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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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

Go back to Magnesium Binding Sites List in 6ftv
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: Mon Dec 14 22:43:03 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy