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Magnesium in PDB 4mku: Frog M Ferritin Mutant H54Q

Enzymatic activity of Frog M Ferritin Mutant H54Q

All present enzymatic activity of Frog M Ferritin Mutant H54Q:
1.16.3.1;

Protein crystallography data

The structure of Frog M Ferritin Mutant H54Q, PDB code: 4mku 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) 20.64 / 1.30
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.580, 184.580, 184.580, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 13.9

Other elements in 4mku:

The structure of Frog M Ferritin Mutant H54Q also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Frog M Ferritin Mutant H54Q (pdb code 4mku). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Frog M Ferritin Mutant H54Q, PDB code: 4mku:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4mku

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Magnesium binding site 1 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:5.4
occ:0.33
 O A:HOH380 1.9 7.5 1.0
O A:HOH368 2.0 8.8 1.0
OE2 A:GLU130 4.1 9.1 1.0
O A:HOH660 4.2 5.2 0.2
O A:HOH394 4.3 9.7 1.0
O A:HOH371 4.4 15.6 1.0
OE1 A:GLU130 4.4 10.7 1.0
CD A:GLU130 4.7 9.2 1.0

Magnesium binding site 2 out of 11 in 4mku

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Magnesium binding site 2 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:12.3
occ:0.60
 OE2 A:GLU57 2.0 10.6 0.6
O A:HOH497 2.1 15.8 0.6
O A:HOH439 2.1 13.7 0.6
OE2 A:GLU53 2.1 11.4 0.5
O A:HOH521 2.2 15.9 0.6
O A:HOH496 2.2 16.9 0.6
CD A:GLU57 3.0 10.9 0.6
CD A:GLU53 3.2 10.8 0.5
OE2 A:GLU53 3.3 10.6 0.3
OE1 A:GLU57 3.4 11.3 0.6
CG A:GLU53 3.5 8.6 0.3
CG A:GLU53 3.7 9.6 0.5
CD A:GLU53 3.9 9.5 0.3
O A:HOH638 4.2 37.1 1.0
O A:HOH377 4.2 16.2 1.0
NH1 A:ARG143 4.2 12.1 0.8
OE1 A:GLU53 4.3 12.2 0.5
CG A:GLU57 4.4 9.9 0.6
O A:HOH672 4.4 29.8 1.0
O A:HOH559 4.4 21.4 1.0
O A:HOH420 4.5 17.4 1.0
NH2 A:ARG143 4.5 12.6 0.8
CZ A:ARG143 4.8 11.7 0.8
CB A:GLU53 4.9 8.9 0.5
CB A:GLU53 4.9 8.2 0.5
O A:HOH643 5.0 10.7 0.9

Magnesium binding site 3 out of 11 in 4mku

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Magnesium binding site 3 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:13.6
occ:0.80
 O A:HOH631 2.0 12.7 0.8
O A:HOH646 2.1 17.8 0.8
O A:HOH656 2.1 15.5 0.8
O A:HOH619 2.1 9.3 0.8
OG A:SER10 2.1 8.7 0.8
O A:HOH460 2.1 18.1 0.8
CB A:SER10 3.2 8.2 1.0
CA A:SER10 3.9 7.2 1.0
O A:SER10 4.1 6.7 1.0
OE1 A:GLU13 4.2 7.5 1.0
O A:HOH367 4.2 14.2 1.0
O A:HOH537 4.3 29.8 1.0
C A:SER10 4.3 6.9 1.0
O A:HOH360 4.4 12.2 1.0
O A:HOH586 4.5 31.8 1.0
O A:HOH593 4.6 31.7 1.0
CD A:GLU13 4.6 6.5 1.0
OE2 A:GLU13 5.0 7.0 1.0

Magnesium binding site 4 out of 11 in 4mku

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Magnesium binding site 4 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:13.1
occ:0.80
 O A:HOH621 2.0 12.7 0.8
O A:HOH650 2.1 14.9 0.8
O A:HOH642 2.1 16.6 0.8
O A:HOH664 4.3 32.4 1.0
O A:HOH512 4.4 29.4 1.0
CD2 A:HIS45 4.5 11.1 0.8
CG A:HIS45 4.9 10.0 0.8

Magnesium binding site 5 out of 11 in 4mku

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Magnesium binding site 5 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:8.9
occ:0.90
 OD2 A:ASP140 2.0 10.2 0.9
OE1 A:GLN54 2.0 9.8 0.9
O A:HOH648 2.0 9.2 0.9
O A:HOH620 2.1 11.1 0.9
O A:HOH643 2.2 10.7 0.9
OE2 A:GLU103 2.2 7.6 0.9
CD A:GLN54 3.1 9.1 0.9
CD A:GLU103 3.1 7.4 0.9
CG A:ASP140 3.2 8.5 0.9
OE1 A:GLU103 3.5 7.7 0.9
NE2 A:GLN54 3.5 11.4 0.9
OE2 A:GLU58 3.9 9.8 1.0
CB A:ASP140 4.0 8.1 1.0
OD1 A:ASP140 4.0 10.8 0.9
OH A:TYR30 4.1 9.0 1.0
OE2 A:GLU136 4.1 11.7 0.8
CE2 A:TYR30 4.3 7.0 1.0
O A:HOH559 4.4 21.4 1.0
OE1 A:GLU57 4.4 11.3 0.6
CG A:GLU103 4.4 7.3 1.0
CG A:GLN54 4.4 8.6 1.0
CZ A:TYR30 4.5 7.5 1.0
CB A:GLN54 4.7 8.2 1.0
O A:HOH321 4.8 9.2 1.0
CD A:GLU58 4.9 9.0 1.0
CA A:GLN54 4.9 7.3 1.0
O A:GLN54 5.0 8.2 1.0

Magnesium binding site 6 out of 11 in 4mku

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Magnesium binding site 6 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:7.4
occ:0.50
 O A:HOH398 1.9 13.6 1.0
O A:HOH429 1.9 11.0 1.0
O A:HOH487 2.0 9.8 0.5
O A:HOH441 2.1 13.2 0.5
O A:HOH347 4.2 11.3 1.0
O A:HOH340 4.4 11.0 1.0
CE A:LYS83 4.4 6.9 0.5
O A:HOH474 4.5 27.7 1.0
CD A:LYS82 4.6 8.4 0.5
CE A:LYS83 4.7 8.4 0.5
NZ A:LYS82 4.8 8.4 0.5
CE A:LYS82 4.8 9.0 0.5

Magnesium binding site 7 out of 11 in 4mku

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Magnesium binding site 7 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:11.6
occ:0.70
 O A:HOH655 2.0 15.6 0.7
O A:HOH644 2.0 15.2 0.7
O A:HOH633 2.1 15.6 0.7
O A:HOH654 2.1 12.1 0.7
O A:HOH622 2.1 13.0 0.7
O A:HOH494 2.2 13.3 0.7

Magnesium binding site 8 out of 11 in 4mku

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Magnesium binding site 8 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:14.5
occ:0.50
 O A:HOH451 1.9 15.4 0.5
O A:HOH543 2.0 14.1 0.5
O A:HOH561 2.0 19.4 0.5
O A:HOH533 2.1 16.6 0.5
O A:HOH352 2.1 7.1 0.5
O A:HOH544 2.2 21.2 0.5
O A:HOH627 4.2 37.2 1.0
O A:HOH513 4.2 24.4 1.0
O A:VAL1 4.5 12.6 0.5
O A:VAL1 4.8 14.5 0.5
N A:GLN3 5.0 6.7 1.0

Magnesium binding site 9 out of 11 in 4mku

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Magnesium binding site 9 out of 11 in the 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 Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:7.1
occ:1.00
 OE1 A:GLU23 2.0 7.4 1.0
OE1 A:GLU58 2.0 9.0 1.0
O A:HOH322 2.0 8.0 1.0
O A:HOH321 2.0 9.2 1.0
ND1 A:HIS61 2.2 8.3 0.9
CD A:GLU23 3.0 7.2 1.0
CD A:GLU58 3.0 9.0 1.0
CE1 A:HIS61 3.1 8.8 0.9
CG A:HIS61 3.2 8.3 0.9
OE2 A:GLU23 3.4 7.8 1.0
OE2 A:GLU58 3.4 9.8 1.0
CB A:HIS61 3.6 7.7 1.0
CG1 A:VAL106 3.9 6.8 1.0
OE1 A:GLN137 4.2 7.6 1.0
NE2 A:HIS61 4.2 9.7 0.9
O A:HOH348 4.2 8.7 1.0
CD2 A:HIS61 4.3 8.8 0.9
CG A:GLU58 4.3 7.8 1.0
CG A:GLU23 4.3 6.4 1.0
CA A:GLU58 4.4 7.4 1.0
CB A:GLU58 4.6 7.4 1.0
CB A:GLU23 4.7 5.7 1.0
CA A:GLU23 4.9 5.4 1.0
CD A:GLN137 4.9 7.3 1.0
CG2 A:VAL106 4.9 6.4 1.0
O A:GLU58 4.9 7.3 1.0
CB A:VAL106 5.0 6.4 1.0

Magnesium binding site 10 out of 11 in 4mku

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Magnesium binding site 10 out of 11 in the 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 10 of Frog M Ferritin Mutant H54Q within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:15.3
occ:0.20
 O A:HOH397 1.5 6.9 0.6
O A:HOH636 2.1 13.6 0.6
OD1 A:ASP127 3.5 12.9 1.0
OG A:SER131 4.1 7.7 0.4
OE1 A:GLU130 4.3 10.7 1.0
O A:HOH530 4.3 26.2 1.0
CG A:ASP127 4.6 10.0 1.0
O A:HOH494 4.8 13.3 0.7
CB A:GLU130 5.0 8.4 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 11 20:29:12 2025

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