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Magnesium in PDB 4lpm: Frog M-Ferritin with Magnesium, D127E Mutant

Enzymatic activity of Frog M-Ferritin with Magnesium, D127E Mutant

All present enzymatic activity of Frog M-Ferritin with Magnesium, D127E Mutant:
1.16.3.1;

Protein crystallography data

The structure of Frog M-Ferritin with Magnesium, D127E Mutant, PDB code: 4lpm was solved by R.Torres, R.Behera, C.W.Goulding, E.C.Theil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 1.65
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 183.913, 183.913, 183.913, 90.00, 90.00, 90.00
R / Rfree (%) 12.6 / 16.4

Other elements in 4lpm:

The structure of Frog M-Ferritin with Magnesium, D127E Mutant also contains other interesting chemical elements:

Chlorine (Cl) 6 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 with Magnesium, D127E Mutant (pdb code 4lpm). 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 with Magnesium, D127E Mutant, PDB code: 4lpm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 4lpm

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Magnesium binding site 1 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:5.8
occ:0.33
 OE2 A:GLU127 2.3 14.8 1.0
OE1 A:GLU130 2.4 19.4 1.0
CD A:GLU127 3.4 14.1 1.0
CD A:GLU130 3.6 17.9 1.0
MG A:MG213 3.7 2.9 0.3
OE1 A:GLU127 4.0 16.8 1.0
HA A:GLU127 4.0 13.2 1.0
HB2 A:GLU127 4.1 15.0 1.0
HB2 A:GLU130 4.1 19.7 1.0
HB3 A:GLU130 4.2 19.7 1.0
O A:HOH311 4.2 13.3 1.0
OE2 A:GLU130 4.4 17.8 1.0
CB A:GLU130 4.5 16.4 1.0
CG A:GLU127 4.6 12.5 1.0
CG A:GLU130 4.6 19.2 1.0
CB A:GLU127 4.7 12.5 1.0
CA A:GLU127 4.8 11.0 1.0
HG2 A:GLU130 5.0 23.1 1.0

Magnesium binding site 2 out of 11 in 4lpm

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Magnesium binding site 2 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:23.0
occ:1.00
 O A:HOH344 2.0 22.2 1.0
OE1 A:GLN137 2.0 20.6 1.0
O A:HOH592 2.0 18.6 1.0
OE1 A:GLU136 2.0 23.4 1.0
O A:HOH389 2.3 28.6 1.0
O A:HOH347 2.3 22.4 1.0
MG A:MG217 2.7 30.2 0.5
CD A:GLU136 2.9 21.7 1.0
HD2 A:HIS61 3.1 31.8 1.0
CD A:GLN137 3.1 18.3 1.0
O A:HOH602 3.2 19.0 1.0
OE2 A:GLU136 3.2 21.6 1.0
HE22 A:GLN137 3.4 21.0 1.0
HA A:GLN137 3.5 16.2 1.0
NE2 A:GLN137 3.6 17.5 1.0
CD2 A:HIS61 3.8 26.5 1.0
HE2 A:HIS61 3.9 35.5 1.0
OE2 A:GLU58 4.0 25.1 1.0
OE1 A:GLU103 4.0 17.0 1.0
HB2 A:GLN137 4.0 18.8 1.0
OE1 A:GLU58 4.0 21.5 1.0
HG11 A:VAL106 4.2 15.5 1.0
NE2 A:HIS61 4.2 29.6 1.0
OD2 A:ASP140 4.2 20.5 1.0
CA A:GLN137 4.2 13.5 1.0
CG A:GLN137 4.3 17.1 1.0
CG A:GLU136 4.3 19.0 1.0
CB A:GLN137 4.4 15.7 1.0
OE1 A:GLU57 4.4 20.9 1.0
CD A:GLU58 4.4 21.3 1.0
HE21 A:GLN137 4.5 21.0 1.0
N A:GLN137 4.5 13.7 1.0
HD2 A:TYR133 4.5 18.9 1.0
HD11 A:LEU110 4.6 16.3 1.0
HG12 A:VAL106 4.7 15.5 1.0
H A:GLN137 4.7 16.4 1.0
OE2 A:GLU23 4.7 23.1 1.0
MG A:MG208 4.7 20.4 1.0
O A:HOH421 4.8 26.9 1.0
HG2 A:GLN137 4.8 20.5 1.0
HB2 A:ASP140 4.9 14.9 1.0
HG3 A:GLN137 4.9 20.5 1.0
CG1 A:VAL106 4.9 12.9 1.0
C A:GLU136 4.9 15.1 1.0

Magnesium binding site 3 out of 11 in 4lpm

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Magnesium binding site 3 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:19.7
occ:1.00
 O A:HOH362 2.0 17.5 1.0
O A:HOH365 2.0 21.1 1.0
OG A:SER10 2.1 14.1 1.0
O A:HOH331 2.1 14.7 1.0
O A:HOH386 2.2 22.8 1.0
O A:HOH414 2.2 21.8 1.0
CB A:SER10 3.2 12.9 1.0
HB2 A:SER10 3.2 15.5 1.0
HA A:SER10 3.5 12.5 1.0
CA A:SER10 3.8 10.4 1.0
HB3 A:SER10 3.9 15.5 1.0
O A:SER10 4.1 10.5 1.0
OE1 A:GLU13 4.1 12.7 1.0
O A:HOH501 4.3 34.1 1.0
O A:HOH425 4.3 31.4 1.0
O A:HOH340 4.3 17.9 1.0
C A:SER10 4.3 9.9 1.0
O A:HOH361 4.4 15.4 1.0
HB3 A:GLU13 4.5 12.2 1.0
O A:HOH576 4.6 45.2 1.0
CD A:GLU13 4.6 9.8 1.0
O A:HOH483 4.7 33.5 1.0
HH12 A:ARG5 4.9 14.6 1.0
HB2 A:ALA14 4.9 12.9 1.0
OE2 A:GLU13 5.0 11.9 1.0

Magnesium binding site 4 out of 11 in 4lpm

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Magnesium binding site 4 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:20.4
occ:1.00
 OE1 A:GLU57 2.0 20.9 1.0
OE2 A:GLU136 2.1 21.6 1.0
O A:HOH358 2.1 17.2 1.0
O A:HOH400 2.1 23.8 1.0
OD2 A:ASP140 2.1 20.5 1.0
O A:HOH367 2.1 21.0 1.0
CG A:ASP140 3.0 17.8 1.0
CD A:GLU57 3.0 21.9 1.0
OD1 A:ASP140 3.3 21.7 1.0
CD A:GLU136 3.3 21.7 1.0
OE2 A:GLU57 3.4 23.9 1.0
O A:GLU136 3.8 15.3 1.0
CB A:GLU136 3.8 19.6 1.0
O A:HOH344 3.9 22.2 1.0
O A:HOH389 3.9 28.6 1.0
HE2 A:HIS61 4.1 35.5 1.0
CG A:GLU136 4.1 19.0 1.0
O A:HOH550 4.2 57.8 1.0
OE1 A:GLU136 4.2 23.4 1.0
HH21 A:ARG143 4.2 46.9 0.4
C A:GLU136 4.2 15.1 1.0
O A:HOH472 4.3 40.1 1.0
CG A:GLU57 4.4 18.7 1.0
CB A:ASP140 4.4 12.4 1.0
HB2 A:ASP140 4.4 14.9 1.0
HH22 A:ARG143 4.5 46.9 0.4
CA A:GLU136 4.5 16.1 1.0
HE1 A:HIS54 4.5 29.0 1.0
O A:HOH538 4.5 43.0 1.0
HA A:GLU136 4.5 19.3 1.0
O A:HOH605 4.6 37.8 1.0
MG A:MG217 4.7 30.2 0.5
NH2 A:ARG143 4.7 39.1 0.4
H A:ASP140 4.7 11.9 1.0
MG A:MG204 4.7 23.0 1.0
NE2 A:HIS61 4.9 29.6 1.0
O A:HOH536 4.9 44.6 1.0
O A:HOH421 4.9 26.9 1.0
HB3 A:ASP140 4.9 14.9 1.0

Magnesium binding site 5 out of 11 in 4lpm

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Magnesium binding site 5 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:12.9
occ:0.33
 O A:HOH319 2.1 15.4 1.0
O A:HOH311 2.1 13.3 1.0
OE2 A:GLU130 3.8 17.8 1.0
O A:HOH343 4.1 13.5 1.0
O A:HOH446 4.2 27.8 1.0
OE1 A:GLU130 4.4 19.4 1.0
CD A:GLU130 4.5 17.9 1.0
HB3 A:CYS126 4.6 12.6 1.0
HE1 A:HIS114 4.7 14.6 1.0
HE2 A:HIS114 4.7 15.3 1.0

Magnesium binding site 6 out of 11 in 4lpm

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Magnesium binding site 6 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:29.0
occ:0.33
 O A:HOH426 2.1 33.4 1.0
O A:HOH335 2.4 18.0 1.0
HG23 A:THR118 3.9 17.6 1.0
O A:HOH446 3.9 27.8 1.0
HG21 A:THR118 4.4 17.6 1.0
O A:HOH549 4.5 43.4 1.0
CG2 A:THR118 4.6 14.6 1.0
O A:HOH515 4.7 19.9 1.0
O A:HOH313 4.8 16.6 1.0
HG22 A:THR118 4.9 17.6 1.0

Magnesium binding site 7 out of 11 in 4lpm

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Magnesium binding site 7 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:14.1
occ:0.50
 O A:HOH322 2.0 13.9 1.0
O A:HOH305 2.0 15.1 0.5
O A:HOH332 2.1 16.2 0.5
O A:HOH336 2.5 16.4 1.0
OD2 A:ASP80 4.0 12.0 1.0
OD1 A:ASP80 4.1 10.4 1.0
CG A:ASP80 4.5 10.3 1.0
O A:HOH519 4.8 25.0 1.0
O A:HOH306 5.0 8.6 1.0

Magnesium binding site 8 out of 11 in 4lpm

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Magnesium binding site 8 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:29.9
occ:0.75
 O A:HOH396 2.0 23.9 1.0
O A:HOH529 2.1 37.3 1.0
O A:HOH468 2.1 48.9 1.0
O A:HOH526 2.2 43.1 1.0
O A:HOH489 2.2 34.4 1.0
O A:HOH408 2.2 37.1 1.0
O A:HOH559 3.8 36.0 1.0
O A:HOH583 4.0 51.2 1.0
HB2 A:SER131 4.2 21.3 1.0
OG A:SER131 4.2 17.6 1.0
O A:HOH571 4.3 54.7 1.0
CB A:SER131 4.6 17.8 1.0
OE1 A:GLU127 4.7 16.8 1.0
OE2 A:GLU132 4.7 29.6 1.0
CL A:CL214 4.7 22.2 0.3
HB3 A:SER131 4.8 21.3 1.0
HG3 A:GLU127 4.8 15.0 1.0
HG A:SER131 4.8 21.1 1.0

Magnesium binding site 9 out of 11 in 4lpm

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Magnesium binding site 9 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:2.9
occ:0.33
 OE1 A:GLU127 2.1 16.8 1.0
CL A:CL214 2.3 22.2 0.3
CD A:GLU127 2.9 14.1 1.0
OE2 A:GLU127 3.1 14.8 1.0
HB3 A:SER131 3.4 21.3 1.0
MG A:MG202 3.7 5.8 0.3
O A:HOH396 4.1 23.9 1.0
CB A:SER131 4.2 17.8 1.0
HB2 A:SER131 4.2 21.3 1.0
CG A:GLU127 4.4 12.5 1.0
HG2 A:GLU127 4.6 15.0 1.0
HG3 A:GLU127 4.6 15.0 1.0
HA A:SER131 4.9 18.2 1.0
O A:HOH529 5.0 37.3 1.0

Magnesium binding site 10 out of 11 in 4lpm

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Magnesium binding site 10 out of 11 in the Frog M-Ferritin with Magnesium, D127E Mutant


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 with Magnesium, D127E Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:22.6
occ:0.71
 O A:HOH485 2.1 28.6 1.0
O A:HOH503 2.1 31.7 1.0
O A:HOH374 2.1 20.0 1.0
O A:HOH541 2.2 33.4 1.0
O A:HOH469 2.5 33.8 1.0
O A:HOH558 3.9 42.5 1.0
HB3 A:GLN3 4.0 11.8 1.0
O A:HOH451 4.3 30.3 1.0
H A:GLN3 4.4 13.6 1.0
O A:VAL1 4.7 18.4 1.0
HA A:SER2 4.9 12.3 1.0
N A:GLN3 4.9 11.3 1.0
CB A:GLN3 5.0 9.8 1.0

Reference:

R.Behera, R.Torres, T.Takehiko, J.Bradley, C.W.Goulding, E.C.Theil. D127E Ion Channel Exit Modification in Ferritin Nanocages Entraps Fe(II) and Impairs Its Distribution to Diiron Catalytic Centers To Be Published.
Page generated: Mon Aug 19 19:58:22 2024

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