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Magnesium in PDB 4lqh: High Resolution Structure of Native Frog M Ferritin

Enzymatic activity of High Resolution Structure of Native Frog M Ferritin

All present enzymatic activity of High Resolution Structure of Native Frog M Ferritin:
1.16.3.1;

Protein crystallography data

The structure of High Resolution Structure of Native Frog M Ferritin, PDB code: 4lqh 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) 21.73 / 1.16
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.410, 184.410, 184.410, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 16

Other elements in 4lqh:

The structure of High Resolution Structure of Native Frog M Ferritin also contains other interesting chemical elements:

Chlorine (Cl) 16 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 9 in 4lqh

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Magnesium binding site 1 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:13.7
occ:0.60
 O A:HOH593 2.0 15.1 0.6
O A:HOH485 2.1 14.6 0.6
O A:HOH618 2.1 16.9 0.6
O A:HOH423 2.1 11.9 0.6
O A:HOH508 2.1 17.7 0.6
O A:HOH479 2.1 18.0 0.6
O A:HOH321 4.0 10.2 1.0
O A:HOH337 4.6 15.2 1.0

Magnesium binding site 2 out of 9 in 4lqh

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Magnesium binding site 2 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:10.2
occ:0.50
 O A:HOH628 1.9 12.4 0.5
OE2 A:GLU136 1.9 11.8 0.5
OE1 A:GLN137 2.0 13.4 0.5
OE1 A:GLN137 2.0 9.0 0.5
O A:HOH627 2.1 10.2 0.5
O A:HOH610 2.1 10.9 0.5
O A:HOH365 2.2 11.0 0.5
MG A:MG209 2.4 15.8 0.5
CD A:GLU136 2.9 11.9 0.5
CD A:GLN137 3.0 9.0 0.5
CD A:GLN137 3.2 13.1 0.5
OE1 A:GLU136 3.2 11.7 0.5
OD2 A:ASP140 3.5 13.9 0.5
NE2 A:GLN137 3.5 9.0 0.5
ND1 A:HIS61 3.9 17.9 0.7
NE2 A:GLN137 3.9 13.2 0.5
CE1 A:HIS61 3.9 17.7 0.7
OE1 A:GLU103 4.0 8.9 0.5
OE2 A:GLU58 4.1 17.8 1.0
OE1 A:GLU58 4.1 15.4 1.0
CB A:GLN137 4.2 12.7 0.5
CA A:GLN137 4.2 12.2 0.5
OE1 A:GLU103 4.2 11.7 0.5
CG A:GLU136 4.2 11.9 0.5
CG A:GLN137 4.2 13.0 0.5
CA A:GLN137 4.3 9.2 0.5
OD2 A:ASP140 4.3 9.0 0.5
CG A:GLN137 4.3 9.1 0.5
CB A:GLN137 4.4 9.2 0.5
OE2 A:GLU57 4.4 10.9 0.5
N A:GLN137 4.5 11.0 1.0
OE2 A:GLU23 4.5 9.3 0.5
CD A:GLU58 4.5 14.4 1.0
CG A:ASP140 4.6 13.5 0.5
MG A:MG203 4.8 11.1 0.5
O A:TYR133 4.9 12.1 1.0
C A:GLU136 4.9 11.6 1.0
O A:HOH433 4.9 21.3 1.0
CG1 A:VAL106 4.9 9.6 1.0

Magnesium binding site 3 out of 9 in 4lqh

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Magnesium binding site 3 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:11.1
occ:0.50
 O A:HOH623 2.0 13.6 0.5
OE2 A:GLU57 2.0 10.9 0.5
OE1 A:GLU136 2.1 11.7 0.5
O A:HOH629 2.1 12.4 0.5
O A:HOH606 2.1 9.8 0.5
OD2 A:ASP140 2.1 9.0 0.5
OD1 A:ASP140 2.6 13.6 0.5
OD2 A:ASP140 3.0 13.9 0.5
CD A:GLU57 3.0 10.9 0.5
CG A:ASP140 3.1 9.1 0.5
CG A:ASP140 3.1 13.5 0.5
CD A:GLU136 3.3 11.9 0.5
OD1 A:ASP140 3.4 9.3 0.5
OE1 A:GLU57 3.4 11.1 0.5
O A:GLU136 3.8 11.9 1.0
CB A:GLU136 3.9 14.3 1.0
O A:HOH628 3.9 12.4 0.5
O A:HOH627 4.1 10.2 0.5
CG A:GLU136 4.1 11.9 0.5
OE2 A:GLU136 4.2 11.8 0.5
C A:GLU136 4.3 11.6 1.0
CG A:GLU57 4.3 10.8 0.5
CB A:ASP140 4.4 9.1 0.5
O A:HOH592 4.4 45.5 1.0
O A:HOH537 4.4 47.8 1.0
CA A:GLU136 4.5 12.7 1.0
CB A:ASP140 4.6 13.2 0.5
MG A:MG209 4.7 15.8 0.5
O A:HOH506 4.7 67.3 1.0
MG A:MG202 4.8 10.2 0.5
NH2 A:ARG143 4.8 17.3 0.5
CE1 A:HIS61 4.9 17.7 0.7
O A:HOH433 4.9 21.3 1.0

Magnesium binding site 4 out of 9 in 4lqh

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Magnesium binding site 4 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:13.4
occ:0.70
 O A:HOH395 2.0 13.9 0.7
O A:HOH603 2.0 17.8 0.7
O A:HOH617 2.1 16.3 0.7
O A:HOH355 2.1 10.1 0.7
O A:HOH404 2.1 17.0 0.7
OG A:SER10 2.1 12.0 1.0
CB A:SER10 3.2 10.6 1.0
CA A:SER10 3.9 9.2 1.0
O A:HOH575 4.0 33.5 1.0
O A:SER10 4.1 8.9 1.0
OE1 A:GLU13 4.2 9.7 1.0
O A:HOH470 4.3 30.2 1.0
O A:HOH334 4.3 15.9 1.0
C A:SER10 4.4 8.8 1.0
O A:HOH391 4.4 14.2 1.0
O A:HOH605 4.4 38.7 1.0
O A:HOH607 4.5 34.0 1.0
CD A:GLU13 4.6 8.5 1.0
O A:HOH514 4.6 33.8 1.0

Magnesium binding site 5 out of 9 in 4lqh

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Magnesium binding site 5 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:5.9
occ:0.40
 O A:HOH431 1.9 11.7 0.8
O A:HOH349 1.9 10.0 0.8
O A:HOH359 2.0 8.6 0.4
O A:HOH438 2.1 9.5 0.4
OD2 A:ASP80 4.0 8.2 1.0
O A:HOH420 4.2 14.0 1.0
OD1 A:ASP80 4.2 6.9 1.0
CG A:ASP80 4.5 7.0 1.0
CL A:CL224 4.5 14.5 0.8

Magnesium binding site 6 out of 9 in 4lqh

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Magnesium binding site 6 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:13.0
occ:0.70
 O A:HOH476 2.0 16.9 0.7
O A:HOH614 2.1 16.3 0.7
O A:HOH399 2.1 13.9 0.7
O A:HOH406 2.1 17.0 0.7
O A:HOH616 2.1 14.7 0.7
O A:HOH394 2.1 14.5 0.7
OD2 A:ASP127 4.0 14.5 1.0
OD1 A:ASP127 4.4 14.9 1.0
O A:HOH540 4.6 43.8 1.0
O A:HOH498 4.6 30.1 1.0
CG A:ASP127 4.7 13.0 1.0
OG A:SER131 4.7 12.0 0.5
O A:HOH549 4.8 31.7 1.0
OG A:SER131 4.9 15.0 0.5

Magnesium binding site 7 out of 9 in 4lqh

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Magnesium binding site 7 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:13.4
occ:0.20
 O A:HOH632 1.6 16.2 0.6
O A:HOH583 2.2 21.6 0.6
OD1 A:ASP127 3.7 14.9 1.0
OE1 A:GLU130 3.7 14.2 0.4
OG A:SER131 4.2 12.0 0.5
O A:HOH498 4.2 30.1 1.0
OE1 A:GLU130 4.3 9.7 0.6
CG A:ASP127 4.8 13.0 1.0
O A:HOH394 4.8 14.5 0.7
CB A:GLU130 4.9 13.3 0.4
CD A:GLU130 4.9 13.7 0.4
CB A:GLU130 5.0 9.9 0.6

Magnesium binding site 8 out of 9 in 4lqh

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Magnesium binding site 8 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:9.1
occ:0.30
 O A:HOH384 2.1 11.4 0.9
O A:HOH345 2.1 10.2 0.9
OE2 A:GLU130 3.8 13.8 0.4
OE2 A:GLU130 3.9 9.7 0.6
O A:HOH499 4.1 16.3 0.5
OE1 A:GLU130 4.3 9.7 0.6
O A:HOH419 4.3 12.9 1.0
O A:HOH381 4.3 18.5 1.0
OE1 A:GLU130 4.4 14.2 0.4
CD A:GLU130 4.5 13.7 0.4
CD A:GLU130 4.5 9.8 0.6

Magnesium binding site 9 out of 9 in 4lqh

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Magnesium binding site 9 out of 9 in the High Resolution Structure of Native 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 High Resolution Structure of Native Frog M Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:15.8
occ:0.50
 O A:HOH627 1.4 10.2 0.5
OE1 A:GLU103 2.0 8.9 0.5
O A:HOH365 2.0 11.0 0.5
OE1 A:GLU103 2.0 11.7 0.5
OD2 A:ASP140 2.2 13.9 0.5
OE1 A:GLN137 2.4 13.4 0.5
MG A:MG202 2.4 10.2 0.5
O A:HOH628 2.6 12.4 0.5
CD A:GLU103 2.8 8.9 0.5
CD A:GLU103 3.0 11.5 0.5
OE2 A:GLU103 3.0 8.9 0.5
O A:HOH433 3.1 21.3 1.0
CD A:GLN137 3.2 13.1 0.5
OD2 A:ASP140 3.3 9.0 0.5
CG A:ASP140 3.3 13.5 0.5
OE2 A:GLU103 3.3 11.9 0.5
OE1 A:GLN137 3.4 9.0 0.5
NE2 A:GLN137 3.4 9.0 0.5
NE2 A:GLN137 3.4 13.2 0.5
OE2 A:GLU58 3.6 17.8 1.0
CD A:GLN137 3.6 9.0 0.5
CB A:ASP140 3.7 13.2 0.5
CB A:ASP140 3.8 9.1 0.5
OE2 A:GLU136 3.9 11.8 0.5
CG A:ASP140 3.9 9.1 0.5
OE1 A:GLU136 4.0 11.7 0.5
OE1 A:GLU58 4.1 15.4 1.0
CD A:GLU58 4.2 14.4 1.0
CG A:GLU103 4.2 8.8 0.5
O A:HOH610 4.2 10.9 0.5
CD A:GLU136 4.4 11.9 0.5
CG A:GLU103 4.4 11.2 0.5
OD1 A:ASP140 4.4 13.6 0.5
OE2 A:GLU57 4.4 10.9 0.5
CG A:GLN137 4.6 13.0 0.5
CA A:GLN137 4.6 12.2 0.5
MG A:MG203 4.7 11.1 0.5
CA A:GLN137 4.7 9.2 0.5
CB A:GLU103 4.7 8.8 0.5
CG A:GLN137 4.8 9.1 0.5
CB A:GLU103 5.0 11.0 0.5
CB A:GLN137 5.0 12.7 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 Dec 14 19:10:23 2020

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