Magnesium in PDB 8pp4: Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)

Enzymatic activity of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)

All present enzymatic activity of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition):
1.16.3.1;

Protein crystallography data

The structure of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition), PDB code: 8pp4 was solved by L.Lang, T.Beck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.36 / 2.00
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 127.039, 127.039, 176.961, 90, 90, 90
R / Rfree (%) 18.1 / 22.1

Other elements in 8pp4:

The structure of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) also contains other interesting chemical elements:

Iron (Fe) 14 atoms
Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) (pdb code 8pp4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition), PDB code: 8pp4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8pp4

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Magnesium binding site 1 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:32.4
occ:1.00
 O B:HOH321 2.0 30.5 1.0
O B:HOH399 2.1 28.8 1.0
O C:HOH349 2.2 32.0 1.0
O C:HOH389 2.2 30.4 1.0
OE2 B:GLU134 3.8 36.4 1.0
OE2 C:GLU134 3.9 30.5 1.0
O C:HOH301 4.2 52.8 1.0
O B:HOH346 4.2 34.2 1.0
OE1 B:GLU134 4.3 38.9 1.0
O C:HOH324 4.3 29.7 1.0
OE1 C:GLU134 4.3 34.3 1.0
O B:HOH412 4.3 30.7 1.0
O C:HOH401 4.3 26.6 1.0
CD B:GLU134 4.5 32.7 1.0
HB3 B:CYS130 4.5 30.2 1.0
CD C:GLU134 4.5 34.6 1.0
HB3 C:CYS130 4.6 28.2 1.0
HE1 B:HIS118 4.8 27.7 1.0
HE1 C:HIS118 4.8 27.6 1.0
HE2 B:HIS118 4.8 28.4 0.0
HE2 C:HIS118 4.9 27.4 0.0

Magnesium binding site 2 out of 7 in 8pp4

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Magnesium binding site 2 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:32.1
occ:1.00
 O D:HOH389 2.1 30.3 1.0
O E:HOH381 2.1 28.8 1.0
O D:HOH320 2.1 33.3 1.0
O E:HOH346 2.1 31.3 1.0
O F:HOH381 2.1 29.9 1.0
O F:HOH325 2.2 35.0 1.0
O F:HOH317 3.5 61.7 1.0
OE2 D:GLU134 3.9 33.1 1.0
O F:HOH357 3.9 66.1 1.0
O D:HOH405 4.0 28.3 1.0
OE2 F:GLU134 4.0 36.1 1.0
OE2 E:GLU134 4.0 33.1 1.0
O E:HOH393 4.1 37.1 1.0
O F:HOH389 4.1 35.0 1.0
O F:HOH316 4.2 35.3 1.0
O E:HOH309 4.2 33.7 1.0
OE1 E:GLU134 4.3 45.1 1.0
OE1 D:GLU134 4.4 36.8 1.0
OE1 F:GLU134 4.4 36.9 1.0
HB3 D:CYS130 4.5 33.2 1.0
HB3 E:CYS130 4.6 31.2 1.0
HE1 D:HIS118 4.6 27.9 1.0
CD D:GLU134 4.6 33.4 1.0
HB3 F:CYS130 4.6 29.4 1.0
CD E:GLU134 4.6 37.5 1.0
CD F:GLU134 4.6 33.3 1.0
HE1 E:HIS118 4.7 30.7 1.0
HE2 F:HIS118 4.8 32.4 0.0
HE2 D:HIS118 4.8 27.9 0.0
HE1 F:HIS118 4.8 30.9 1.0
HE2 E:HIS118 4.9 28.7 0.0

Magnesium binding site 3 out of 7 in 8pp4

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Magnesium binding site 3 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:73.8
occ:1.00
 O E:HOH301 2.2 45.7 1.0
O F:HOH301 2.2 46.9 1.0
O D:HOH344 2.5 45.9 1.0
O F:HOH319 2.6 50.7 1.0
OE1 E:GLU134 2.8 45.1 1.0
OD1 D:ASP131 2.9 39.5 1.0
HA D:ASP131 3.2 31.2 1.0
OE1 D:GLU134 3.4 36.8 1.0
HB2 D:ASP131 3.5 35.4 1.0
O F:HOH314 3.5 45.4 1.0
HB3 E:GLU134 3.8 33.2 1.0
CG D:ASP131 3.8 38.8 1.0
HB2 E:GLU134 3.8 33.2 1.0
HB2 D:GLU134 3.9 32.4 1.0
CB D:ASP131 3.9 36.4 1.0
OE1 F:GLU134 3.9 36.9 1.0
CD E:GLU134 3.9 37.5 1.0
CA D:ASP131 3.9 30.4 1.0
CB E:GLU134 4.2 32.7 1.0
OD1 F:ASP131 4.2 34.0 1.0
CD D:GLU134 4.3 33.4 1.0
O D:HOH320 4.3 33.3 1.0
HA E:ASP131 4.3 32.0 1.0
OD1 E:ASP131 4.4 32.8 1.0
OG1 D:THR135 4.5 33.2 1.0
HB3 D:GLU134 4.5 32.4 1.0
HG1 D:THR135 4.5 33.8 0.0
CB D:GLU134 4.6 32.9 1.0
CG E:GLU134 4.6 37.0 1.0
O D:ASP131 4.7 28.8 1.0
OE2 D:GLU134 4.8 33.1 1.0
OE2 E:GLU134 4.8 33.1 1.0
C D:ASP131 4.8 28.8 1.0
HB3 D:ASP131 4.9 35.4 1.0
HA F:ASP131 4.9 29.7 1.0
O E:HOH346 4.9 31.3 1.0
O F:HOH325 4.9 35.0 1.0
OD2 D:ASP131 5.0 46.7 1.0
N D:ASP131 5.0 30.7 1.0
O E:HOH391 5.0 36.5 1.0
HB2 F:ASP131 5.0 31.0 1.0

Magnesium binding site 4 out of 7 in 8pp4

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Magnesium binding site 4 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg202

b:40.8
occ:1.00
 O H:HOH306 2.1 40.5 1.0
O L:HOH329 2.1 36.7 1.0
O L:HOH321 2.2 42.9 1.0
O H:HOH344 2.2 38.2 1.0
OE2 H:GLU134 3.7 42.7 1.0
OE2 L:GLU134 3.8 44.0 1.0
O H:HOH301 4.2 39.2 1.0
OE1 H:GLU134 4.3 58.1 1.0
OE1 L:GLU134 4.3 52.8 1.0
CD H:GLU134 4.4 46.8 1.0
CD L:GLU134 4.5 47.9 1.0
HB3 H:CYS130 4.5 39.5 1.0
HB3 L:CYS130 4.6 37.0 1.0
HE1 H:HIS118 4.8 34.1 1.0
HE1 L:HIS118 4.8 44.0 1.0
HE2 H:HIS118 4.9 33.8 0.0

Magnesium binding site 5 out of 7 in 8pp4

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Magnesium binding site 5 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg203

b:64.1
occ:1.00
 OE1 H:GLU134 2.9 58.1 1.0
OD1 L:ASP131 3.2 38.7 1.0
OE1 L:GLU134 3.3 52.8 1.0
OD1 H:ASP131 3.4 44.5 1.0
HA H:ASP131 4.1 36.6 1.0
HA L:ASP131 4.1 39.6 1.0
CD H:GLU134 4.2 46.8 1.0
HB3 H:GLU134 4.2 41.9 1.0
HB2 H:GLU134 4.2 41.9 1.0
HB2 L:GLU134 4.3 40.3 1.0
HB3 L:GLU134 4.3 40.3 1.0
CG L:ASP131 4.4 38.5 1.0
CD L:GLU134 4.4 47.9 1.0
HB2 L:ASP131 4.5 39.1 1.0
CG H:ASP131 4.6 43.7 1.0
CB H:GLU134 4.6 40.8 1.0
CB L:GLU134 4.7 41.1 1.0
OG1 H:THR135 4.7 38.4 1.0
HB2 H:ASP131 4.8 39.5 1.0
CB L:ASP131 4.8 38.4 1.0
O H:HOH306 4.8 40.5 1.0
HG1 H:THR135 4.9 38.6 0.0
OG1 L:THR135 4.9 40.3 1.0
CA L:ASP131 4.9 41.2 1.0
CG H:GLU134 4.9 47.1 1.0
O L:HOH321 5.0 42.9 1.0
CA H:ASP131 5.0 36.4 1.0

Magnesium binding site 6 out of 7 in 8pp4

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Magnesium binding site 6 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg202

b:36.7
occ:1.00
 O I:HOH348 1.8 41.7 1.0
O J:HOH347 2.0 35.3 1.0
O I:HOH317 2.1 34.9 1.0
O J:HOH309 2.2 37.0 1.0
OE2 J:GLU134 3.7 43.0 1.0
OE2 I:GLU134 3.8 40.8 1.0
OE1 J:GLU134 4.1 47.9 1.0
OE1 I:GLU134 4.1 47.2 1.0
CD J:GLU134 4.3 43.5 1.0
CD I:GLU134 4.4 38.5 1.0
O I:HOH333 4.4 37.7 1.0
HB3 I:CYS130 4.4 39.0 1.0
HB3 J:CYS130 4.5 36.4 1.0
HE2 I:HIS118 4.8 39.8 0.0
HE1 J:HIS118 4.8 37.4 1.0
HE2 J:HIS118 4.9 38.4 0.0

Magnesium binding site 7 out of 7 in 8pp4

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Magnesium binding site 7 out of 7 in the Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Binary Crystal Structure of Positively Supercharged Ferritin Variant Ftn(Pos) and Reduced Charge Negatively Supercharged Ferritin Variant Ftn(Neg)-M3 (Mg Formate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg202

b:64.6
occ:1.00
 OD1 I:ASP131 2.9 49.0 1.0
OE1 J:GLU134 3.3 47.9 1.0
OD1 J:ASP131 3.4 41.4 1.0
OE1 I:GLU134 3.7 47.2 1.0
HA I:ASP131 4.2 35.9 1.0
CG I:ASP131 4.2 40.8 1.0
HA J:ASP131 4.2 33.6 1.0
HB3 J:GLU134 4.3 39.6 1.0
HB2 I:GLU134 4.4 38.5 1.0
HB2 J:GLU134 4.4 39.6 1.0
CD J:GLU134 4.5 43.5 1.0
CG J:ASP131 4.6 40.7 1.0
HB3 I:GLU134 4.6 38.6 1.0
CD I:GLU134 4.7 38.5 1.0
HB2 I:ASP131 4.7 37.3 1.0
CB J:GLU134 4.8 38.8 1.0
CB I:ASP131 4.9 36.5 1.0
HB2 J:ASP131 4.9 36.1 1.0
CA I:ASP131 5.0 36.0 1.0
CB I:GLU134 5.0 38.9 1.0

Reference:

L.Lang, H.Bohler, H.Wagler, T.Beck. Assembly Requirements For the Construction of Large-Scale Binary Protein Structures. Biomacromolecules 2023.
ISSN: ESSN 1526-4602
PubMed: 38059469
DOI: 10.1021/ACS.BIOMAC.3C00891
Page generated: Fri Oct 4 16:09:13 2024

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