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Magnesium in PDB 5jkm: Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)

Enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)

All present enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition):
1.16.3.1;

Protein crystallography data

The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition), PDB code: 5jkm 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) 47.60 / 1.80
Space group P 4
Cell size a, b, c (Å), α, β, γ (°) 126.840, 126.840, 175.020, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.1

Other elements in 5jkm:

The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) also contains other interesting chemical elements:

Iron (Fe) 12 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

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

Magnesium binding site 1 out of 17 in 5jkm

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Magnesium binding site 1 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:17.7
occ:1.00
 O C:HOH354 2.0 20.0 1.0
O C:HOH447 2.1 23.9 1.0
O A:HOH425 2.1 20.2 1.0
O A:HOH360 2.1 21.5 1.0
OE2 A:GLU134 3.9 18.6 1.0
OE2 C:GLU134 3.9 18.3 1.0
O C:HOH368 4.2 23.9 1.0
O A:HOH391 4.2 23.6 1.0
OE1 A:GLU134 4.2 21.7 1.0
OE1 C:GLU134 4.2 22.5 1.0
O C:HOH455 4.3 25.4 1.0
O A:HOH433 4.3 27.7 1.0
CD A:GLU134 4.5 21.7 1.0
CD C:GLU134 4.5 18.8 1.0

Magnesium binding site 2 out of 17 in 5jkm

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Magnesium binding site 2 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:18.9
occ:0.50
 O A:HOH306 1.6 26.4 0.5
O A:HOH314 1.8 25.9 0.5
OE1 A:GLN58 2.0 27.6 1.0
O A:HOH432 2.2 23.2 0.5
CD A:GLN58 3.3 27.0 1.0
NE2 A:GLN58 4.1 31.5 1.0
OE2 A:GLU62 4.2 22.7 1.0
CG A:GLN58 4.2 19.9 1.0
OE2 A:GLU107 4.3 34.0 1.0
CB A:GLN58 4.3 17.1 1.0
CA A:GLN58 4.4 15.6 1.0
CB A:GLU61 4.5 20.3 1.0
CB A:ALA144 4.6 15.3 1.0
O A:HOH340 4.7 30.2 1.0
CG A:GLU61 4.8 30.2 1.0
O A:GLN58 4.8 15.6 1.0
O A:HOH308 4.8 35.9 1.0

Magnesium binding site 3 out of 17 in 5jkm

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Magnesium binding site 3 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:24.2
occ:0.50
 OE1 B:GLN58 2.1 25.0 1.0
OE1 B:GLU61 2.5 46.7 1.0
CD B:GLN58 3.3 26.5 1.0
CD B:GLU61 3.8 40.0 1.0
OE2 B:GLU107 4.0 31.1 1.0
NE2 B:GLN58 4.1 31.4 1.0
OE2 B:GLU62 4.2 25.0 1.0
CG B:GLN58 4.3 18.9 1.0
CB B:GLN58 4.4 17.1 1.0
CB B:GLU61 4.4 23.6 1.0
CA B:GLN58 4.5 13.9 1.0
CG B:GLU61 4.6 29.7 1.0
CB B:ALA144 4.6 16.4 1.0
OE2 B:GLU61 4.7 50.6 1.0
O B:HOH316 4.7 31.2 1.0
O B:GLN58 4.9 14.7 1.0

Magnesium binding site 4 out of 17 in 5jkm

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Magnesium binding site 4 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:23.6
occ:0.50
 O C:HOH301 1.5 15.0 0.5
O C:HOH305 1.8 16.4 0.5
OE1 C:GLN58 2.1 26.8 1.0
O C:HOH365 2.1 15.7 0.5
CD C:GLN58 3.2 26.4 1.0
OE2 C:GLU107 3.3 36.0 1.0
OE2 C:GLU62 3.9 28.6 1.0
CG C:GLN58 4.1 21.3 1.0
NE2 C:GLN58 4.1 31.4 1.0
O C:HOH439 4.2 31.8 1.0
CB C:GLN58 4.2 17.1 1.0
CD C:GLU107 4.4 31.1 1.0
CB C:ALA144 4.5 15.9 1.0
CA C:GLN58 4.5 15.7 1.0
OH C:TYR34 4.6 27.0 1.0
CB C:GLU61 4.7 21.8 1.0
CG C:GLU61 4.7 35.1 1.0
CE2 C:TYR34 4.7 18.5 1.0
OE2 C:GLU61 4.7 47.8 1.0
O C:GLN58 4.8 13.2 1.0
CZ C:TYR34 4.9 24.3 1.0
OE1 C:GLU107 4.9 32.8 1.0
CD C:GLU62 4.9 23.2 1.0

Magnesium binding site 5 out of 17 in 5jkm

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Magnesium binding site 5 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:18.6
occ:1.00
 O D:HOH442 2.0 21.5 1.0
O F:HOH317 2.0 17.3 1.0
O E:HOH417 2.1 20.2 1.0
O F:HOH426 2.1 17.7 1.0
O E:HOH365 2.1 18.4 1.0
O D:HOH312 2.1 20.7 1.0
OE2 D:GLU134 3.8 17.7 1.0
OE2 F:GLU134 3.8 18.7 1.0
OE2 E:GLU134 3.8 17.4 1.0
O D:HOH376 4.2 23.7 1.0
OE1 F:GLU134 4.2 19.6 1.0
O F:HOH325 4.3 23.5 1.0
O D:HOH452 4.3 25.4 1.0
O F:HOH437 4.3 28.6 1.0
OE1 E:GLU134 4.3 20.8 1.0
O E:HOH326 4.3 22.5 1.0
OE1 D:GLU134 4.3 20.3 1.0
CD D:GLU134 4.5 20.3 1.0
CD F:GLU134 4.5 17.7 1.0
CD E:GLU134 4.5 19.0 1.0

Magnesium binding site 6 out of 17 in 5jkm

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Magnesium binding site 6 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:29.1
occ:0.50
 O D:HOH301 1.4 16.4 0.5
OE1 D:GLN58 2.3 25.4 1.0
O D:HOH370 2.4 18.6 0.5
OE2 D:GLU107 3.1 34.4 1.0
OE2 D:GLU61 3.2 56.5 1.0
CD D:GLN58 3.4 25.3 1.0
OE2 D:GLU62 3.5 30.2 1.0
CD D:GLU61 3.9 47.1 1.0
CG D:GLN58 4.1 18.9 1.0
CB D:GLN58 4.1 14.9 1.0
CD D:GLU107 4.1 27.4 1.0
OH D:TYR34 4.2 27.0 1.0
CE2 D:TYR34 4.3 16.6 1.0
CB D:ALA144 4.4 14.6 1.0
NE2 D:GLN58 4.4 30.6 1.0
CZ D:TYR34 4.5 21.7 1.0
CA D:GLN58 4.5 14.7 1.0
CG D:GLU61 4.6 31.5 1.0
CD D:GLU62 4.6 22.2 1.0
OE1 D:GLU107 4.6 33.1 1.0
OE1 D:GLU61 4.7 48.6 1.0
O D:GLN58 4.7 13.5 1.0
O D:HOH333 4.9 23.9 1.0
CB D:GLU61 4.9 23.0 1.0

Magnesium binding site 7 out of 17 in 5jkm

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Magnesium binding site 7 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate 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 and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:38.8
occ:1.00
 O D:HOH317 1.9 38.5 1.0
O E:HOH334 1.9 26.1 1.0
O F:HOH305 1.9 30.4 1.0
O D:HOH339 2.0 30.1 1.0
O D:HOH303 2.0 30.5 1.0
OD1 E:ASP131 3.4 22.4 1.0
OD2 F:ASP131 3.5 21.2 1.0
OD1 D:ASP131 3.6 24.3 1.0
OG1 F:THR135 4.2 18.2 1.0
OG1 E:THR135 4.2 18.3 1.0
OE1 F:GLU134 4.3 19.6 1.0
OE1 D:GLU134 4.3 20.3 1.0
OE1 E:GLU134 4.4 20.8 1.0
O D:HOH380 4.4 32.1 1.0
OG1 D:THR135 4.5 18.8 1.0
CG E:ASP131 4.5 20.8 1.0
O F:HOH386 4.5 34.5 1.0
CG F:ASP131 4.6 20.1 1.0
CG D:ASP131 4.8 21.2 1.0
CB F:GLU134 4.9 15.2 1.0

Magnesium binding site 8 out of 17 in 5jkm

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Magnesium binding site 8 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:21.2
occ:0.50
 OE1 F:GLU61 1.7 39.2 1.0
OE1 F:GLN58 2.1 25.6 1.0
CD F:GLU61 2.6 38.5 1.0
O F:HOH308 3.3 34.5 1.0
CD F:GLN58 3.3 23.7 1.0
OE2 F:GLU61 3.5 49.7 1.0
CG F:GLU61 3.5 31.4 1.0
OE2 F:GLU62 4.0 23.9 1.0
OE2 F:GLU107 4.1 29.4 1.0
NE2 F:GLN58 4.2 26.8 1.0
CG F:GLN58 4.2 18.0 1.0
CB F:GLN58 4.3 14.6 1.0
CA F:GLN58 4.4 13.5 1.0
CB F:GLU61 4.4 20.9 1.0
CB F:ALA144 4.6 14.4 1.0
O F:GLN58 4.8 12.7 1.0

Magnesium binding site 9 out of 17 in 5jkm

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Magnesium binding site 9 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg202

b:50.2
occ:1.00
 O G:HOH301 1.8 35.0 1.0
O G:HOH345 1.8 35.5 1.0
O G:HOH305 2.4 40.3 1.0
OD1 I:ASP131 3.1 32.4 1.0
OD1 G:ASP131 3.5 27.9 1.0
OE1 I:GLU134 4.1 29.5 1.0
CG I:ASP131 4.2 25.4 1.0
OG1 I:THR135 4.3 24.3 1.0
OE1 G:GLU134 4.3 27.0 1.0
O I:HOH391 4.3 37.4 1.0
OG1 G:THR135 4.6 24.4 1.0
CG G:ASP131 4.6 29.7 1.0
CB I:ASP131 4.8 20.6 1.0
CA I:ASP131 5.0 21.7 1.0

Magnesium binding site 10 out of 17 in 5jkm

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Magnesium binding site 10 out of 17 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Acetate Condition) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg203

b:21.0
occ:1.00
 O I:HOH406 2.0 26.1 1.0
O I:HOH327 2.0 24.9 1.0
O G:HOH326 2.0 26.6 1.0
O G:HOH417 2.1 25.5 1.0
OE2 I:GLU134 3.8 24.8 1.0
OE2 G:GLU134 3.9 24.2 1.0
OE1 I:GLU134 4.2 29.5 1.0
O I:HOH326 4.3 32.8 1.0
O G:HOH317 4.3 26.2 1.0
OE1 G:GLU134 4.3 27.0 1.0
CD I:GLU134 4.5 26.0 1.0
CD G:GLU134 4.5 24.6 1.0

Reference:

M.Kunzle, T.Eckert, T.Beck. Binary Protein Crystals For the Assembly of Inorganic Nanoparticle Superlattices. J.Am.Chem.Soc. V. 138 12731 2016.
ISSN: ESSN 1520-5126
PubMed: 27617514
DOI: 10.1021/JACS.6B07260
Page generated: Sun Sep 29 17:49:40 2024

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