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Magnesium in PDB 5z8u: Human Mitochondrial Ferritin Mutant - C102A/C130A

Enzymatic activity of Human Mitochondrial Ferritin Mutant - C102A/C130A

All present enzymatic activity of Human Mitochondrial Ferritin Mutant - C102A/C130A:
1.16.3.1;

Protein crystallography data

The structure of Human Mitochondrial Ferritin Mutant - C102A/C130A, PDB code: 5z8u was solved by J.Zang, B.Zheng, G.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.85 / 1.90
Space group F 2 3
Cell size a, b, c (Å), α, β, γ (°) 179.071, 179.071, 179.071, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Mitochondrial Ferritin Mutant - C102A/C130A (pdb code 5z8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Mitochondrial Ferritin Mutant - C102A/C130A, PDB code: 5z8u:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5z8u

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Magnesium binding site 1 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:25.3
occ:0.33
 O A:HOH320 1.9 37.5 1.0
O A:HOH435 2.2 35.3 1.0
O A:HOH312 2.5 28.4 1.0
O A:HOH315 2.5 31.1 1.0
O A:HOH437 2.5 39.0 1.0
O A:HOH302 3.6 35.2 1.0
O A:HOH321 3.9 20.5 1.0
OE2 A:GLU134 4.0 17.6 1.0
O A:HOH431 4.4 16.4 1.0
OE1 A:GLU134 4.6 21.3 1.0
CD A:GLU134 4.7 16.5 1.0

Magnesium binding site 2 out of 6 in 5z8u

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Magnesium binding site 2 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:6.1
occ:1.00
 OE2 A:GLU27 1.9 11.9 1.0
OE1 A:GLU62 2.0 10.1 1.0
ND1 A:HIS65 2.1 16.3 1.0
O A:HOH318 2.3 15.1 1.0
O A:HOH303 2.8 19.1 1.0
CD A:GLU27 2.9 11.0 1.0
CD A:GLU62 3.0 10.8 1.0
CE1 A:HIS65 3.1 16.5 1.0
CG A:HIS65 3.1 14.4 1.0
OE2 A:GLU62 3.3 15.3 1.0
OE1 A:GLU27 3.3 11.8 1.0
CB A:HIS65 3.4 11.5 1.0
OE1 A:GLN141 3.6 23.4 1.0
O A:HOH352 4.0 22.4 1.0
NE2 A:HIS65 4.2 19.9 1.0
CD2 A:HIS65 4.2 16.5 1.0
CG A:GLU27 4.3 8.8 1.0
CG1 A:VAL110 4.3 12.7 1.0
CG A:GLU62 4.3 10.2 1.0
CA A:GLU62 4.4 10.2 1.0
O A:HOH313 4.5 23.6 1.0
CB A:GLU62 4.6 7.3 1.0
CB A:GLU27 4.6 9.1 1.0
CA A:GLU27 4.8 8.9 1.0
CD A:GLN141 4.8 16.5 1.0
O A:GLU62 4.9 9.2 1.0
OE2 A:GLU140 4.9 28.8 1.0
CA A:HIS65 4.9 9.3 1.0
OE1 A:GLU107 5.0 22.9 1.0

Magnesium binding site 3 out of 6 in 5z8u

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Magnesium binding site 3 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:15.3
occ:0.33
 O B:HOH321 1.8 19.2 1.0
O B:HOH425 2.0 24.4 1.0
O B:HOH349 2.6 35.5 1.0
O B:HOH356 3.1 33.2 1.0
O B:HOH317 3.7 34.6 1.0
OE2 B:GLU134 3.8 15.8 1.0
O B:HOH330 4.0 18.6 1.0
O B:HOH433 4.2 16.6 1.0
O B:HOH414 4.2 38.6 1.0
O B:HOH430 4.3 39.2 1.0
OE1 B:GLU134 4.4 22.9 1.0
CD B:GLU134 4.5 16.4 1.0

Magnesium binding site 4 out of 6 in 5z8u

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Magnesium binding site 4 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:6.1
occ:1.00
 OE2 B:GLU27 1.9 11.9 1.0
OE1 B:GLU62 2.0 10.7 1.0
ND1 B:HIS65 2.1 18.7 1.0
O B:HOH313 2.3 13.5 1.0
CD B:GLU27 2.9 11.7 1.0
O B:HOH303 2.9 18.2 1.0
CD B:GLU62 3.0 10.6 1.0
CE1 B:HIS65 3.1 18.9 1.0
CG B:HIS65 3.1 15.8 1.0
OE1 B:GLU27 3.3 12.0 1.0
OE2 B:GLU62 3.3 15.6 1.0
CB B:HIS65 3.4 11.4 1.0
OE1 B:GLN141 3.7 24.7 1.0
O B:HOH368 4.1 22.7 1.0
NE2 B:HIS65 4.2 22.1 1.0
CD2 B:HIS65 4.2 17.1 1.0
CG B:GLU27 4.2 7.8 1.0
CG1 B:VAL110 4.3 13.9 1.0
CG B:GLU62 4.3 10.0 1.0
CA B:GLU62 4.4 9.8 1.0
O B:HOH316 4.5 25.1 1.0
CB B:GLU62 4.6 7.8 1.0
CB B:GLU27 4.6 8.9 1.0
CA B:GLU27 4.8 8.8 1.0
CD B:GLN141 4.8 18.0 1.0
O B:GLU62 4.9 9.8 1.0
CA B:HIS65 4.9 9.6 1.0
OE1 B:GLU140 4.9 30.6 1.0
CB B:ALA30 5.0 6.5 1.0

Magnesium binding site 5 out of 6 in 5z8u

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Magnesium binding site 5 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:18.9
occ:1.00
 O B:HOH429 2.0 12.0 1.0
O B:HOH382 2.0 32.1 1.0
O B:HOH336 2.3 17.9 1.0
OD2 B:ASP84 3.9 11.8 1.0
OD1 B:ASP84 4.0 9.4 1.0
O A:HOH396 4.1 38.3 1.0
O A:HOH424 4.2 48.0 1.0
CG B:ASP84 4.3 12.1 1.0
O A:HOH332 4.4 11.1 1.0
O A:HOH440 4.4 28.2 1.0
O B:HOH360 4.4 6.6 1.0
O A:HOH433 4.6 15.5 1.0
CE A:LYS87 4.8 20.8 1.0
CD A:LYS86 4.8 16.5 1.0

Magnesium binding site 6 out of 6 in 5z8u

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Magnesium binding site 6 out of 6 in the Human Mitochondrial Ferritin Mutant - C102A/C130A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Mitochondrial Ferritin Mutant - C102A/C130A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:31.0
occ:1.00
 O A:HOH422 1.7 22.1 1.0
O B:HOH437 2.1 15.3 1.0
O A:HOH341 2.3 12.7 1.0
O A:HOH316 2.3 15.5 1.0
O B:HOH418 2.5 35.8 1.0
O B:HOH439 4.0 27.4 1.0
OD1 A:ASP84 4.0 9.8 1.0
OD2 A:ASP84 4.0 10.9 1.0
O A:HOH366 4.0 6.1 1.0
O A:HOH305 4.1 35.4 1.0
CE B:LYS87 4.3 22.0 1.0
CG A:ASP84 4.4 12.2 1.0
O B:HOH329 4.5 12.2 1.0
CD B:LYS87 4.6 15.1 1.0
O B:HOH426 4.6 16.1 1.0
CG B:LYS87 4.7 10.7 1.0
NZ B:LYS87 5.0 29.7 1.0

Reference:

J.Zang, B.Zheng, X.Zhang, P.Arosio, G.Zhao. Design and Site-Directed Compartmentalization of Gold Nanoclusters Within the Intrasubunit Interfaces of Ferritin Nanocage. J Nanobiotechnology V. 17 79 2019.
ISSN: ISSN 1477-3155
PubMed: 31277668
DOI: 10.1186/S12951-019-0512-0
Page generated: Mon Sep 30 11:47:20 2024

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