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Magnesium in PDB 4lqj: Two Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Two Minutes Iron Loaded Frog M Ferritin

All present enzymatic activity of Two Minutes Iron Loaded Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Two Minutes Iron Loaded Frog M Ferritin, PDB code: 4lqj 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) 46.14 / 1.20
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.548, 184.548, 184.548, 90.00, 90.00, 90.00
R / Rfree (%) 13.6 / 14.5

Other elements in 4lqj:

The structure of Two Minutes Iron Loaded Frog M Ferritin also contains other interesting chemical elements:

Iron (Fe) 3 atoms
Chlorine (Cl) 12 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 10 in 4lqj

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Magnesium binding site 1 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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 Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:15.0
occ:0.60
 O A:HOH642 2.0 17.4 0.6
O A:HOH533 2.0 17.2 0.6
O A:HOH619 2.1 19.1 0.6
O A:HOH626 2.1 18.9 0.6
O A:HOH541 2.1 11.2 0.6
O A:HOH540 2.3 21.3 0.6
O A:HOH503 4.3 24.2 1.0
O A:VAL1 4.7 17.6 1.0
N A:GLN3 5.0 7.8 1.0

Magnesium binding site 2 out of 10 in 4lqj

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Magnesium binding site 2 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:13.8
occ:0.80
 O A:HOH485 2.0 13.7 0.8
O A:HOH638 2.1 18.2 0.8
O A:HOH423 2.1 10.7 0.8
O A:HOH613 2.1 17.6 0.8
O A:HOH448 2.1 17.8 0.8
OG A:SER10 2.1 11.5 1.0
CB A:SER10 3.2 10.0 1.0
CA A:SER10 3.9 8.5 1.0
O A:SER10 4.1 8.0 1.0
OE1 A:GLU13 4.2 8.7 1.0
O A:HOH338 4.3 14.9 1.0
C A:SER10 4.3 7.9 1.0
O A:HOH634 4.4 46.6 1.0
O A:HOH547 4.4 28.5 1.0
O A:HOH368 4.4 13.2 1.0
O A:HOH599 4.4 32.7 1.0
O A:HOH568 4.6 32.8 1.0
CD A:GLU13 4.6 7.8 1.0

Magnesium binding site 3 out of 10 in 4lqj

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Magnesium binding site 3 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:11.1
occ:0.50
 O A:HOH640 2.0 13.4 0.5
OE2 A:GLU57 2.0 10.8 0.5
OE1 A:GLU136 2.1 11.9 0.5
O A:HOH596 2.2 12.2 0.5
OD2 A:ASP140 2.2 13.5 0.7
O A:HOH629 2.2 9.9 0.5
CG A:ASP140 3.1 12.8 0.7
CD A:GLU57 3.1 10.8 0.5
CD A:GLU136 3.3 12.0 0.5
OD1 A:ASP140 3.3 15.5 0.7
OE1 A:GLU57 3.5 11.2 0.5
O A:HOH583 3.8 12.0 0.5
O A:GLU136 3.8 10.7 1.0
CB A:GLU136 3.8 13.9 1.0
O A:HOH440 4.0 9.0 0.4
CG A:GLU136 4.1 12.0 0.5
OE2 A:GLU136 4.2 12.1 0.5
C A:GLU136 4.3 11.0 1.0
CG A:GLU57 4.4 10.7 0.5
MG A:MG213 4.4 16.9 0.3
CB A:ASP140 4.4 10.6 1.0
CA A:GLU136 4.5 10.2 1.0
O A:HOH394 4.6 27.0 1.0
O A:HOH608 4.7 45.1 1.0
NE2 A:HIS61 4.7 9.3 0.5
CE1 A:HIS61 4.7 11.0 0.5
O A:HOH630 4.7 32.9 1.0
CE1 A:HIS61 4.7 9.3 0.5
MG A:MG212 4.7 9.0 0.4
OE1 A:GLU57 4.8 16.1 0.4

Magnesium binding site 4 out of 10 in 4lqj

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Magnesium binding site 4 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:9.3
occ:0.20
 O A:HOH509 1.7 14.3 0.6
O A:HOH549 2.2 19.0 0.6
OD1 A:ASP127 3.8 12.5 1.0
OG A:SER131 4.2 10.4 0.5
O A:HOH467 4.2 25.1 1.0
OE1 A:GLU130 4.3 11.7 1.0
O A:HOH414 4.9 12.5 0.8
CG A:ASP127 4.9 11.0 1.0
CB A:GLU130 4.9 9.3 1.0

Magnesium binding site 5 out of 10 in 4lqj

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Magnesium binding site 5 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:11.8
occ:0.80
 O A:HOH411 2.0 15.4 0.8
O A:HOH611 2.1 12.4 0.8
O A:HOH628 2.1 14.7 0.8
O A:HOH476 2.1 15.8 0.8
O A:HOH414 2.1 12.5 0.8
O A:HOH637 2.1 13.0 0.8
OD2 A:ASP127 4.1 12.8 1.0
OD1 A:ASP127 4.4 12.5 1.0
O A:HOH467 4.6 25.1 1.0
CG A:ASP127 4.7 11.0 1.0
OG A:SER131 4.7 10.4 0.5
O A:HOH515 4.7 36.6 1.0
O A:HOH519 4.8 26.6 1.0
OG A:SER131 4.8 12.4 0.5

Magnesium binding site 6 out of 10 in 4lqj

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Magnesium binding site 6 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:13.7
occ:0.50
 O A:HOH653 1.9 25.6 0.5
O A:HOH643 1.9 17.4 0.5
O A:HOH468 2.0 20.2 0.5
O A:HOH652 2.0 16.5 0.5
O A:HOH644 2.0 16.0 0.5
O A:HOH598 2.1 11.0 0.5
OD2 A:ASP146 4.0 9.8 1.0
O A:HOH401 4.2 22.2 1.0
O A:HOH457 4.3 24.4 1.0
O A:HOH352 4.4 13.9 1.0
O A:HOH473 4.7 58.6 1.0
O A:HOH351 4.7 13.8 1.0

Magnesium binding site 7 out of 10 in 4lqj

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Magnesium binding site 7 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:7.6
occ:0.33
 O A:HOH366 2.0 9.9 1.0
O A:HOH313 2.1 9.2 1.0
OE2 A:GLU130 3.9 10.1 1.0
OE1 A:GLU130 4.3 11.7 1.0
O A:HOH422 4.3 10.4 1.0
O A:HOH342 4.3 13.6 1.0
CD A:GLU130 4.5 10.4 1.0

Magnesium binding site 8 out of 10 in 4lqj

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Magnesium binding site 8 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:11.4
occ:0.50
 O A:HOH449 2.0 12.5 1.0
O A:HOH413 2.0 16.8 0.5
O A:HOH484 2.1 12.9 0.5
O A:HOH435 2.1 15.4 1.0
O A:HOH331 4.2 12.0 1.0
O A:HOH367 4.5 12.8 1.0
CE A:LYS83 4.5 8.0 0.5
NZ A:LYS82 4.6 9.2 0.5
CE A:LYS82 4.6 9.9 0.5
CD A:LYS82 4.6 9.8 0.5
O A:HOH456 4.7 22.8 1.0
CD A:LYS82 4.7 9.0 0.5
CE A:LYS83 4.8 8.7 0.5

Magnesium binding site 9 out of 10 in 4lqj

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Magnesium binding site 9 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:9.0
occ:0.40
 OE2 A:GLU136 1.8 12.1 0.5
O A:HOH583 2.0 12.0 0.5
OE1 A:GLN137 2.0 15.8 1.0
O A:HOH440 2.1 9.0 0.4
O A:HOH651 2.2 14.8 1.0
MG A:MG213 2.3 16.9 0.3
O A:HOH639 2.3 22.3 1.0
CD A:GLU136 2.8 12.0 0.5
CE1 A:HIS61 3.0 9.3 0.5
CD A:GLN137 3.1 12.5 1.0
OE1 A:GLU136 3.2 11.9 0.5
FE A:FE2201 3.2 10.3 0.5
FE A:FE2202 3.5 13.6 0.3
ND1 A:HIS61 3.5 9.3 0.5
NE2 A:GLN137 3.6 13.3 1.0
ND1 A:HIS61 3.7 11.0 0.5
CE1 A:HIS61 3.8 11.0 0.5
OE1 A:GLU103 4.0 13.9 1.0
NE2 A:HIS61 4.0 9.3 0.5
OE2 A:GLU58 4.1 10.5 0.6
CG A:GLU136 4.2 12.0 0.5
OE1 A:GLU58 4.2 10.2 0.6
OD2 A:ASP140 4.3 13.5 0.7
CA A:GLN137 4.3 9.3 1.0
CG A:GLN137 4.3 13.0 1.0
CB A:GLN137 4.5 10.9 1.0
N A:GLN137 4.5 10.0 1.0
OE2 A:GLU57 4.5 10.8 0.5
O A:HOH394 4.5 27.0 1.0
OE2 A:GLU58 4.5 10.9 0.4
OE2 A:GLU23 4.6 9.0 0.5
O A:HOH502 4.6 24.1 1.0
CD A:GLU58 4.6 10.0 0.6
CG A:HIS61 4.7 9.1 0.5
OE1 A:GLU58 4.7 10.9 0.4
MG A:MG206 4.7 11.1 0.5
C A:GLU136 4.9 11.0 1.0
O A:TYR133 4.9 9.6 1.0
CG1 A:VAL106 4.9 8.7 1.0
CD2 A:HIS61 4.9 9.2 0.5

Magnesium binding site 10 out of 10 in 4lqj

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Magnesium binding site 10 out of 10 in the Two Minutes Iron Loaded Frog M Ferritin


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

b:16.9
occ:0.30
 O A:HOH440 1.2 9.0 0.4
FE A:FE2202 2.1 13.6 0.3
O A:HOH651 2.2 14.8 1.0
OE1 A:GLU103 2.2 13.9 1.0
MG A:MG212 2.3 9.0 0.4
O A:HOH583 2.5 12.0 0.5
O A:HOH394 2.6 27.0 1.0
OD2 A:ASP140 3.0 13.5 0.7
CD A:GLU103 3.1 12.2 1.0
OE1 A:GLN137 3.2 15.8 1.0
OE2 A:GLU103 3.4 15.7 1.0
NE2 A:GLN137 3.5 13.3 1.0
CD A:GLN137 3.5 12.5 1.0
OE2 A:GLU58 3.6 10.5 0.6
OE2 A:GLU58 3.6 10.9 0.4
OE2 A:GLU136 3.6 12.1 0.5
OE1 A:GLU136 3.7 11.9 0.5
CG A:ASP140 3.8 12.8 0.7
CB A:ASP140 3.9 10.6 1.0
CD A:GLU136 4.1 12.0 0.5
CE1 A:HIS61 4.1 9.3 0.5
OE2 A:GLU57 4.2 10.8 0.5
OE1 A:GLU58 4.2 10.2 0.6
CD A:GLU58 4.3 10.0 0.6
O A:HOH639 4.3 22.3 1.0
FE A:FE2201 4.3 10.3 0.5
MG A:MG206 4.4 11.1 0.5
CG A:GLU103 4.5 10.2 1.0
CA A:GLN137 4.6 9.3 1.0
CD A:GLU58 4.6 10.7 0.4
ND1 A:HIS61 4.8 9.3 0.5
CG A:GLN137 4.8 13.0 1.0
O A:GLU136 4.9 10.7 1.0
OE1 A:GLU58 4.9 10.9 0.4
OD1 A:ASP140 4.9 15.5 0.7
CD A:GLU57 5.0 10.8 0.5

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 20:01:12 2024

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