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Magnesium in PDB 4my7: Frog M Ferritin Iron-Loaded Under Anaerobic Environment

Enzymatic activity of Frog M Ferritin Iron-Loaded Under Anaerobic Environment

All present enzymatic activity of Frog M Ferritin Iron-Loaded Under Anaerobic Environment:
1.16.3.1;

Protein crystallography data

The structure of Frog M Ferritin Iron-Loaded Under Anaerobic Environment, PDB code: 4my7 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) 41.11 / 1.48
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 (%) 17.4 / 19.5

Other elements in 4my7:

The structure of Frog M Ferritin Iron-Loaded Under Anaerobic Environment also contains other interesting chemical elements:

Iron (Fe) 5 atoms
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment (pdb code 4my7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment, PDB code: 4my7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4my7

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Magnesium binding site 1 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:12.8
occ:0.50
 O A:HOH318 2.0 13.7 1.0
O A:HOH358 2.0 12.2 0.5
O A:HOH395 2.1 12.2 0.5
O A:HOH642 2.1 15.2 1.0
O A:HOH346 4.2 13.7 1.0
CD A:LYS82 4.5 9.6 0.5
NZ A:LYS82 4.5 9.9 0.5
O A:HOH411 4.5 20.9 1.0
CE A:LYS83 4.5 9.7 0.5
O A:HOH462 4.7 23.3 1.0
CE A:LYS82 4.7 9.6 0.5
CE A:LYS83 4.8 9.8 0.5
CD A:LYS82 4.9 10.4 0.5

Magnesium binding site 2 out of 8 in 4my7

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Magnesium binding site 2 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:9.6
occ:0.33
 O A:HOH316 2.0 11.5 1.0
O A:HOH348 2.1 12.9 1.0
OE2 A:GLU130 3.9 12.6 1.0
O A:HOH498 4.1 26.5 1.0
OE1 A:GLU130 4.2 14.0 1.0
O A:HOH391 4.3 17.0 1.0
O A:HOH365 4.3 15.3 1.0
CD A:GLU130 4.5 12.9 1.0

Magnesium binding site 3 out of 8 in 4my7

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Magnesium binding site 3 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:10.0
occ:0.50
 O A:HOH428 2.1 21.5 1.0
O A:HOH416 2.1 21.3 1.0
O A:HOH378 2.1 17.8 1.0
O A:HOH399 2.1 21.5 1.0
OG A:SER10 2.1 12.5 1.0
O A:HOH323 2.1 15.1 1.0
CB A:SER10 3.2 11.2 1.0
CA A:SER10 3.9 10.7 1.0
O A:SER10 4.1 10.1 1.0
OE1 A:GLU13 4.2 10.5 1.0
O A:HOH338 4.2 16.8 1.0
C A:SER10 4.3 10.5 1.0
O A:HOH506 4.4 30.0 1.0
O A:HOH373 4.4 15.8 1.0
O A:HOH465 4.5 32.4 1.0
O A:HOH581 4.5 45.0 1.0
O A:HOH518 4.6 32.8 1.0
CD A:GLU13 4.7 9.8 1.0
O A:HOH482 5.0 27.2 1.0

Magnesium binding site 4 out of 8 in 4my7

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Magnesium binding site 4 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:10.6
occ:0.50
 O A:HOH598 2.0 24.7 1.0
O A:HOH370 2.0 20.8 1.0
O A:HOH638 2.1 31.4 1.0
O A:HOH616 2.1 30.6 1.0
O A:HOH626 2.2 33.3 1.0
O A:HOH347 2.3 15.8 1.0
OD1 A:ASN21 4.3 8.2 1.0
O A:HOH419 4.3 21.2 1.0
O A:ARG18 4.4 9.3 1.0
O A:HOH461 4.4 14.0 1.0
O A:HOH432 4.5 22.2 1.0
O A:HOH420 4.6 21.6 1.0
O A:HOH551 4.7 31.6 1.0
CB A:LEU22 4.9 8.6 1.0

Magnesium binding site 5 out of 8 in 4my7

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Magnesium binding site 5 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:17.7
occ:0.80
 O A:HOH569 2.0 26.7 1.0
O A:HOH623 2.0 20.1 1.0
O A:HOH402 2.1 27.0 1.0
O A:HOH453 2.1 22.1 1.0
O A:HOH476 2.1 25.8 1.0
O A:HOH539 2.2 21.7 1.0
OD2 A:ASP127 4.1 14.1 1.0
O A:HOH570 4.3 31.1 1.0
O A:HOH552 4.5 29.7 1.0
O A:HOH545 4.6 35.2 1.0
OD1 A:ASP127 4.6 14.8 1.0
OG A:SER131 4.7 12.7 0.5
OG A:SER131 4.8 12.8 0.5
CG A:ASP127 4.8 12.9 1.0
O A:HOH513 5.0 34.0 1.0

Magnesium binding site 6 out of 8 in 4my7

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Magnesium binding site 6 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:20.9
occ:0.20
 O A:HOH345 1.9 15.0 1.0
O A:HOH637 2.0 27.1 1.0
OD1 A:ASP127 3.5 14.8 1.0
OG A:SER131 4.0 12.7 0.5
O A:HOH552 4.1 29.7 1.0
OE1 A:GLU130 4.5 14.0 1.0
CG A:ASP127 4.6 12.9 1.0
O A:HOH453 4.7 22.1 1.0
CB A:GLU130 5.0 11.8 1.0

Magnesium binding site 7 out of 8 in 4my7

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Magnesium binding site 7 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:17.6
occ:0.33
 O A:HOH499 2.1 26.8 1.0
O A:HOH380 2.3 22.8 1.0
O A:HOH391 4.2 17.0 1.0
CG2 A:THR118 4.4 11.0 1.0
O A:HOH574 4.5 39.2 1.0
O A:HOH344 4.6 15.9 1.0
O A:HOH406 4.7 16.7 1.0

Magnesium binding site 8 out of 8 in 4my7

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Magnesium binding site 8 out of 8 in the Frog M Ferritin Iron-Loaded Under Anaerobic Environment


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Frog M Ferritin Iron-Loaded Under Anaerobic Environment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:21.7
occ:0.80
 O A:HOH627 1.9 26.1 0.8
O A:HOH475 2.0 27.0 1.0
O A:HOH376 2.0 18.2 1.0
O A:HOH484 2.1 27.1 1.0
O A:HOH445 2.2 24.6 0.8
O A:HOH485 2.3 27.9 0.8
NE2 A:HIS45 3.9 11.6 0.5
CD2 A:HIS45 4.0 11.7 0.5
CE1 A:HIS45 4.1 11.8 0.5
CG A:HIS45 4.3 11.4 0.5
ND1 A:HIS45 4.3 11.7 0.5
O A:HOH505 4.3 35.9 1.0
O A:HOH619 4.7 42.2 1.0
CD2 A:HIS45 4.8 11.6 0.5
CG A:HIS45 4.9 11.4 0.5
O A:HOH629 5.0 23.4 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 23:23:20 2024

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