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Magnesium in PDB 4ml5: One Minute Iron Loaded Frog M Ferritin Mutant H54Q

Enzymatic activity of One Minute Iron Loaded Frog M Ferritin Mutant H54Q

All present enzymatic activity of One Minute Iron Loaded Frog M Ferritin Mutant H54Q:
1.16.3.1;

Protein crystallography data

The structure of One Minute Iron Loaded Frog M Ferritin Mutant H54Q, PDB code: 4ml5 was solved by S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.71 / 1.22
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.230, 184.230, 184.230, 90.00, 90.00, 90.00
R / Rfree (%) 13.9 / 15.4

Other elements in 4ml5:

The structure of One Minute Iron Loaded Frog M Ferritin Mutant H54Q also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q (pdb code 4ml5). 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 Frog M Ferritin Mutant H54Q, PDB code: 4ml5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4ml5

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Magnesium binding site 1 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:11.6
occ:0.70
 O A:HOH529 2.0 11.4 0.7
O A:HOH530 2.0 13.7 0.7
O A:HOH591 2.0 15.0 0.7
O A:HOH362 2.1 8.4 0.7
OG A:SER10 2.1 9.8 1.0
O A:HOH441 2.2 15.7 0.7
CB A:SER10 3.2 8.5 1.0
CA A:SER10 3.9 7.4 1.0
O A:SER10 4.1 6.7 1.0
OE1 A:GLU13 4.2 7.5 1.0
O A:HOH366 4.2 13.4 1.0
C A:SER10 4.3 7.0 1.0
O A:HOH592 4.4 24.8 1.0
O A:HOH361 4.4 11.8 1.0
O A:HOH579 4.5 27.3 1.0
O A:HOH588 4.6 28.6 1.0
CD A:GLU13 4.6 6.7 1.0

Magnesium binding site 2 out of 9 in 4ml5

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Magnesium binding site 2 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:6.6
occ:0.33
 O A:HOH337 2.0 8.6 1.0
O A:HOH312 2.1 8.0 1.0
OE2 A:GLU130 3.9 8.9 1.0
O A:HOH491 4.1 18.6 1.0
OE1 A:GLU130 4.3 10.1 1.0
O A:HOH355 4.3 9.4 1.0
O A:HOH372 4.3 13.9 1.0
CD A:GLU130 4.5 9.4 1.0

Magnesium binding site 3 out of 9 in 4ml5

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Magnesium binding site 3 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:14.8
occ:0.20
 O A:HOH378 1.5 6.2 0.6
O A:HOH674 2.1 13.2 0.6
OD1 A:ASP127 3.6 12.0 1.0
OG A:SER131 4.2 9.6 0.5
O A:HOH508 4.2 23.8 1.0
OE1 A:GLU130 4.3 10.1 1.0
CG A:ASP127 4.7 9.7 1.0
O A:HOH438 4.8 14.9 1.0
CB A:GLU130 5.0 8.5 1.0

Magnesium binding site 4 out of 9 in 4ml5

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Magnesium binding site 4 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:7.3
occ:0.50
 O A:HOH475 1.9 14.8 1.0
O A:HOH593 2.0 12.5 1.0
O A:HOH676 2.1 17.1 1.0
O A:HOH590 2.1 15.2 1.0
O A:HOH471 2.1 16.6 1.0
O A:HOH664 2.1 16.7 1.0
O A:HOH387 4.2 16.4 1.0
O A:HOH391 4.2 11.9 0.7
O A:HOH565 4.4 29.7 1.0
O A:HOH403 4.5 19.6 1.0
O A:HOH501 4.6 24.1 1.0
ND1 A:HIS45 4.6 9.6 1.0
O A:HOH655 4.6 34.5 1.0
CG A:HIS45 4.9 8.7 1.0

Magnesium binding site 5 out of 9 in 4ml5

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Magnesium binding site 5 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:10.3
occ:0.50
 O A:HOH680 2.0 11.8 0.5
O A:HOH456 2.0 11.2 1.0
O A:HOH681 2.1 11.8 0.5
O A:HOH396 2.1 13.5 1.0
O A:HOH338 4.2 11.2 1.0
CD A:LYS82 4.4 7.7 0.5
O A:HOH357 4.5 11.5 1.0
CE A:LYS82 4.5 8.0 0.5
CE A:LYS83 4.5 7.1 0.5
NZ A:LYS82 4.6 7.8 0.5
O A:HOH462 4.7 22.0 1.0
CE A:LYS83 4.8 7.1 0.5
CD A:LYS82 4.9 7.4 0.5

Magnesium binding site 6 out of 9 in 4ml5

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Magnesium binding site 6 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:8.0
occ:0.50
 O A:HOH679 2.0 18.4 1.0
O A:HOH644 2.0 19.0 1.0
O A:HOH665 2.1 17.6 1.0
O A:HOH460 2.1 14.8 1.0
O A:HOH399 2.1 14.7 1.0
O A:HOH438 2.2 14.9 1.0
O A:SER131 4.2 10.5 1.0
O A:HOH476 4.3 24.0 1.0
O A:GLU130 4.3 10.2 1.0
O A:HOH597 4.4 27.9 1.0
CA A:SER131 4.4 9.1 0.5
CA A:SER131 4.4 9.0 0.5
O A:HOH508 4.6 23.8 1.0
C A:SER131 4.7 9.1 1.0
CB A:GLU135 4.7 9.2 1.0
O A:HOH617 4.7 29.6 1.0
CG A:GLU135 4.9 9.7 1.0

Magnesium binding site 7 out of 9 in 4ml5

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Magnesium binding site 7 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:15.1
occ:0.60
 O A:HOH533 2.0 20.3 1.0
O A:HOH365 2.1 13.7 1.0
O A:HOH555 2.1 23.1 1.0
O A:HOH447 2.1 21.1 1.0
O A:HOH601 2.2 25.1 1.0
O A:HOH561 2.2 25.8 1.0
O A:HOH625 4.0 37.7 1.0
O A:HOH367 4.2 14.4 1.0
O A:HOH351 4.5 11.4 1.0
O A:HOH503 4.6 23.2 1.0

Magnesium binding site 8 out of 9 in 4ml5

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Magnesium binding site 8 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:21.2
occ:0.60
 O A:HOH490 2.0 15.3 0.6
O A:HOH567 2.0 17.5 0.6
O A:HOH587 2.1 21.8 0.6
O A:HOH578 2.3 21.5 0.6
O A:HOH425 3.8 20.9 1.0
O A:HOH516 4.1 23.8 1.0
OE1 A:GLU136 4.3 11.5 0.7
O A:HOH393 4.3 12.9 1.0
O A:GLU132 4.5 9.9 1.0
O A:HOH597 4.5 27.9 1.0
CB A:GLU136 4.6 9.4 1.0
O A:HOH392 4.8 17.1 1.0
CG A:GLU136 4.9 10.5 1.0
CD A:GLU136 4.9 10.6 0.7
NZ A:LYS64 4.9 14.9 1.0

Magnesium binding site 9 out of 9 in 4ml5

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Magnesium binding site 9 out of 9 in the One Minute Iron Loaded Frog M Ferritin Mutant H54Q


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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:14.3
occ:0.50
 O A:HOH429 1.7 10.8 0.5
O A:HOH553 1.8 18.8 0.5
O A:HOH650 2.1 23.3 0.5
O A:HOH348 2.3 6.3 0.5
O A:HOH623 2.3 23.1 0.5
O A:HOH600 2.4 16.5 0.5
O A:HOH572 3.6 24.8 1.0
O A:HOH420 4.1 16.9 1.0
OD1 A:ASN21 4.2 6.2 1.0
O A:ARG18 4.4 6.3 1.0
O A:HOH452 4.4 18.3 1.0
O A:HOH469 4.4 12.9 1.0
O A:HOH618 4.5 32.6 1.0
O A:HOH641 4.5 42.0 1.0
CB A:LEU22 4.9 6.2 1.0
O A:HOH406 4.9 13.4 1.0
O A:HOH444 5.0 17.8 1.0

Reference:

S.Mangani, F.Di Pisa, C.Pozzi, P.Turano, D.Lalli. Crystallographic Snapshots of Iron in Frog M Ferritin To Be Published.
Page generated: Mon Aug 19 23:13:57 2024

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