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Magnesium in PDB 4lyx: Five Minutes Iron Loaded Frog M Ferritin

Enzymatic activity of Five Minutes Iron Loaded Frog M Ferritin

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

Protein crystallography data

The structure of Five Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyx 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) 20.22 / 1.23
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.180, 184.180, 184.180, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 17.5

Other elements in 4lyx:

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

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

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Five Minutes Iron Loaded Frog M Ferritin (pdb code 4lyx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Five Minutes Iron Loaded Frog M Ferritin, PDB code: 4lyx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4lyx

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Magnesium binding site 1 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:15.7
occ:0.60
 O A:HOH498 2.0 18.2 0.6
O A:HOH566 2.1 21.1 0.6
O A:HOH536 2.1 20.7 0.6
O A:HOH412 2.1 12.9 0.6
O A:HOH516 2.1 20.5 0.6
O A:HOH472 2.1 17.8 0.6
O A:VAL1 4.4 18.7 0.5
O A:HOH478 4.4 28.6 1.0
O A:HOH594 4.7 45.4 1.0
O A:VAL1 4.7 17.2 0.5

Magnesium binding site 2 out of 11 in 4lyx

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Magnesium binding site 2 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:13.8
occ:0.70
 O A:HOH387 2.0 14.6 0.7
O A:HOH503 2.0 18.4 0.7
O A:HOH458 2.0 17.5 0.7
O A:HOH325 2.1 10.6 0.7
O A:HOH446 2.1 17.3 0.7
OG A:SER10 2.1 13.2 1.0
CB A:SER10 3.2 12.7 1.0
CA A:SER10 3.9 10.3 1.0
O A:HOH604 4.0 47.2 1.0
O A:SER10 4.1 9.4 1.0
OE1 A:GLU13 4.2 10.4 1.0
O A:HOH339 4.3 17.1 1.0
C A:SER10 4.4 9.4 1.0
O A:HOH486 4.4 32.2 1.0
O A:HOH502 4.4 32.4 1.0
O A:HOH398 4.4 15.6 1.0
O A:HOH627 4.5 42.2 1.0
O A:HOH499 4.6 34.7 1.0
CD A:GLU13 4.6 9.2 1.0

Magnesium binding site 3 out of 11 in 4lyx

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Magnesium binding site 3 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:13.8
occ:0.60
 O A:HOH527 2.0 17.4 0.6
O A:HOH393 2.0 15.1 0.6
O A:HOH512 2.1 17.8 0.6
O A:HOH558 2.1 20.0 0.6
O A:HOH529 2.1 19.1 0.6
O A:HOH344 2.2 10.1 0.6
O A:HOH440 4.1 23.2 1.0
OD1 A:ASN21 4.3 8.5 1.0
O A:HOH432 4.3 20.6 1.0
O A:ARG18 4.4 8.8 1.0
O A:HOH406 4.5 13.4 1.0
O A:HOH426 4.5 21.0 1.0
O A:HOH598 4.7 45.5 1.0
O A:HOH641 4.7 47.0 1.0
CB A:LEU22 4.8 9.2 1.0
O A:HOH418 4.8 19.8 1.0
O A:HOH422 4.9 22.9 1.0
O A:HOH632 5.0 46.2 1.0

Magnesium binding site 4 out of 11 in 4lyx

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Magnesium binding site 4 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:15.1
occ:0.50
 OE1 A:GLU136 2.0 15.5 0.5
OE2 A:GLU57 2.0 13.7 0.5
O A:HOH537 2.1 18.4 0.5
O A:HOH434 2.1 15.6 0.5
O A:HOH403 2.2 13.1 0.5
OD2 A:ASP140 2.2 21.6 1.0
CG A:ASP140 3.0 17.9 1.0
CD A:GLU57 3.0 14.1 0.5
CD A:GLU136 3.2 16.1 0.5
OD1 A:ASP140 3.2 23.6 1.0
OE1 A:GLU57 3.4 14.9 0.5
O A:HOH664 3.6 11.9 0.3
CB A:GLU136 3.8 18.7 1.0
O A:GLU136 3.8 13.5 1.0
O A:HOH497 3.9 30.4 1.0
CG A:GLU136 4.0 15.0 0.5
OE2 A:GLU136 4.1 16.5 0.5
C A:GLU136 4.2 13.2 1.0
CG A:GLU57 4.3 13.2 0.5
CB A:ASP140 4.4 13.5 1.0
CA A:GLU136 4.4 14.2 1.0
O A:HOH441 4.5 27.8 1.0
OE1 A:GLU57 4.6 19.8 0.5
NE2 A:HIS61 4.6 12.3 0.5
CE1 A:HIS61 4.7 12.6 0.5
MG A:MG211 4.7 9.1 0.3
O A:HOH559 4.7 44.3 1.0
NE2 A:HIS61 4.8 14.2 0.5
CD A:GLU57 5.0 18.9 0.5
O A:HOH541 5.0 40.5 1.0

Magnesium binding site 5 out of 11 in 4lyx

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Magnesium binding site 5 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:14.0
occ:0.15
 O A:HOH661 1.9 9.0 0.5
O A:HOH545 2.0 16.9 0.5
OD1 A:ASP127 3.6 17.4 1.0
OE1 A:GLU130 3.7 15.0 0.5
OG A:SER131 4.1 13.3 0.5
OE1 A:GLU130 4.3 9.1 0.5
O A:HOH534 4.4 30.9 1.0
CG A:ASP127 4.7 14.1 1.0
O A:HOH439 4.7 17.1 0.7
CB A:GLU130 4.9 12.6 0.5
CD A:GLU130 5.0 13.6 0.5

Magnesium binding site 6 out of 11 in 4lyx

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Magnesium binding site 6 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:14.6
occ:0.70
 O A:HOH483 2.0 22.0 0.7
O A:HOH650 2.0 18.0 0.7
O A:HOH658 2.1 16.3 0.7
O A:HOH524 2.1 20.9 0.7
O A:HOH521 2.1 16.3 0.7
O A:HOH439 2.1 17.1 0.7
OD2 A:ASP127 4.0 17.1 1.0
O A:HOH569 4.5 37.2 1.0
OD1 A:ASP127 4.5 17.4 1.0
O A:HOH534 4.6 30.9 1.0
CG A:ASP127 4.7 14.1 1.0
OG A:SER131 4.7 13.3 0.5
O A:HOH578 4.7 34.6 1.0
OG A:SER131 4.8 14.5 0.5
CB A:SER131 5.0 13.3 0.5
CB A:SER131 5.0 14.0 0.5

Magnesium binding site 7 out of 11 in 4lyx

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Magnesium binding site 7 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:15.7
occ:0.50
 O A:HOH625 1.9 22.3 0.5
O A:HOH660 1.9 24.7 0.5
O A:HOH629 1.9 19.8 0.5
O A:HOH425 2.0 11.8 0.5
O A:HOH501 2.0 22.1 0.5
O A:HOH538 2.1 22.3 0.5
OD2 A:ASP146 4.0 12.8 1.0
O A:HOH444 4.2 27.3 1.0
O A:HOH438 4.2 28.1 1.0
O A:HOH575 4.3 40.0 1.0
O A:HOH346 4.3 16.1 1.0
O A:HOH612 4.5 44.3 1.0
O A:HOH354 4.6 17.3 1.0

Magnesium binding site 8 out of 11 in 4lyx

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Magnesium binding site 8 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:9.1
occ:0.30
 OE2 A:GLU136 1.8 16.5 0.5
OE1 A:GLN137 1.9 19.9 1.0
O A:HOH664 2.0 11.9 0.3
O A:HOH301 2.2 12.6 0.6
O A:HOH497 2.4 30.4 1.0
O A:HOH481 2.5 23.3 1.0
CD A:GLU136 2.8 16.1 0.5
CE1 A:HIS61 3.0 12.6 0.5
CD A:GLN137 3.0 15.9 1.0
OE1 A:GLU136 3.2 15.5 0.5
FE A:FE2201 3.2 12.2 0.5
ND1 A:HIS61 3.4 12.4 0.5
FE A:FE2202 3.5 16.0 0.3
NE2 A:GLN137 3.6 15.7 1.0
CD2 A:HIS61 3.8 13.7 0.5
NE2 A:HIS61 4.0 14.2 0.5
NE2 A:HIS61 4.0 12.3 0.5
OE1 A:GLU103 4.0 11.2 0.5
OE2 A:GLU58 4.1 13.6 0.5
OE1 A:GLU58 4.2 13.3 0.5
CG A:GLU136 4.2 15.0 0.5
OD2 A:ASP140 4.2 21.6 1.0
OE1 A:GLU103 4.2 13.6 0.5
CG A:GLN137 4.3 17.6 1.0
CA A:GLN137 4.3 11.0 1.0
CB A:GLN137 4.4 14.0 1.0
N A:GLN137 4.4 12.8 1.0
OE2 A:GLU57 4.4 13.7 0.5
OE2 A:GLU23 4.5 8.7 0.3
OE2 A:GLU58 4.5 13.7 0.5
CD A:GLU58 4.6 13.1 0.5
CG A:HIS61 4.6 11.9 0.5
O A:HOH441 4.7 27.8 1.0
OE1 A:GLU58 4.7 13.7 0.5
MG A:MG207 4.7 15.1 0.5
C A:GLU136 4.8 13.2 1.0
O A:TYR133 4.8 12.1 1.0
CG1 A:VAL106 4.9 10.7 1.0
CD2 A:HIS61 4.9 12.2 0.5
O A:GLU136 5.0 13.5 1.0
CG A:HIS61 5.0 12.4 0.5

Magnesium binding site 9 out of 11 in 4lyx

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Magnesium binding site 9 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:11.1
occ:0.33
 O A:HOH400 2.0 13.8 1.0
O A:HOH324 2.1 12.7 1.0
OE2 A:GLU130 3.9 13.1 0.5
OE2 A:GLU130 3.9 9.5 0.5
O A:HOH447 4.1 13.0 0.5
O A:HOH409 4.3 14.7 1.0
O A:HOH390 4.3 22.3 1.0
OE1 A:GLU130 4.3 9.1 0.5
OE1 A:GLU130 4.5 15.0 0.5
CD A:GLU130 4.5 9.4 0.5
CD A:GLU130 4.6 13.6 0.5

Magnesium binding site 10 out of 11 in 4lyx

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Magnesium binding site 10 out of 11 in the Five 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 Five Minutes Iron Loaded Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:12.2
occ:0.50
 O A:HOH396 2.0 12.5 1.0
O A:HOH382 2.0 14.2 0.5
O A:HOH424 2.1 13.6 0.5
O A:HOH433 2.2 15.5 1.0
O A:HOH331 4.2 13.8 1.0
CD A:LYS82 4.4 9.9 0.5
O A:HOH410 4.4 16.2 1.0
NZ A:LYS82 4.5 10.8 0.5
CE A:LYS83 4.6 8.2 0.5
CE A:LYS82 4.6 11.0 0.5
O A:HOH404 4.7 21.9 1.0
CE A:LYS83 4.7 12.3 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 20:09:08 2024

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