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:
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
Go back to
Magnesium Binding Sites List in 5n27
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
|