Iron in PDB 5jkl: Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
All present enzymatic activity of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition):
1.16.3.1;
Protein crystallography data
The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition), PDB code: 5jkl
was solved by
M.Kuenzle,
T.Beck,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
48.85 /
1.80
|
Space group
|
P 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.620,
126.620,
174.860,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.7 /
17.6
|
Other elements in 5jkl:
The structure of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) also contains other interesting chemical elements:
Iron Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
18;
Binding sites:
The binding sites of Iron atom in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
(pdb code 5jkl). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 18 binding sites of Iron where determined in the
Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition), PDB code: 5jkl:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Iron binding site 1 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 1 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:26.7
occ:1.00
|
OE1
|
A:GLU62
|
2.1
|
21.8
|
1.0
|
OE1
|
A:GLU27
|
2.1
|
17.5
|
1.0
|
O
|
A:HOH304
|
2.2
|
18.1
|
1.0
|
O
|
A:HOH305
|
2.2
|
28.9
|
1.0
|
ND1
|
A:HIS65
|
2.3
|
24.9
|
1.0
|
CD
|
A:GLU62
|
3.0
|
22.1
|
1.0
|
CD
|
A:GLU27
|
3.0
|
18.4
|
1.0
|
CE1
|
A:HIS65
|
3.2
|
26.6
|
1.0
|
OE2
|
A:GLU62
|
3.3
|
24.0
|
1.0
|
CG
|
A:HIS65
|
3.3
|
19.2
|
1.0
|
OE2
|
A:GLU27
|
3.3
|
19.0
|
1.0
|
CB
|
A:HIS65
|
3.6
|
15.2
|
1.0
|
OE1
|
A:GLN141
|
4.0
|
28.1
|
1.0
|
CG
|
A:GLU27
|
4.3
|
14.9
|
1.0
|
CG1
|
A:VAL110
|
4.3
|
17.6
|
1.0
|
CG
|
A:GLU62
|
4.3
|
16.2
|
1.0
|
NE2
|
A:HIS65
|
4.4
|
23.2
|
1.0
|
CD2
|
A:HIS65
|
4.4
|
22.1
|
1.0
|
CA
|
A:GLU62
|
4.5
|
13.4
|
1.0
|
CB
|
A:GLU62
|
4.6
|
13.5
|
1.0
|
CB
|
A:GLU27
|
4.6
|
13.5
|
1.0
|
CD
|
A:GLN141
|
4.9
|
23.0
|
1.0
|
CA
|
A:GLU27
|
5.0
|
12.6
|
1.0
|
|
Iron binding site 2 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 2 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:21.8
occ:0.25
|
NE2
|
A:HIS173
|
2.3
|
20.7
|
1.0
|
CL
|
A:CL205
|
2.3
|
28.0
|
0.2
|
CE1
|
A:HIS173
|
3.0
|
21.4
|
1.0
|
CD2
|
A:HIS173
|
3.4
|
24.9
|
1.0
|
ND1
|
A:HIS173
|
4.2
|
23.7
|
1.0
|
CG
|
A:HIS173
|
4.4
|
17.8
|
1.0
|
|
Iron binding site 3 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 3 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:23.8
occ:1.00
|
OE1
|
B:GLU27
|
2.0
|
17.1
|
1.0
|
OE1
|
B:GLU62
|
2.1
|
19.0
|
1.0
|
ND1
|
B:HIS65
|
2.1
|
19.4
|
1.0
|
O
|
B:HOH312
|
2.1
|
27.2
|
1.0
|
O
|
B:HOH345
|
2.2
|
17.1
|
1.0
|
CD
|
B:GLU62
|
3.0
|
21.3
|
1.0
|
CE1
|
B:HIS65
|
3.0
|
24.1
|
1.0
|
CD
|
B:GLU27
|
3.1
|
17.5
|
1.0
|
CG
|
B:HIS65
|
3.2
|
18.7
|
1.0
|
OE2
|
B:GLU62
|
3.3
|
31.7
|
1.0
|
OE2
|
B:GLU27
|
3.4
|
18.1
|
1.0
|
CB
|
B:HIS65
|
3.6
|
14.6
|
1.0
|
OE1
|
B:GLN141
|
4.0
|
25.3
|
1.0
|
NE2
|
B:HIS65
|
4.2
|
21.8
|
1.0
|
CG1
|
B:VAL110
|
4.3
|
17.4
|
1.0
|
CD2
|
B:HIS65
|
4.3
|
21.7
|
1.0
|
CG
|
B:GLU62
|
4.3
|
15.4
|
1.0
|
CG
|
B:GLU27
|
4.4
|
17.0
|
1.0
|
CA
|
B:GLU62
|
4.5
|
15.0
|
1.0
|
CB
|
B:GLU62
|
4.6
|
14.5
|
1.0
|
CB
|
B:GLU27
|
4.8
|
14.2
|
1.0
|
CD
|
B:GLN141
|
4.9
|
23.4
|
1.0
|
|
Iron binding site 4 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 4 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:24.3
occ:1.00
|
OE1
|
C:GLU27
|
2.0
|
19.4
|
1.0
|
OE1
|
C:GLU62
|
2.1
|
23.8
|
1.0
|
O
|
C:HOH313
|
2.1
|
25.9
|
1.0
|
ND1
|
C:HIS65
|
2.1
|
18.8
|
1.0
|
O
|
C:HOH327
|
2.1
|
15.6
|
1.0
|
CE1
|
C:HIS65
|
3.0
|
24.7
|
1.0
|
CD
|
C:GLU62
|
3.0
|
25.4
|
1.0
|
CD
|
C:GLU27
|
3.1
|
17.9
|
1.0
|
CG
|
C:HIS65
|
3.2
|
16.0
|
1.0
|
OE2
|
C:GLU62
|
3.3
|
31.6
|
1.0
|
OE2
|
C:GLU27
|
3.5
|
19.7
|
1.0
|
CB
|
C:HIS65
|
3.6
|
14.5
|
1.0
|
OE1
|
C:GLN141
|
4.0
|
25.1
|
1.0
|
NE2
|
C:HIS65
|
4.2
|
21.1
|
1.0
|
CG1
|
C:VAL110
|
4.3
|
19.7
|
1.0
|
CD2
|
C:HIS65
|
4.3
|
20.7
|
1.0
|
CG
|
C:GLU27
|
4.4
|
15.6
|
1.0
|
CG
|
C:GLU62
|
4.4
|
17.1
|
1.0
|
CA
|
C:GLU62
|
4.5
|
13.9
|
1.0
|
CB
|
C:GLU62
|
4.7
|
15.3
|
1.0
|
CB
|
C:GLU27
|
4.7
|
13.5
|
1.0
|
O
|
C:HOH421
|
4.8
|
26.9
|
0.5
|
CD
|
C:GLN141
|
4.8
|
22.1
|
1.0
|
OE1
|
C:GLU107
|
4.9
|
36.8
|
1.0
|
|
Iron binding site 5 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 5 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:25.6
occ:1.00
|
OE1
|
D:GLU27
|
2.0
|
20.5
|
1.0
|
OE1
|
D:GLU62
|
2.0
|
22.6
|
1.0
|
O
|
D:HOH319
|
2.1
|
26.2
|
1.0
|
O
|
D:HOH314
|
2.1
|
20.6
|
1.0
|
ND1
|
D:HIS65
|
2.2
|
21.9
|
1.0
|
CD
|
D:GLU62
|
3.0
|
24.1
|
1.0
|
CD
|
D:GLU27
|
3.0
|
18.8
|
1.0
|
CE1
|
D:HIS65
|
3.1
|
25.7
|
1.0
|
OE2
|
D:GLU62
|
3.2
|
33.8
|
1.0
|
CG
|
D:HIS65
|
3.2
|
18.8
|
1.0
|
OE2
|
D:GLU27
|
3.4
|
21.3
|
1.0
|
CB
|
D:HIS65
|
3.6
|
15.9
|
1.0
|
OE1
|
D:GLN141
|
4.0
|
25.2
|
1.0
|
NE2
|
D:HIS65
|
4.3
|
24.6
|
1.0
|
CG
|
D:GLU62
|
4.3
|
17.6
|
1.0
|
CG
|
D:GLU27
|
4.3
|
16.8
|
1.0
|
CD2
|
D:HIS65
|
4.4
|
21.2
|
1.0
|
CG1
|
D:VAL110
|
4.4
|
19.8
|
1.0
|
CA
|
D:GLU62
|
4.6
|
14.4
|
1.0
|
CB
|
D:GLU62
|
4.6
|
15.0
|
1.0
|
CB
|
D:GLU27
|
4.7
|
15.7
|
1.0
|
CD
|
D:GLN141
|
4.9
|
21.8
|
1.0
|
|
Iron binding site 6 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 6 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe202
b:22.9
occ:1.00
|
CL
|
D:CL205
|
2.3
|
28.9
|
1.0
|
NE2
|
D:HIS173
|
2.3
|
24.3
|
1.0
|
CE1
|
D:HIS173
|
3.0
|
23.4
|
1.0
|
CD2
|
D:HIS173
|
3.5
|
28.2
|
1.0
|
ND1
|
D:HIS173
|
4.2
|
21.5
|
1.0
|
CG
|
D:HIS173
|
4.5
|
18.2
|
1.0
|
|
Iron binding site 7 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 7 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:25.4
occ:1.00
|
OE1
|
E:GLU27
|
2.0
|
19.6
|
1.0
|
OE1
|
E:GLU62
|
2.1
|
20.6
|
1.0
|
ND1
|
E:HIS65
|
2.1
|
24.3
|
1.0
|
O
|
E:HOH318
|
2.1
|
29.9
|
1.0
|
O
|
E:HOH314
|
2.1
|
19.7
|
1.0
|
CD
|
E:GLU62
|
3.0
|
25.1
|
1.0
|
CD
|
E:GLU27
|
3.0
|
18.4
|
1.0
|
CE1
|
E:HIS65
|
3.0
|
26.9
|
1.0
|
CG
|
E:HIS65
|
3.2
|
22.4
|
1.0
|
OE2
|
E:GLU62
|
3.3
|
27.6
|
1.0
|
OE2
|
E:GLU27
|
3.4
|
21.2
|
1.0
|
CB
|
E:HIS65
|
3.6
|
16.6
|
1.0
|
OE1
|
E:GLN141
|
4.0
|
24.6
|
1.0
|
NE2
|
E:HIS65
|
4.2
|
26.2
|
1.0
|
CD2
|
E:HIS65
|
4.3
|
24.8
|
1.0
|
CG
|
E:GLU27
|
4.3
|
15.2
|
1.0
|
CG
|
E:GLU62
|
4.3
|
17.6
|
1.0
|
CG1
|
E:VAL110
|
4.4
|
22.9
|
1.0
|
CA
|
E:GLU62
|
4.6
|
15.5
|
1.0
|
CB
|
E:GLU62
|
4.6
|
16.6
|
1.0
|
CB
|
E:GLU27
|
4.7
|
13.9
|
1.0
|
CD
|
E:GLN141
|
4.9
|
21.8
|
1.0
|
OE1
|
E:GLU107
|
5.0
|
34.6
|
1.0
|
|
Iron binding site 8 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 8 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:24.0
occ:1.00
|
OE1
|
F:GLU27
|
2.0
|
19.5
|
1.0
|
OE1
|
F:GLU62
|
2.0
|
21.3
|
1.0
|
O
|
F:HOH313
|
2.1
|
28.2
|
1.0
|
O
|
F:HOH310
|
2.1
|
19.1
|
1.0
|
ND1
|
F:HIS65
|
2.2
|
23.2
|
1.0
|
CD
|
F:GLU62
|
3.0
|
22.2
|
1.0
|
CD
|
F:GLU27
|
3.0
|
19.1
|
1.0
|
CE1
|
F:HIS65
|
3.1
|
26.3
|
1.0
|
CG
|
F:HIS65
|
3.2
|
20.3
|
1.0
|
OE2
|
F:GLU62
|
3.2
|
27.4
|
1.0
|
OE2
|
F:GLU27
|
3.4
|
18.8
|
1.0
|
CB
|
F:HIS65
|
3.6
|
16.1
|
1.0
|
OE1
|
F:GLN141
|
4.0
|
25.9
|
1.0
|
NE2
|
F:HIS65
|
4.2
|
24.0
|
1.0
|
CG1
|
F:VAL110
|
4.3
|
18.7
|
1.0
|
CG
|
F:GLU27
|
4.3
|
15.5
|
1.0
|
CD2
|
F:HIS65
|
4.3
|
22.1
|
1.0
|
CG
|
F:GLU62
|
4.3
|
17.0
|
1.0
|
CA
|
F:GLU62
|
4.6
|
14.0
|
1.0
|
CB
|
F:GLU62
|
4.7
|
15.0
|
1.0
|
CB
|
F:GLU27
|
4.7
|
14.3
|
1.0
|
CD
|
F:GLN141
|
4.9
|
25.5
|
1.0
|
|
Iron binding site 9 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 9 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe202
b:22.5
occ:0.25
|
NE2
|
F:HIS173
|
2.2
|
22.6
|
1.0
|
CL
|
F:CL204
|
2.5
|
33.4
|
0.2
|
CE1
|
F:HIS173
|
2.9
|
22.3
|
1.0
|
CD2
|
F:HIS173
|
3.4
|
26.3
|
1.0
|
ND1
|
F:HIS173
|
4.1
|
22.8
|
1.0
|
CG
|
F:HIS173
|
4.4
|
18.1
|
1.0
|
|
Iron binding site 10 out
of 18 in 5jkl
Go back to
Iron Binding Sites List in 5jkl
Iron binding site 10 out
of 18 in the Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition)
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 10 of Binary Crystal Structure of Positively and Negatively Supercharged Variants Ftn(Pos) and Ftn(Neg) From Human Heavy Chain Ferritin (Mg Formate Condition) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Fe201
b:27.4
occ:1.00
|
OE1
|
G:GLU27
|
2.0
|
17.9
|
1.0
|
OE1
|
G:GLU62
|
2.1
|
22.3
|
1.0
|
O
|
G:HOH334
|
2.1
|
18.6
|
1.0
|
ND1
|
G:HIS65
|
2.2
|
27.9
|
1.0
|
O
|
G:HOH305
|
2.2
|
39.2
|
1.0
|
CD
|
G:GLU27
|
3.0
|
19.2
|
1.0
|
CD
|
G:GLU62
|
3.0
|
22.4
|
1.0
|
CE1
|
G:HIS65
|
3.0
|
28.4
|
1.0
|
CG
|
G:HIS65
|
3.2
|
22.0
|
1.0
|
OE2
|
G:GLU62
|
3.3
|
27.6
|
1.0
|
OE2
|
G:GLU27
|
3.4
|
21.4
|
1.0
|
CB
|
G:HIS65
|
3.6
|
18.6
|
1.0
|
OE1
|
G:GLN141
|
3.9
|
26.8
|
1.0
|
NE2
|
G:HIS65
|
4.2
|
30.2
|
1.0
|
CD2
|
G:HIS65
|
4.3
|
26.4
|
1.0
|
CG
|
G:GLU27
|
4.3
|
16.6
|
1.0
|
CG
|
G:GLU62
|
4.4
|
17.8
|
1.0
|
CG1
|
G:VAL110
|
4.5
|
19.4
|
1.0
|
CA
|
G:GLU62
|
4.6
|
15.3
|
1.0
|
CB
|
G:GLU62
|
4.7
|
15.8
|
1.0
|
CB
|
G:GLU27
|
4.7
|
15.9
|
1.0
|
CD
|
G:GLN141
|
4.8
|
25.7
|
1.0
|
OE1
|
G:GLU107
|
4.9
|
36.9
|
1.0
|
|
Reference:
M.Kunzle,
T.Eckert,
T.Beck.
Binary Protein Crystals For the Assembly of Inorganic Nanoparticle Superlattices. J.Am.Chem.Soc. V. 138 12731 2016.
ISSN: ESSN 1520-5126
PubMed: 27617514
DOI: 10.1021/JACS.6B07260
Page generated: Tue Aug 6 02:31:31 2024
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