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Magnesium in PDB 5xhi: Crystal Structure of Frog M-Ferritin D38A Mutant

Enzymatic activity of Crystal Structure of Frog M-Ferritin D38A Mutant

All present enzymatic activity of Crystal Structure of Frog M-Ferritin D38A Mutant:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of Frog M-Ferritin D38A Mutant, PDB code: 5xhi 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) 31.12 / 1.26
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 184.090, 184.090, 184.090, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 15.3

Other elements in 5xhi:

The structure of Crystal Structure of Frog M-Ferritin D38A Mutant also contains other interesting chemical elements:

Chlorine (Cl) 27 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Frog M-Ferritin D38A Mutant (pdb code 5xhi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the Crystal Structure of Frog M-Ferritin D38A Mutant, PDB code: 5xhi:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 5xhi

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Magnesium binding site 1 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:11.3
occ:0.75
 OE2 A:GLU57 2.0 11.9 0.8
OE1 A:GLU136 2.0 7.5 0.5
O A:HOH423 2.0 16.6 1.0
OD2 A:ASP140 2.1 13.8 1.0
O A:HOH327 2.1 16.9 1.0
O A:HOH395 2.1 13.8 1.0
CG A:ASP140 3.0 11.2 1.0
CD A:GLU57 3.0 10.5 0.5
CD A:GLU136 3.3 8.0 0.5
OD1 A:ASP140 3.3 15.9 1.0
OE1 A:GLU57 3.4 9.5 0.5
O A:GLU136 3.8 10.0 1.0
CB A:GLU136 3.9 12.7 1.0
O A:HOH317 3.9 15.7 1.0
O A:HOH383 4.0 15.3 1.0
CG A:GLU136 4.1 13.5 1.0
O A:HOH523 4.2 38.9 1.0
OE2 A:GLU136 4.2 7.8 0.5
C A:GLU136 4.3 9.5 1.0
CG A:GLU57 4.3 12.7 1.0
CB A:ASP140 4.4 10.3 1.0
CA A:GLU136 4.5 10.8 1.0
O A:HOH482 4.5 37.1 1.0
O A:HOH462 4.6 34.0 1.0
CE1 A:HIS61 4.8 34.1 1.0
MG A:MG209 4.8 6.5 0.5
O A:HOH348 4.9 19.0 1.0

Magnesium binding site 2 out of 11 in 5xhi

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Magnesium binding site 2 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:13.4
occ:0.75
 O A:HOH507 2.0 23.6 1.0
O A:HOH351 2.0 15.4 1.0
O A:HOH428 2.0 20.6 1.0
O A:HOH430 2.1 21.9 1.0
OG A:SER10 2.1 12.5 1.0
O A:HOH406 2.1 12.2 1.0
CB A:SER10 3.2 10.6 1.0
CA A:SER10 3.9 8.2 1.0
O A:SER10 4.1 8.0 1.0
OE1 A:GLU13 4.2 9.6 1.0
O A:HOH483 4.3 33.3 1.0
O A:HOH336 4.3 16.5 1.0
O A:HOH487 4.3 32.7 1.0
C A:SER10 4.4 7.3 1.0
O A:HOH475 4.4 14.0 1.0
O A:HOH561 4.6 37.9 1.0
CD A:GLU13 4.7 7.0 1.0

Magnesium binding site 3 out of 11 in 5xhi

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Magnesium binding site 3 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:10.6
occ:0.75
 O A:HOH344 2.0 17.5 1.0
OD2 A:ASP127 4.0 13.2 1.0
O A:HOH533 4.2 27.9 1.0
OD1 A:ASP127 4.4 13.3 1.0
O A:HOH484 4.4 66.7 1.0
CG A:ASP127 4.6 11.8 1.0
O A:HOH369 4.7 26.3 1.0
OG A:SER131 4.7 13.5 0.7
O A:HOH519 4.8 31.6 1.0
OG A:SER131 4.9 14.3 0.3

Magnesium binding site 4 out of 11 in 5xhi

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Magnesium binding site 4 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:6.4
occ:0.25
 O A:HOH563 2.1 10.7 1.0
O A:HOH339 2.1 9.5 1.0
OE2 A:GLU130 3.9 10.1 1.0
OE1 A:GLU130 4.3 14.7 1.0
O A:HOH510 4.3 10.8 1.0
O A:HOH567 4.3 14.0 1.0
CD A:GLU130 4.5 11.1 1.0

Magnesium binding site 5 out of 11 in 5xhi

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Magnesium binding site 5 out of 11 in the Crystal Structure of Frog M-Ferritin D38A Mutant


Mono view


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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:17.3
occ:0.70
 O A:HOH546 1.8 23.6 1.0
O A:HOH566 1.9 29.4 1.0
O A:HOH505 2.1 16.0 1.0
O A:HOH557 2.1 26.8 1.0
O A:HOH410 2.1 32.6 1.0
O A:HOH508 2.5 35.7 1.0
O A:HOH441 3.9 9.8 1.0
O A:HOH503 4.4 29.6 1.0
O A:VAL1 4.7 18.9 1.0

Magnesium binding site 6 out of 11 in 5xhi

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Magnesium binding site 6 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:11.5
occ:0.25
 O A:HOH343 1.8 28.5 1.0
O A:HOH310 2.1 31.8 1.0
OD1 A:ASP127 3.8 13.3 1.0
OG A:SER131 4.1 13.5 0.7
OE1 A:GLU130 4.2 14.7 1.0
O A:HOH369 4.2 26.3 1.0
CB A:GLU130 4.8 9.1 1.0
CG A:ASP127 4.9 11.8 1.0
O A:HOH490 4.9 14.9 1.0
CD A:GLU130 5.0 11.1 1.0

Magnesium binding site 7 out of 11 in 5xhi

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Magnesium binding site 7 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:6.9
occ:0.35
 CD A:LYS82 4.3 9.8 0.3
O A:HOH558 4.4 16.0 1.0
CE A:LYS83 4.5 10.2 0.7
CE A:LYS82 4.6 8.3 0.3
NZ A:LYS82 4.8 15.7 0.7
CE A:LYS83 4.8 5.5 0.3
O A:HOH456 4.9 58.6 1.0
CD A:LYS82 4.9 10.4 0.7

Magnesium binding site 8 out of 11 in 5xhi

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Magnesium binding site 8 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:13.9
occ:0.15
 O A:HOH538 2.9 15.0 1.0
O A:HOH567 4.2 14.0 1.0
CG2 A:THR118 4.4 11.0 1.0
O A:HOH539 4.7 17.6 1.0
CL A:CL230 4.8 18.4 0.7

Magnesium binding site 9 out of 11 in 5xhi

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Magnesium binding site 9 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:6.5
occ:0.50
 O A:HOH317 2.0 15.7 1.0
OE1 A:GLN137 2.0 12.6 0.9
OE2 A:GLU136 2.0 7.8 0.5
O A:HOH389 2.1 15.3 1.0
O A:HOH383 2.1 15.3 1.0
O A:HOH332 2.2 14.5 1.0
CD A:GLU136 3.0 8.0 0.5
CD A:GLN137 3.0 12.2 1.0
OE1 A:GLU136 3.3 7.5 0.5
NE2 A:GLN137 3.6 12.5 1.0
ND1 A:HIS61 3.9 26.9 1.0
OE1 A:GLU103 4.0 12.2 1.0
CE1 A:HIS61 4.0 34.1 1.0
OE1 A:GLU58 4.0 13.2 1.0
OE2 A:GLU58 4.0 17.4 1.0
CA A:GLN137 4.2 7.8 1.0
CG A:GLN137 4.2 11.0 1.0
OD2 A:ASP140 4.3 13.8 1.0
CB A:GLN137 4.3 11.2 1.0
CG A:GLU136 4.4 13.5 1.0
OE2 A:GLU57 4.5 11.9 0.8
CD A:GLU58 4.5 12.5 1.0
N A:GLN137 4.5 9.1 1.0
OE2 A:GLU23 4.6 13.6 1.0
O A:HOH348 4.8 19.0 1.0
MG A:MG201 4.8 11.3 0.8
CG1 A:VAL106 4.9 9.1 1.0
C A:GLU136 4.9 9.5 1.0

Magnesium binding site 10 out of 11 in 5xhi

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Magnesium binding site 10 out of 11 in the Crystal Structure of Frog M-Ferritin D38A 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 D38A Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:0.7
occ:0.25
 NE2 A:HIS169 3.2 10.2 1.0
CE1 A:HIS169 3.9 12.1 1.0
CD2 A:LEU165 3.9 11.9 1.0
CD2 A:HIS169 4.3 8.2 1.0
MG A:MG211 4.9 0.0 0.3

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 Sep 30 09:22:21 2024

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