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Magnesium in PDB 5jkk: Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin

Enzymatic activity of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin

All present enzymatic activity of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin:
1.16.3.1;

Protein crystallography data

The structure of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin, PDB code: 5jkk was solved by M.Kuenzle, T.Beck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 1.60
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 180.980, 180.980, 180.980, 90.00, 90.00, 90.00
R / Rfree (%) 12.4 / 14.3

Other elements in 5jkk:

The structure of Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin also contains other interesting chemical elements:

Iron (Fe) 10 atoms
Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin (pdb code 5jkk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin, PDB code: 5jkk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 5jkk

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Magnesium binding site 1 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:12.7
occ:0.50
 O A:HOH347 1.9 22.2 0.5
O A:HOH407 2.0 34.9 1.0
O A:HOH503 2.1 15.7 0.5
OE1 A:GLN58 2.1 17.6 1.0
O A:HOH315 2.1 14.1 0.5
CD A:GLN58 3.3 16.9 1.0
O A:HOH441 3.9 33.2 1.0
NE2 A:GLN58 4.1 21.3 1.0
OE2 A:GLU62 4.1 19.8 1.0
CG A:GLN58 4.3 11.9 1.0
O A:HOH478 4.3 22.6 1.0
O A:HOH394 4.4 20.5 1.0
OE2 A:GLU107 4.4 24.1 1.0
CB A:GLN58 4.5 10.6 1.0
CB A:GLU61 4.5 13.5 1.0
CA A:GLN58 4.6 8.0 1.0
CB A:ALA144 4.6 9.2 1.0
CG A:GLU61 4.9 20.9 1.0

Magnesium binding site 2 out of 17 in 5jkk

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Magnesium binding site 2 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:30.3
occ:0.33
 O A:HOH373 1.7 15.8 1.0
O A:HOH329 1.8 28.0 1.0
OD2 A:ASP131 3.5 18.7 1.0
O A:HOH326 4.1 32.3 1.0
OG1 A:THR135 4.2 15.5 1.0
OE1 A:GLU134 4.4 18.5 1.0
CG A:ASP131 4.6 13.0 1.0

Magnesium binding site 3 out of 17 in 5jkk

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Magnesium binding site 3 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:12.2
occ:0.50
 O B:HOH340 2.0 12.7 0.5
O B:HOH389 2.0 31.3 1.0
OE1 B:GLN58 2.1 20.4 1.0
O B:HOH484 2.1 32.1 1.0
O B:HOH301 2.3 21.4 0.5
OE2 B:GLU61 2.4 39.4 1.0
CD B:GLN58 3.3 17.7 1.0
CD B:GLU61 3.7 34.5 1.0
O B:HOH443 4.0 37.3 1.0
NE2 B:GLN58 4.1 22.6 1.0
OE2 B:GLU62 4.2 19.5 1.0
O B:HOH478 4.2 23.3 1.0
CG B:GLN58 4.3 11.8 1.0
O B:HOH481 4.3 24.8 1.0
CB B:GLN58 4.3 10.6 1.0
OE2 B:GLU107 4.4 20.6 1.0
CB B:GLU61 4.5 12.4 1.0
O B:HOH406 4.5 21.7 1.0
OE1 B:GLU61 4.5 52.4 1.0
CA B:GLN58 4.5 9.1 1.0
CB B:ALA144 4.7 9.1 1.0
CG B:GLU61 4.7 19.6 1.0

Magnesium binding site 4 out of 17 in 5jkk

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Magnesium binding site 4 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:8.8
occ:1.00
 O C:HOH345 2.0 12.6 1.0
O D:HOH480 2.0 15.7 1.0
O C:HOH486 2.1 14.8 1.0
O D:HOH337 2.1 14.4 1.0
O B:HOH333 2.1 13.2 1.0
O B:HOH491 2.1 16.2 1.0
OE2 D:GLU134 3.9 10.9 1.0
OE2 C:GLU134 3.9 12.1 1.0
OE2 B:GLU134 3.9 11.4 1.0
O B:HOH408 4.2 16.2 1.0
O C:HOH384 4.2 16.7 1.0
O B:HOH509 4.2 17.5 1.0
OE1 C:GLU134 4.2 19.0 1.0
O D:HOH367 4.2 18.4 1.0
OE1 D:GLU134 4.3 19.1 1.0
O C:HOH504 4.3 18.5 1.0
OE1 B:GLU134 4.3 18.1 1.0
O D:HOH500 4.3 19.0 1.0
CD C:GLU134 4.5 14.6 1.0
CD D:GLU134 4.5 14.8 1.0
CD B:GLU134 4.5 14.4 1.0

Magnesium binding site 5 out of 17 in 5jkk

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Magnesium binding site 5 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:12.6
occ:0.50
 OE2 C:GLU61 2.0 41.1 1.0
O C:HOH317 2.0 13.5 0.5
O C:HOH386 2.0 19.1 0.5
O C:HOH389 2.1 16.4 0.5
OE1 C:GLN58 2.1 17.6 1.0
CD C:GLU61 3.2 41.2 1.0
CD C:GLN58 3.3 18.2 1.0
CG C:GLU61 4.1 24.0 1.0
NE2 C:GLN58 4.1 23.2 1.0
O C:HOH477 4.1 25.4 1.0
OE2 C:GLU62 4.1 19.9 1.0
OE1 C:GLU61 4.2 42.1 1.0
CG C:GLN58 4.3 12.3 1.0
O C:HOH475 4.3 26.4 1.0
OE2 C:GLU107 4.4 23.6 1.0
CB C:GLN58 4.4 10.0 1.0
CB C:GLU61 4.5 13.7 1.0
CA C:GLN58 4.5 8.3 1.0
O C:HOH408 4.6 22.0 1.0
CB C:ALA144 4.6 9.0 1.0
O C:HOH332 5.0 25.6 1.0

Magnesium binding site 6 out of 17 in 5jkk

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Magnesium binding site 6 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:32.4
occ:1.00
 O D:HOH372 1.8 17.8 1.0
O B:HOH327 1.8 18.3 1.0
O C:HOH339 1.8 29.1 1.0
O D:HOH322 1.8 16.3 1.0
O D:HOH308 1.9 31.5 1.0
O B:HOH330 1.9 28.6 1.0
OD1 C:ASP131 3.4 16.3 1.0
OD1 D:ASP131 3.4 18.7 1.0
OD1 B:ASP131 3.5 18.2 1.0
O C:HOH347 4.1 26.3 1.0
O B:HOH315 4.1 28.9 1.0
O D:HOH395 4.1 27.4 1.0
OG1 C:THR135 4.2 16.4 1.0
OG1 D:THR135 4.2 15.8 1.0
OG1 B:THR135 4.3 16.1 1.0
OE1 D:GLU134 4.4 19.1 1.0
OE1 B:GLU134 4.4 18.1 1.0
OE1 C:GLU134 4.5 19.0 1.0
CG C:ASP131 4.5 12.6 1.0
CG D:ASP131 4.6 13.5 1.0
CG B:ASP131 4.7 13.7 1.0

Magnesium binding site 7 out of 17 in 5jkk

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Magnesium binding site 7 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:7.6
occ:0.50
 O H:HOH343 2.0 7.7 1.0
OD2 C:ASP84 2.1 6.8 1.0
O C:HOH403 2.2 7.9 1.0
CG C:ASP84 3.2 7.9 1.0
CB C:ASP84 3.6 7.1 1.0
OE1 H:GLN86 4.2 18.3 1.0
NE2 H:GLN86 4.2 12.1 1.0
OD1 C:ASP84 4.2 7.0 1.0
OD2 H:ASP84 4.2 10.8 1.0
O C:HOH362 4.3 12.6 1.0
O C:HOH507 4.4 21.2 1.0
O C:HOH374 4.6 10.2 1.0
CD H:GLN86 4.6 14.0 1.0
O H:HOH326 4.8 12.7 1.0
O C:HOH327 4.9 24.2 1.0

Magnesium binding site 8 out of 17 in 5jkk

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Magnesium binding site 8 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:13.2
occ:0.50
 O D:HOH305 1.8 20.8 0.5
OE1 D:GLN58 2.0 18.0 1.0
O D:HOH323 2.1 26.4 1.0
O D:HOH394 2.1 20.9 0.5
O D:HOH497 2.1 26.0 1.0
CD D:GLN58 3.3 18.1 1.0
NE2 D:GLN58 4.1 21.8 1.0
OE2 D:GLU62 4.2 22.2 1.0
CG D:GLN58 4.3 11.8 1.0
OE2 D:GLU107 4.3 22.6 1.0
O D:HOH468 4.4 23.4 1.0
CB D:GLN58 4.4 9.8 1.0
CB D:GLU61 4.5 12.8 1.0
O D:HOH388 4.5 21.7 1.0
CA D:GLN58 4.6 8.7 1.0
CB D:ALA144 4.6 8.4 1.0
CG D:GLU61 4.9 19.6 1.0

Magnesium binding site 9 out of 17 in 5jkk

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Magnesium binding site 9 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:10.5
occ:0.50
 O D:HOH375 2.0 11.5 1.0
OD2 D:ASP84 2.1 9.6 1.0
O D:HOH452 2.2 11.5 1.0
CG D:ASP84 3.2 8.5 1.0
CB D:ASP84 3.6 6.6 1.0
OD1 D:ASP84 4.2 8.2 1.0
NE2 G:GLN86 4.3 13.6 1.0
OE1 G:GLN86 4.3 23.1 1.0
O D:HOH334 4.3 17.5 1.0
OD2 G:ASP84 4.4 13.1 1.0
O D:HOH320 4.5 13.3 1.0
O D:HOH309 4.7 15.2 1.0
CD G:GLN86 4.7 18.0 1.0
O D:HOH332 4.8 19.9 1.0

Magnesium binding site 10 out of 17 in 5jkk

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Magnesium binding site 10 out of 17 in the Crystal Structure of the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin


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 the Negatively Supercharged Variant Ftn(Neg) of Human Heavy Chain Ferritin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:11.3
occ:0.50
 O E:HOH409 2.0 20.1 0.5
O E:HOH310 2.0 24.9 1.0
OE1 E:GLN58 2.1 19.4 1.0
O E:HOH302 2.1 25.3 1.0
OE2 E:GLU61 2.8 49.3 1.0
CD E:GLN58 3.2 17.5 1.0
CD E:GLU61 3.4 43.2 1.0
OE1 E:GLU61 3.9 47.4 1.0
OE2 E:GLU62 4.0 21.6 1.0
NE2 E:GLN58 4.0 23.2 1.0
O E:HOH472 4.2 24.7 1.0
CG E:GLN58 4.2 11.5 1.0
OE2 E:GLU107 4.3 24.2 1.0
CB E:GLN58 4.3 10.3 1.0
CG E:GLU61 4.4 22.9 1.0
O E:HOH407 4.5 21.1 1.0
CA E:GLN58 4.6 8.6 1.0
CB E:ALA144 4.6 9.3 1.0
CB E:GLU61 4.6 14.3 1.0

Reference:

M.Kuenzle, T.Eckert, T.Beck. Self-Assembly of Charged Protein Containers Enables Positioning of Nanoparticles in A 3-D Lattice to Form Biohybrid Materials To Be Published.
Page generated: Sun Sep 29 17:48:44 2024

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