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Magnesium in PDB 6ftv: X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A

Enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A

All present enzymatic activity of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A:
1.16.3.1;

Protein crystallography data

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A, PDB code: 6ftv was solved by A.Merlino, G.Ferraro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 105.30 / 1.58
Space group F 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 182.380, 182.380, 182.380, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 18.3

Other elements in 6ftv:

The structure of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms
Chlorine (Cl) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A (pdb code 6ftv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A, PDB code: 6ftv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 6ftv

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Magnesium binding site 1 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:20.9
occ:0.80
 OE2 A:GLU27 2.0 25.4 1.0
OE2 A:GLU62 2.0 29.1 1.0
O A:HOH312 2.1 48.4 0.8
O A:HOH365 2.1 23.9 1.0
O A:HOH326 2.1 33.6 1.0
ND1 A:HIS65 2.1 32.9 1.0
CE1 A:HIS65 2.9 36.5 1.0
CD A:GLU27 3.1 23.6 1.0
CD A:GLU62 3.1 28.5 1.0
CG A:HIS65 3.3 28.7 1.0
OE1 A:GLU27 3.4 24.3 1.0
OE1 A:GLU62 3.4 35.9 1.0
CB A:HIS65 3.7 21.7 1.0
O A:HOH429 4.0 38.2 1.0
OE1 A:GLN141 4.0 30.6 1.0
NE2 A:HIS65 4.1 36.1 1.0
CG A:GLU27 4.3 19.8 1.0
CD2 A:HIS65 4.3 33.7 1.0
CG1 A:VAL110 4.4 24.5 1.0
CG A:GLU62 4.4 22.8 1.0
CA A:GLU62 4.6 18.0 1.0
O A:HOH357 4.6 62.6 1.0
CB A:GLU62 4.6 19.0 1.0
CB A:GLU27 4.7 17.8 1.0
CD A:GLN141 4.8 26.2 1.0
OE1 A:GLU107 4.9 36.5 1.0
CA A:GLU27 5.0 19.4 1.0
O A:HOH405 5.0 45.0 1.0

Magnesium binding site 2 out of 10 in 6ftv

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Magnesium binding site 2 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg209

b:76.0
occ:0.80
 O A:HOH640 2.2 72.3 1.0
SG A:CYS90 2.8 81.1 1.0
CB A:CYS90 3.2 61.6 1.0
O A:HOH479 3.2 37.2 1.0
CA A:CYS90 3.6 57.9 1.0
O A:HOH348 3.7 77.2 1.0
O A:ASP92 4.2 43.5 1.0
O A:HOH540 4.5 65.0 1.0
N A:CYS90 4.5 60.9 1.0
O A:ASP89 4.6 56.6 1.0
C A:CYS90 4.8 53.5 1.0
N A:ASP91 4.8 43.2 1.0
C A:ASP89 4.9 58.6 1.0

Magnesium binding site 3 out of 10 in 6ftv

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Magnesium binding site 3 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg210

b:17.8
occ:0.30
 O A:HOH533 2.0 23.4 1.0
O A:HOH310 2.1 22.8 1.0
OE2 A:GLU134 3.8 20.8 0.5
OE2 A:GLU134 3.9 23.8 0.5
O A:HOH438 4.2 29.9 1.0
OE1 A:GLU134 4.2 15.3 0.5
O A:HOH612 4.2 26.4 1.0
CD A:GLU134 4.5 18.9 0.5
OE1 A:GLU134 4.6 25.2 0.5
CD A:GLU134 4.6 22.3 0.5

Magnesium binding site 4 out of 10 in 6ftv

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Magnesium binding site 4 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg211

b:11.6
occ:0.25
 O A:HOH641 1.9 29.6 0.5
O A:HOH340 4.0 27.8 1.0
CD A:LYS86 4.3 30.9 0.5
O A:HOH634 4.4 45.1 1.0
O A:HOH583 4.6 43.8 1.0
CE A:LYS87 4.6 39.8 1.0
NZ A:LYS86 4.7 22.0 0.5
CE A:LYS86 4.8 36.4 0.5
CD A:LYS86 5.0 19.9 0.5

Magnesium binding site 5 out of 10 in 6ftv

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Magnesium binding site 5 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg212

b:20.9
occ:0.30
 O A:HOH396 2.0 26.1 0.3
OD2 A:ASP150 2.0 21.7 1.0
O A:HOH504 2.1 16.9 0.3
O A:HOH475 2.1 14.9 0.3
O A:HOH601 2.1 17.9 0.3
O A:HOH415 2.5 31.5 1.0
O A:HOH592 2.5 38.2 0.7
CG A:ASP150 3.1 20.6 1.0
CB A:ASP150 3.6 16.5 1.0
O A:HOH435 4.0 50.2 1.0
OD1 A:ASP150 4.0 18.6 1.0
O A:HOH459 4.2 24.3 0.7
O A:HOH632 4.3 39.0 1.0
NZ A:LYS146 4.5 19.1 1.0
O A:HOH426 4.6 21.5 1.0

Magnesium binding site 6 out of 10 in 6ftv

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Magnesium binding site 6 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:22.8
occ:0.60
 O A:HOH620 2.0 28.6 0.6
O A:HOH376 2.1 26.1 0.6
O A:HOH427 2.3 34.2 1.0
OD2 A:ASP131 4.0 29.4 1.0
O A:HOH530 4.3 23.7 0.4
O A:HOH617 4.3 57.1 1.0
CG2 A:THR135 4.3 30.2 1.0
OG1 A:THR135 4.5 26.6 1.0
O A:HOH530 4.5 29.1 0.6
O A:HOH511 4.5 30.0 0.6
OD1 A:ASP131 4.6 28.6 1.0
CG A:ASP131 4.7 23.5 1.0
CB A:THR135 4.9 23.3 1.0

Magnesium binding site 7 out of 10 in 6ftv

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Magnesium binding site 7 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:32.8
occ:0.50
 MG A:MG214 0.0 32.8 0.5
MG A:MG214 1.5 36.3 0.5
O A:HOH651 2.0 35.9 0.5
SG A:CYS102 2.5 24.5 0.5
O A:HOH573 2.6 40.6 0.5
O A:HOH651 2.7 33.8 0.5
SG A:CYS102 2.7 44.2 0.5
O A:HOH548 3.2 52.6 0.5
CB A:CYS102 3.2 30.5 0.5
CB A:CYS102 3.2 21.6 0.5
O A:HOH540 3.7 65.0 1.0
O A:HOH467 3.7 60.8 1.0
CA A:CYS102 3.8 25.1 0.5
CA A:CYS102 3.9 20.4 0.5
CZ3 A:TRP93 4.2 39.3 1.0
O A:HOH563 4.5 93.2 1.0
SG A:CYS90 4.5 81.1 1.0
C A:CYS102 4.8 20.2 0.5
O A:CYS102 4.8 19.5 0.5
C A:CYS102 4.8 22.6 0.5
N A:CYS102 4.8 20.2 0.5
N A:CYS102 4.9 18.0 0.5
O A:CYS102 4.9 21.0 0.5

Magnesium binding site 8 out of 10 in 6ftv

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Magnesium binding site 8 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


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 in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:36.3
occ:0.50
 MG A:MG214 0.0 36.3 0.5
MG A:MG214 1.5 32.8 0.5
O A:HOH651 2.0 33.8 0.5
SG A:CYS102 2.1 24.5 0.5
O A:HOH548 2.3 52.6 0.5
O A:HOH651 2.4 35.9 0.5
O A:HOH563 3.1 93.2 1.0
CB A:CYS102 3.2 21.6 0.5
CB A:CYS102 3.2 30.5 0.5
CA A:CYS102 3.5 25.1 0.5
CA A:CYS102 3.5 20.4 0.5
SG A:CYS102 3.5 44.2 0.5
O A:HOH540 3.6 65.0 1.0
O A:HOH573 4.0 40.6 0.5
N A:CYS102 4.1 20.2 0.5
N A:CYS102 4.1 18.0 0.5
O A:HOH467 4.3 60.8 1.0
CD2 A:HIS105 4.5 45.9 0.5
O A:HOH330 4.6 65.2 1.0
C A:CYS102 4.7 20.2 0.5
C A:CYS102 4.7 22.6 0.5
O A:CYS102 4.8 19.5 0.5
C A:GLU101 4.9 21.0 1.0
O A:CYS102 4.9 21.0 0.5

Magnesium binding site 9 out of 10 in 6ftv

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Magnesium binding site 9 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:48.2
occ:0.70
 OD1 A:ASP42 2.2 22.1 1.0
O A:HOH378 2.5 30.3 1.0
CG A:ASP42 3.5 20.7 1.0
O A:HOH451 3.9 25.0 1.0
O A:HOH394 4.2 19.2 1.0
O A:ASP42 4.2 18.1 1.0
OD2 A:ASP42 4.3 20.9 1.0
CB A:ASP42 4.4 19.2 1.0
CA A:ASP42 4.5 16.7 1.0
C A:ASP42 4.8 17.6 1.0
O A:HOH469 4.9 29.1 1.0

Magnesium binding site 10 out of 10 in 6ftv

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Magnesium binding site 10 out of 10 in the X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of X-Ray Structure of Human Heavy Chain Ferritin in Complex with Nami A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:33.5
occ:0.70
 O A:HOH307 1.7 32.2 0.7
O A:HOH432 2.1 29.3 0.7
OE1 A:GLN58 2.1 21.8 0.3
OE1 A:GLN58 2.2 27.6 0.7
OE1 A:GLU61 2.3 38.3 0.7
O A:HOH342 2.3 27.0 0.7
O A:HOH539 2.7 41.3 0.7
CD A:GLN58 2.9 21.9 0.3
NE2 A:GLN58 2.9 24.6 0.3
CD A:GLN58 3.4 26.3 0.7
CD A:GLU61 3.6 31.5 0.7
O A:HOH371 3.8 44.8 1.0
O A:HOH357 3.9 62.6 1.0
OE2 A:GLU107 4.2 45.5 1.0
NE2 A:GLN58 4.2 30.4 0.7
CG A:GLN58 4.3 21.6 0.3
OE1 A:GLU62 4.3 35.9 1.0
O A:HOH505 4.3 33.4 1.0
CG A:GLN58 4.4 22.5 0.7
OE2 A:GLU61 4.4 40.5 0.7
CB A:GLU61 4.4 22.8 0.7
CB A:ALA144 4.4 21.7 1.0
CB A:GLN58 4.5 19.8 0.7
O A:HOH401 4.5 34.4 1.0
CA A:GLN58 4.6 19.4 0.7
CA A:GLN58 4.6 19.4 0.3
CG A:GLU61 4.6 29.3 0.7
CB A:GLU61 4.6 23.9 0.3
CB A:GLN58 4.7 20.4 0.3
O A:HOH474 4.7 49.2 1.0
O A:GLN58 4.8 18.3 0.3
O A:GLN58 4.9 18.6 0.7

Reference:

S.Ciambellotti, A.Pratesi, M.Severi, G.Ferraro, E.Alessio, A.Merlino, L.Messori. The Nami A - Human Ferritin System: A Biophysical Characterization. Dalton Trans V. 47 11429 2018.
ISSN: ESSN 1477-9234
PubMed: 30063237
DOI: 10.1039/C8DT00860D
Page generated: Tue Oct 1 00:52:23 2024

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