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Magnesium in PDB 6i9p: Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N

Enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N

All present enzymatic activity of Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N:
1.16.3.1;

Protein crystallography data

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6i9p 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) 21.10 / 1.25
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.910, 183.910, 183.910, 90.00, 90.00, 90.00
R / Rfree (%) 11.7 / 13.3

Other elements in 6i9p:

The structure of Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N (pdb code 6i9p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N, PDB code: 6i9p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 6i9p

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Magnesium binding site 1 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:9.3
occ:0.50
 OE1 A:GLU58 1.7 10.4 0.3
OE1 A:GLU23 1.9 8.7 0.5
OE2 A:GLU23 2.0 11.0 0.5
OE1 A:GLU58 2.0 13.8 0.7
OE1 A:GLU23 2.0 11.1 0.5
O A:HOH353 2.1 10.5 0.5
O A:HOH381 2.1 11.0 0.5
ND1 A:HIS61 2.3 9.6 0.5
CD A:GLU23 2.3 9.9 0.5
O A:HOH353 2.5 5.8 0.1
CD A:GLU58 2.8 9.8 0.3
O A:HOH381 2.9 8.2 0.1
CD A:GLU23 2.9 8.4 0.5
CD A:GLU58 3.0 13.1 0.7
CE1 A:HIS61 3.1 9.7 0.5
CD2 A:HIS61 3.1 15.9 0.5
O A:HOH367 3.2 5.5 0.1
O A:HOH381 3.3 17.3 0.4
OE2 A:GLU23 3.3 9.2 0.5
OE2 A:GLU58 3.3 10.6 0.3
CG A:HIS61 3.3 9.2 0.5
O A:HOH367 3.3 16.5 0.4
MG A:MG211 3.4 4.6 0.1
OE2 A:GLU58 3.4 15.0 0.7
CB A:HIS61 3.7 8.5 0.5
CG A:HIS61 3.7 14.3 0.5
CG A:GLU23 3.8 9.3 0.5
CB A:HIS61 3.8 12.6 0.5
CG A:GLU58 4.0 9.4 0.3
CG1 A:VAL106 4.0 8.6 1.0
CG A:GLU23 4.3 8.1 0.5
NE2 A:HIS61 4.3 16.8 0.5
CG A:GLU58 4.3 11.7 0.7
O A:HOH492 4.3 15.6 0.8
NE2 A:HIS61 4.3 10.0 0.5
MG A:MG211 4.4 11.8 0.4
CA A:GLU58 4.4 9.0 0.3
CA A:GLU58 4.4 10.0 0.7
OE1 A:GLN137 4.4 13.2 0.9
CD2 A:HIS61 4.4 9.4 0.5
CB A:GLU58 4.4 9.1 0.3
OE1 A:GLN137 4.4 8.6 0.1
CB A:GLU58 4.5 10.7 0.7
O A:HOH492 4.6 6.3 0.1
CB A:GLU23 4.6 8.8 0.5
CB A:GLU23 4.6 7.6 0.5
CA A:GLU23 4.9 7.2 0.5
CA A:GLU23 4.9 8.1 0.5
O A:GLU58 5.0 8.0 1.0

Magnesium binding site 2 out of 14 in 6i9p

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Magnesium binding site 2 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:17.9
occ:0.70
 O A:HOH653 2.1 22.6 0.7
O A:HOH578 2.1 10.7 0.7
O A:HOH442 2.1 18.7 0.7
O A:HOH593 2.2 23.8 0.7
O A:HOH573 4.3 30.0 1.0
O A:HOH603 4.5 51.4 1.0
O A:VAL1 4.6 16.5 0.6
O A:VAL1 4.8 19.8 0.4
N A:GLN3 5.0 7.7 1.0

Magnesium binding site 3 out of 14 in 6i9p

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Magnesium binding site 3 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:15.4
occ:1.00
 O A:HOH465 2.0 17.9 1.0
O A:HOH359 2.0 15.6 1.0
O A:HOH595 2.0 20.0 1.0
O A:HOH450 2.0 19.7 1.0
OG A:SER10 2.1 11.2 1.0
O A:HOH453 2.1 11.4 1.0
CB A:SER10 3.2 9.7 1.0
CA A:SER10 3.8 8.0 1.0
O A:SER10 4.1 7.6 1.0
OE1 A:GLU13 4.2 8.8 1.0
O A:HOH345 4.2 14.6 1.0
O A:HOH559 4.3 34.4 1.0
O A:HOH650 4.3 45.9 1.0
C A:SER10 4.3 7.4 1.0
O A:HOH554 4.4 31.2 1.0
O A:HOH550 4.4 13.3 1.0
O A:HOH660 4.5 39.5 1.0
CD A:GLU13 4.6 7.2 1.0

Magnesium binding site 4 out of 14 in 6i9p

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Magnesium binding site 4 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:14.2
occ:0.70
 O A:HOH666 2.0 23.9 0.7
O A:HOH435 2.0 15.5 0.7
O A:HOH664 2.0 20.4 0.7
O A:HOH588 2.0 19.9 0.7
O A:HOH571 2.0 19.3 0.7
O A:HOH455 2.1 11.2 0.7
O A:HOH435 2.3 13.8 0.3
O A:HOH455 2.6 11.7 0.3
O A:HOH649 4.1 24.9 1.0
OD1 A:ASN21 4.3 7.0 1.0
O A:HOH572 4.3 22.8 1.0
O A:ARG18 4.4 7.0 1.0
O A:HOH580 4.5 12.7 1.0
O A:HOH537 4.5 27.1 0.5
O A:HOH551 4.5 19.5 1.0
O A:HOH635 4.8 17.7 1.0
CB A:LEU22 4.8 7.4 1.0
O A:HOH669 4.8 43.3 1.0
O A:HOH655 5.0 23.9 1.0

Magnesium binding site 5 out of 14 in 6i9p

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Magnesium binding site 5 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:14.1
occ:0.50
 O A:HOH557 2.1 18.3 0.5
O A:HOH585 2.1 19.6 0.5
NE2 A:HIS45 3.6 10.0 0.5
CD2 A:HIS45 3.6 9.6 0.5
CE1 A:HIS45 4.1 10.2 0.5
CG A:HIS45 4.2 9.2 0.5
ND1 A:HIS45 4.5 9.9 0.5
ND1 A:HIS45 4.7 13.3 0.5

Magnesium binding site 6 out of 14 in 6i9p

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Magnesium binding site 6 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:10.7
occ:0.50
 O A:HOH337 2.0 12.2 1.0
O A:HOH325 2.0 7.3 0.5
O A:HOH574 2.1 15.1 1.0
OD2 A:ASP80 4.0 7.3 1.0
OD1 A:ASP80 4.1 6.2 1.0
CG A:ASP80 4.5 6.2 1.0
O A:HOH423 4.7 6.8 1.0

Magnesium binding site 7 out of 14 in 6i9p

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Magnesium binding site 7 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:13.1
occ:0.20
 O A:HOH430 1.6 8.0 0.6
O A:HOH658 1.9 19.2 0.6
OD1 A:ASP127 3.6 15.5 1.0
OG A:SER131 4.2 11.2 0.5
OE1 A:GLU130 4.3 12.7 1.0
O A:HOH405 4.3 31.8 1.0
CG A:ASP127 4.7 12.4 1.0
O A:HOH434 4.8 15.1 0.8
CB A:GLU130 4.9 9.9 1.0

Magnesium binding site 8 out of 14 in 6i9p

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Magnesium binding site 8 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:14.4
occ:0.80
 O A:HOH448 2.0 18.3 0.8
O A:HOH609 2.1 18.5 0.8
O A:HOH434 2.1 15.1 0.8
OD2 A:ASP127 4.1 15.6 1.0
O A:HOH674 4.1 32.1 1.0
OD1 A:ASP127 4.5 15.5 1.0
O A:HOH405 4.6 31.8 1.0
O A:HOH592 4.6 21.5 0.5
O A:HOH614 4.7 40.0 1.0
CG A:ASP127 4.7 12.4 1.0
OG A:SER131 4.8 11.2 0.5
OG A:SER131 4.9 15.0 0.5

Magnesium binding site 9 out of 14 in 6i9p

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Magnesium binding site 9 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:21.6
occ:0.40
 O A:HOH498 1.9 26.8 0.4
O A:HOH538 1.9 29.2 0.4
O A:HOH477 2.0 23.3 0.4
O A:HOH667 2.0 26.5 0.4
O A:HOH317 2.0 20.4 0.4
O A:HOH474 2.1 24.7 0.4
OD1 A:ASP140 4.1 12.7 0.6
OE1 A:GLU57 4.2 25.5 0.7
OE2 A:GLU57 4.4 23.9 0.7
O A:HOH370 4.4 39.8 1.0
CD A:GLU136 4.5 21.5 0.6
OE1 A:GLU136 4.5 23.3 0.6
OD2 A:ASP140 4.6 14.4 0.6
OE2 A:GLU136 4.6 22.4 0.6
OD1 A:ASP140 4.7 12.4 0.4
CD A:GLU57 4.7 24.3 0.7
CG A:GLU136 4.7 13.0 0.1
CG A:ASP140 4.8 12.3 0.6
CG A:GLU136 4.9 20.1 0.6
O A:HOH348 4.9 25.8 0.5
O A:HOH581 5.0 39.4 1.0

Magnesium binding site 10 out of 14 in 6i9p

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Magnesium binding site 10 out of 14 in the Iron-Free State of 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 Iron-Free State of Rana Catesbeiana H' Ferritin Variant H54N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:7.8
occ:0.33
 O A:HOH360 2.0 9.3 1.0
O A:HOH543 2.0 10.2 1.0
OE2 A:GLU130 3.9 10.2 1.0
O A:HOH324 4.0 13.5 0.5
OE1 A:GLU130 4.2 12.7 1.0
O A:HOH425 4.3 18.0 1.0
O A:HOH596 4.3 11.5 1.0
CD A:GLU130 4.5 10.7 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: Tue Oct 1 03:01:44 2024

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