Magnesium in PDB 5xhm: Crystal Structure of Frog M-Ferritin D40A Mutant

Enzymatic activity of Crystal Structure of Frog M-Ferritin D40A Mutant

All present enzymatic activity of Crystal Structure of Frog M-Ferritin D40A Mutant:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Frog M-Ferritin D40A Mutant, PDB code: 5xhm was solved by M.K.Jagdev, D.Vasudevan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.98 / 1.70
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.170, 184.170, 184.170, 90.00, 90.00, 90.00
R / Rfree (%) 15.6 / 18.7

Other elements in 5xhm:

The structure of Crystal Structure of Frog M-Ferritin D40A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Frog M-Ferritin D40A Mutant (pdb code 5xhm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Frog M-Ferritin D40A Mutant, PDB code: 5xhm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 5xhm

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Magnesium binding site 1 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:26.0
occ:0.97
 OE2 A:GLU57 2.1 24.6 1.0
O A:HOH318 2.1 25.0 1.0
O A:HOH441 2.1 25.6 1.0
O A:HOH429 2.1 19.7 1.0
OE1 A:GLU136 2.1 27.0 1.0
OD2 A:ASP140 2.2 24.2 1.0
CG A:ASP140 2.9 17.9 1.0
CD A:GLU57 3.1 30.0 1.0
OD1 A:ASP140 3.1 22.3 1.0
CD A:GLU136 3.4 34.9 1.0
OE1 A:GLU57 3.4 27.1 1.0
O A:GLU136 3.8 16.4 1.0
CB A:GLU136 3.8 22.5 1.0
O A:HOH311 4.0 24.1 1.0
CG A:GLU136 4.1 24.1 1.0
O A:HOH313 4.2 27.4 1.0
C A:GLU136 4.3 15.6 1.0
OE2 A:GLU136 4.3 29.7 1.0
CB A:ASP140 4.3 15.4 1.0
CG A:GLU57 4.4 21.3 1.0
CA A:GLU136 4.5 17.0 1.0
O A:HOH523 4.5 36.6 1.0
MG A:MG207 4.7 24.4 0.9
CE1 A:HIS61 4.8 31.8 1.0

Magnesium binding site 2 out of 10 in 5xhm

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Magnesium binding site 2 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:22.4
occ:0.97
 O A:HOH398 2.1 17.5 1.0
O A:HOH527 2.1 22.7 1.0
O A:HOH465 2.1 24.3 1.0
O A:HOH439 2.1 21.6 1.0
O A:HOH405 2.1 15.9 1.0
OG A:SER10 2.1 18.4 1.0
CB A:SER10 3.2 14.0 1.0
CA A:SER10 3.9 12.5 1.0
O A:SER10 4.0 12.3 1.0
O A:HOH494 4.1 41.0 1.0
OE1 A:GLU13 4.2 14.3 1.0
O A:HOH319 4.2 18.0 1.0
C A:SER10 4.3 12.4 1.0
O A:HOH504 4.3 30.6 1.0
O A:HOH563 4.5 37.0 1.0
O A:HOH483 4.6 15.1 1.0
CD A:GLU13 4.6 13.3 1.0
OE2 A:GLU13 5.0 13.3 1.0

Magnesium binding site 3 out of 10 in 5xhm

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Magnesium binding site 3 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:20.3
occ:1.00
 O A:HOH529 2.1 22.7 1.0
O A:HOH364 2.1 23.2 1.0
O A:HOH376 2.1 22.1 1.0
OD2 A:ASP127 4.0 19.1 1.0
O A:HOH500 4.3 40.2 1.0
OD1 A:ASP127 4.4 17.4 1.0
CG A:ASP127 4.6 15.3 1.0
O A:HOH421 4.6 33.7 1.0
OG A:SER131 4.7 25.6 1.0
O A:HOH524 4.8 35.9 1.0

Magnesium binding site 4 out of 10 in 5xhm

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Magnesium binding site 4 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:12.9
occ:0.33
 O A:HOH343 2.1 11.8 1.0
O A:HOH488 2.1 12.2 1.0
OE2 A:GLU130 3.9 14.4 1.0
OE1 A:GLU130 4.3 18.4 1.0
O A:HOH428 4.3 17.6 1.0
O A:HOH532 4.3 14.0 1.0
CD A:GLU130 4.5 16.8 1.0

Magnesium binding site 5 out of 10 in 5xhm

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Magnesium binding site 5 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:24.2
occ:0.33
 O A:HOH325 1.9 31.0 1.0
O A:HOH312 2.1 33.5 1.0
OD1 A:ASP127 3.9 17.4 1.0
OE1 A:GLU130 4.0 18.4 1.0
OG A:SER131 4.3 25.6 1.0
O A:HOH421 4.4 33.7 1.0
CD A:GLU130 4.8 16.8 1.0
CB A:GLU130 4.8 13.9 1.0
CG A:ASP127 5.0 15.3 1.0
O A:HOH376 5.0 22.1 1.0

Magnesium binding site 6 out of 10 in 5xhm

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Magnesium binding site 6 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:9.6
occ:0.33
 O A:HOH496 2.1 16.6 1.0
O A:HOH352 4.2 16.9 1.0
O A:HOH538 4.5 22.2 1.0
CE A:LYS83 4.6 19.4 0.8
NZ A:LYS82 4.6 27.6 1.0
CE A:LYS83 4.8 7.7 0.2
CD A:LYS82 4.8 18.3 1.0

Magnesium binding site 7 out of 10 in 5xhm

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Magnesium binding site 7 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:24.4
occ:0.90
 O A:HOH311 1.9 24.1 1.0
OE2 A:GLU136 2.0 29.7 1.0
O A:HOH353 2.1 20.6 1.0
O A:HOH313 2.1 27.4 1.0
OE1 A:GLN137 2.2 23.0 1.0
O A:HOH357 2.2 22.3 1.0
CD A:GLU136 2.8 34.9 1.0
OE1 A:GLU136 3.1 27.0 1.0
CD A:GLN137 3.2 22.5 1.0
ND1 A:HIS61 3.7 30.9 1.0
NE2 A:GLN137 3.7 18.7 1.0
CE1 A:HIS61 3.8 31.8 1.0
OE2 A:GLU58 3.8 26.7 1.0
OE1 A:GLU58 4.0 16.4 1.0
OD2 A:ASP140 4.0 24.2 1.0
OE1 A:GLU103 4.0 17.9 1.0
CG A:GLU136 4.3 24.1 1.0
OE2 A:GLU57 4.3 24.6 1.0
CA A:GLN137 4.3 14.3 1.0
CD A:GLU58 4.4 20.7 1.0
CG A:GLN137 4.4 18.0 1.0
N A:GLN137 4.5 13.4 1.0
CB A:GLN137 4.5 16.0 1.0
OE2 A:GLU23 4.6 22.5 1.0
MG A:MG201 4.7 26.0 1.0
O A:HOH367 4.7 22.6 1.0
C A:GLU136 4.9 15.6 1.0
O A:TYR133 4.9 13.3 1.0
CG1 A:VAL106 5.0 14.4 1.0

Magnesium binding site 8 out of 10 in 5xhm

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Magnesium binding site 8 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:56.2
occ:0.33
 O A:HOH552 2.8 16.5 1.0
O A:HOH564 3.5 33.2 1.0
O A:HOH428 4.2 17.6 1.0
CG2 A:THR118 4.4 12.9 1.0
O A:HOH407 4.7 18.6 1.0
O A:HOH537 4.8 22.5 1.0

Magnesium binding site 9 out of 10 in 5xhm

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Magnesium binding site 9 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:11.9
occ:0.25
 CE1 A:HIS169 3.7 20.5 1.0
ND1 A:HIS169 4.5 18.5 1.0
NE2 A:HIS169 4.6 14.9 1.0
MG A:MG210 4.9 9.4 0.2

Magnesium binding site 10 out of 10 in 5xhm

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Magnesium binding site 10 out of 10 in the Crystal Structure of Frog M-Ferritin D40A Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of Frog M-Ferritin D40A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:9.4
occ:0.25
 NE2 A:HIS169 3.2 14.9 1.0
CE1 A:HIS169 3.9 20.5 1.0
CD2 A:LEU165 3.9 14.0 1.0
CD2 A:HIS169 4.3 14.1 1.0
MG A:MG209 4.9 11.9 0.2

Reference:

B.Subhadarshanee, A.Mohanty, M.K.Jagdev, D.Vasudevan, R.K.Behera. Surface Charge Dependent Separation of Modified and Hybrid Ferritin in Native Page: Impact of Lysine 104 Biochim. Biophys. Acta V.1865 1267 2017.
ISSN: ISSN 0006-3002
PubMed: 28739445
DOI: 10.1016/J.BBAPAP.2017.07.012
Page generated: Mon Dec 14 22:08:49 2020

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