10.5 0.5
CB A:ASP140 4.1 10.2 0.5
O A:HOH324 4.1 14.3 0.5
OE2 A:GLU136 4.3 14.3 0.5
CB A:ASP140 4.3 13.2 0.5
CG A:GLU57 4.4 12.4 0.5
C A:GLU136 4.4 11.2 0.5
C A:GLU136 4.4 11.3 0.5
CA A:GLU136 4.5 12.2 0.5
CA A:GLU136 4.5 11.8 0.5
O A:HOH556 4.5 19.6 0.3
O A:HOH521 4.7 19.7 0.3
O A:HOH371 4.7 14.1 0.5
CD A:GLU57 4.7 11.7 0.5
NE2 A:HIS61 4.7 6.5 0.4
CE1 A:HIS61 4.7 6.4 0.4
MG A:MG211 4.8 13.1 0.5
CE1 A:HIS61 4.8 15.1 0.6
O A:HOH456 4.9 16.5 0.6

Magnesium binding site 3 out of 13 in 6i9t

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Magnesium binding site 3 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:14.1
occ:0.50
O A:HOH550 2.0 19.2 0.5
O A:HOH588 2.2 19.8 0.5
NE2 A:HIS45 3.5 10.4 0.5
CD2 A:HIS45 3.6 10.0 0.5
CE1 A:HIS45 4.1 10.4 0.5
O A:HOH665 4.1 40.4 1.0
CG A:HIS45 4.2 9.4 0.5
O A:HOH574 4.3 18.1 0.5
ND1 A:HIS45 4.5 10.4 0.5
ND1 A:HIS45 4.6 13.2 0.5

Magnesium binding site 4 out of 13 in 6i9t

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Magnesium binding site 4 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:13.8
occ:0.90
O A:HOH473 2.0 15.4 0.9
O A:HOH594 2.0 19.0 0.9
O A:HOH372 2.0 13.6 0.9
O A:HOH459 2.1 16.3 0.9
OG A:SER10 2.1 10.8 1.0
O A:HOH444 2.1 11.2 1.0
CB A:SER10 3.2 9.2 1.0
CA A:SER10 3.8 7.6 1.0
O A:SER10 4.1 7.0 1.0
OE1 A:GLU13 4.2 8.2 1.0
O A:HOH560 4.2 37.4 1.0
O A:HOH358 4.3 14.3 1.0
O A:HOH641 4.3 47.6 1.0
O A:HOH543 4.3 32.4 1.0
C A:SER10 4.3 6.7 1.0
O A:HOH546 4.4 12.8 1.0
O A:HOH656 4.5 37.4 1.0
CD A:GLU13 4.6 6.7 1.0

Magnesium binding site 5 out of 13 in 6i9t

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Magnesium binding site 5 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:11.5
occ:0.50
O A:HOH419 1.7 13.8 0.5
O A:HOH585 1.9 16.9 0.5
O A:HOH449 2.0 10.4 0.5
O A:HOH659 2.0 18.1 0.5
O A:HOH567 2.0 15.2 0.5
O A:HOH655 2.0 16.6 0.5
O A:HOH438 2.0 10.2 0.5
O A:HOH627 2.3 19.2 0.5
O A:HOH449 2.5 10.5 0.5
O A:HOH653 3.8 31.3 1.0
O A:HOH649 4.0 22.9 1.0
O A:HOH529 4.3 12.2 0.5
OD1 A:ASN21 4.3 6.6 1.0
O A:HOH580 4.3 22.2 1.0
O A:ARG18 4.4 6.5 1.0
O A:HOH581 4.5 12.9 1.0
O A:HOH527 4.6 23.4 0.4
O A:HOH664 4.8 37.2 1.0
CB A:LEU22 4.8 6.7 1.0
O A:HOH529 4.8 13.4 0.5
O A:HOH628 4.8 17.3 1.0
O A:HOH647 4.9 22.3 1.0
O A:HOH666 5.0 55.1 1.0

Magnesium binding site 6 out of 13 in 6i9t

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Magnesium binding site 6 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:7.6
occ:0.50
O A:HOH551 1.9 12.9 1.0
O A:HOH590 1.9 10.9 1.0
O A:HOH617 2.1 10.0 0.5
O A:HOH390 4.0 11.6 1.0
CD A:LYS82 4.1 8.8 0.5
O A:HOH650 4.2 13.4 1.0
CE A:LYS82 4.3 9.3 0.5
NZ A:LYS82 4.4 8.6 0.5
O A:HOH404 4.5 16.8 0.5
CE A:LYS83 4.6 7.5 0.5
CD A:LYS82 4.8 8.1 0.5
O A:HOH513 4.8 10.9 0.5
CE A:LYS82 4.9 8.5 0.5
CE A:LYS83 4.9 7.6 0.5

Magnesium binding site 7 out of 13 in 6i9t

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Magnesium binding site 7 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:6.3
occ:0.30
O A:HOH535 2.0 9.4 1.0
O A:HOH651 2.1 9.0 1.0
OE2 A:GLU130 3.9 9.1 1.0
OE1 A:GLU130 4.3 12.4 1.0
O A:HOH431 4.3 15.7 1.0
O A:HOH592 4.3 10.6 1.0
CD A:GLU130 4.5 10.3 1.0

Magnesium binding site 8 out of 13 in 6i9t

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Magnesium binding site 8 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:8.0
occ:0.20
O A:HOH330 1.8 10.2 0.6
O A:HOH310 2.0 16.5 0.6
OD1 A:ASP127 3.7 13.7 1.0
OG A:SER131 4.2 11.6 0.6
OE1 A:GLU130 4.2 12.4 1.0
O A:HOH427 4.3 24.9 1.0
CG A:ASP127 4.8 11.1 1.0
O A:HOH414 4.9 15.2 1.0
CB A:GLU130 4.9 8.8 1.0

Magnesium binding site 9 out of 13 in 6i9t

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Magnesium binding site 9 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:12.6
occ:0.90
O A:HOH406 2.0 18.6 1.0
O A:HOH661 2.0 18.3 1.0
O A:HOH579 2.1 15.1 1.0
O A:HOH614 2.1 17.8 1.0
O A:HOH662 2.1 15.0 1.0
O A:HOH414 2.1 15.2 1.0
OD2 A:ASP127 4.0 14.3 1.0
OD1 A:ASP127 4.4 13.7 1.0
O A:HOH427 4.6 24.9 1.0
CG A:ASP127 4.7 11.1 1.0
OG A:SER131 4.7 11.6 0.6
O A:HOH610 4.8 33.4 1.0
OG A:SER131 4.9 11.9 0.4

Magnesium binding site 10 out of 13 in 6i9t

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Magnesium binding site 10 out of 13 in the Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Two Minutes Iron Loaded Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:22.3
occ:0.50
O A:HOH316 1.7 19.6 0.5
O A:HOH462 1.8 22.9 0.5
O A:GLU158 2.1 12.3 1.0
O A:HOH602 2.1 26.5 0.5
O A:HOH502 2.1 32.2 0.5
O A:HOH487 2.2 13.4 0.5
C A:GLU158 3.3 10.1 1.0
O A:HOH436 4.0 37.5 1.0
CA A:GLU158 4.0 11.4 1.0
N A:GLY160 4.3 7.7 1.0
N A:ASN159 4.3 8.7 1.0
CB A:GLU158 4.3 12.4 1.0
CA A:ASN159 4.5 8.0 1.0
O A:HOH557 4.5 17.4 1.0
C A:ASN159 4.9 7.2 1.0
O A:HOH616 5.0 21.0 1.0

Reference:

C.Pozzi, F.Di Pisa, D.Lalli, C.Rosa, P.Turano, S.Mangani. Effect of the Point Mutation H54N on the Ferroxidase Process of Rana Catesbeiana H' Ferritin. J.Inorg.Biochem. V. 197 10697 2019.
ISSN: ISSN 0162-0134
PubMed: 31075719
DOI: 10.1016/J.JINORGBIO.2019.110697
Page generated: Mon Dec 14 22:56:29 2020

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