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Magnesium in PDB 5n27: X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)

Enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)

All present enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form):
1.16.3.1;

Protein crystallography data

The structure of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form), PDB code: 5n27 was solved by G.Ferraro, A.Merlino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.63 / 1.74
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.955, 182.955, 182.955, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 19.1

Other elements in 5n27:

The structure of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) (pdb code 5n27). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form), PDB code: 5n27:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5n27

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Magnesium binding site 1 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:15.4
occ:0.33
 O A:HOH354 2.0 15.4 1.0
O A:HOH529 2.1 16.1 1.0
OE2 A:GLU134 3.9 11.6 0.5
OE2 A:GLU134 3.9 20.1 0.5
O A:HOH588 4.3 18.0 1.0
O A:HOH404 4.3 20.9 1.0
OE1 A:GLU134 4.3 9.5 0.5
OE1 A:GLU134 4.4 22.5 0.5
CD A:GLU134 4.5 11.2 0.5
CD A:GLU134 4.6 19.1 0.5

Magnesium binding site 2 out of 8 in 5n27

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Magnesium binding site 2 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:19.2
occ:0.50
 O A:HOH617 2.1 18.3 0.5
O A:HOH553 2.2 20.0 1.0
O A:HOH375 4.1 16.6 1.0
O A:HOH468 4.4 49.7 1.0
CD A:LYS86 4.5 17.6 0.5
O A:HOH616 4.5 23.6 1.0
CE A:LYS86 4.6 18.6 0.5
NZ A:LYS86 4.7 13.9 0.5
O A:HOH548 4.8 34.7 1.0
CE A:LYS87 4.8 29.6 1.0

Magnesium binding site 3 out of 8 in 5n27

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Magnesium binding site 3 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:20.1
occ:0.60
 O A:HOH610 2.0 23.7 0.6
O A:HOH351 2.1 23.7 0.6
O A:HOH387 2.3 20.1 0.6
OD2 A:ASP131 4.0 25.2 1.0
O A:HOH607 4.3 50.9 1.0
CG2 A:THR135 4.4 24.1 1.0
OD1 A:ASP131 4.5 24.6 1.0
OG1 A:THR135 4.5 24.0 1.0
CG A:ASP131 4.7 18.6 1.0
O A:HOH531 4.7 34.1 1.0
CB A:THR135 5.0 20.1 1.0

Magnesium binding site 4 out of 8 in 5n27

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Magnesium binding site 4 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:24.0
occ:0.80
 SG A:CYS102 2.0 16.3 0.8
O A:HOH571 2.2 35.8 0.8
CB A:CYS102 2.9 19.7 0.2
CB A:CYS102 3.0 15.1 0.8
SG A:CYS102 3.2 24.1 0.2
O A:HOH474 3.3 39.6 1.0
O A:HOH619 3.6 46.5 1.0
CA A:CYS102 3.6 15.8 0.8
O A:HOH566 3.7 27.4 1.0
CA A:CYS102 3.7 18.4 0.2
O A:HOH504 3.7 36.2 1.0
O A:HOH436 4.2 29.8 1.0
N A:CYS102 4.4 14.1 0.8
O A:HOH321 4.4 40.0 1.0
CZ3 A:TRP93 4.5 19.8 1.0
N A:CYS102 4.6 17.4 0.2
SG A:CYS90 4.6 19.2 0.5
C A:CYS102 4.8 14.9 0.8
C A:CYS102 4.8 16.8 0.2
O A:CYS102 5.0 16.1 0.8

Magnesium binding site 5 out of 8 in 5n27

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Magnesium binding site 5 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:56.3
occ:1.00
 OD1 A:ASP42 2.4 17.0 1.0
O A:HOH386 2.7 22.9 1.0
CG A:ASP42 3.6 16.0 1.0
O A:HOH407 3.9 19.1 1.0
O A:ASP42 4.1 13.5 1.0
O A:HOH355 4.3 13.9 1.0
O A:HOH587 4.3 51.6 1.0
OD2 A:ASP42 4.4 15.2 1.0
CB A:ASP42 4.5 14.5 1.0
CA A:ASP42 4.6 14.3 1.0
C A:ASP42 4.8 14.4 1.0

Magnesium binding site 6 out of 8 in 5n27

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Magnesium binding site 6 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:25.9
occ:0.60
 O A:HOH352 1.8 21.4 0.6
OE1 A:GLU61 2.0 22.4 0.5
OE1 A:GLN58 2.2 38.9 1.0
O A:HOH577 2.3 33.8 0.6
O A:HOH413 2.4 33.5 0.6
O A:HOH361 2.5 21.9 0.6
CD A:GLU61 3.3 21.6 0.5
CD A:GLN58 3.3 28.3 1.0
O A:HOH352 3.3 21.6 0.4
O A:HOH450 3.5 53.0 1.0
O A:HOH393 3.5 49.0 1.0
O A:HOH491 3.8 31.5 0.5
NE2 A:GLN58 4.0 36.5 1.0
OE2 A:GLU61 4.1 25.0 0.5
CB A:GLU61 4.2 18.5 0.5
CG A:GLU61 4.3 20.3 0.5
O A:HOH303 4.4 29.3 1.0
O A:HOH469 4.4 40.3 1.0
OE2 A:GLU107 4.4 37.8 1.0
OE1 A:GLU62 4.5 32.5 1.0
CG A:GLN58 4.5 23.1 1.0
CB A:ALA144 4.5 16.5 1.0
CB A:GLU61 4.5 20.7 0.5
O A:HOH483 4.6 33.5 1.0
CA A:GLN58 4.6 16.4 1.0
OE2 A:GLU140 4.6 35.8 0.6
CB A:GLN58 4.7 18.4 1.0
CD A:GLU140 4.7 31.6 0.4
O A:GLN58 4.9 17.2 1.0
OE1 A:GLU140 4.9 37.2 0.4
CE1 A:HIS65 5.0 35.1 1.0

Magnesium binding site 7 out of 8 in 5n27

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Magnesium binding site 7 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:19.2
occ:0.80
 OE2 A:GLU27 1.9 19.3 1.0
OE2 A:GLU62 2.0 24.4 1.0
O A:HOH339 2.1 14.1 0.8
ND1 A:HIS65 2.1 28.3 1.0
O A:HOH330 2.2 23.4 0.8
O A:HOH306 2.3 57.2 0.8
CE1 A:HIS65 3.0 35.1 1.0
CD A:GLU27 3.0 16.9 1.0
CD A:GLU62 3.0 26.9 1.0
CG A:HIS65 3.3 25.7 1.0
OE1 A:GLU27 3.3 19.8 1.0
OE1 A:GLU62 3.4 32.5 1.0
CB A:HIS65 3.7 18.6 1.0
O A:HOH408 4.1 30.5 1.0
OE1 A:GLN141 4.1 26.4 1.0
NE2 A:HIS65 4.2 38.0 1.0
CG A:GLU27 4.3 15.5 1.0
CG1 A:VAL110 4.3 18.4 1.0
CD2 A:HIS65 4.3 31.5 1.0
O A:HOH316 4.3 57.0 0.8
CG A:GLU62 4.4 20.2 1.0
CA A:GLU62 4.6 15.2 1.0
CB A:GLU27 4.7 14.9 1.0
CB A:GLU62 4.7 17.0 1.0
O A:HOH450 4.7 53.0 1.0
CA A:GLU27 4.9 14.3 1.0
CD A:GLN141 4.9 20.6 1.0
OE1 A:GLU107 4.9 31.7 1.0

Magnesium binding site 8 out of 8 in 5n27

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Magnesium binding site 8 out of 8 in the X-Ray Structure of Human Heavy Chain Ferritin (Apo Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of X-Ray Structure of Human Heavy Chain Ferritin (Apo Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:51.7
occ:1.00
 O A:HOH319 1.9 29.2 1.0
O A:HOH564 2.1 37.2 1.0
O A:HOH389 2.1 18.2 1.0
O A:HOH544 2.4 37.5 1.0
O A:HOH618 2.4 42.7 1.0
O A:HOH625 2.5 48.2 1.0
OD1 A:ASN25 4.1 13.8 1.0
O A:HOH606 4.2 27.7 0.5
O A:ARG22 4.3 13.2 1.0
O A:HOH560 4.3 29.1 1.0
O A:HOH621 4.3 49.7 1.0
O A:HOH590 4.4 19.0 1.0
O A:HOH360 4.6 25.9 1.0
O A:HOH606 4.7 9.8 0.5
CB A:LEU26 4.7 13.5 1.0
CB A:ASN25 4.8 13.5 1.0
CG A:ASN25 4.8 14.2 1.0
N A:LEU26 4.8 12.7 1.0
O A:HOH589 5.0 44.2 1.0
CD1 A:LEU26 5.0 16.9 1.0
CA A:LEU26 5.0 13.2 1.0

Reference:

G.Ferraro, S.Ciambellotti, L.Messori, A.Merlino. Cisplatin Binding Sites in Human H-Chain Ferritin. Inorg Chem V. 56 9064 2017.
ISSN: ISSN 1520-510X
PubMed: 28737381
DOI: 10.1021/ACS.INORGCHEM.7B01072
Page generated: Sun Sep 29 23:03:37 2024

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