Iron in PDB 6wyg: Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
All present enzymatic activity of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent:
1.16.3.1;
Protein crystallography data
The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent, PDB code: 6wyg
was solved by
J.B.Bailey,
L.Zhang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.07 /
2.27
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
126.810,
126.810,
281.285,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.8 /
26
|
Other elements in 6wyg:
The structure of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
(pdb code 6wyg). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 9 binding sites of Iron where determined in the
Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent, PDB code: 6wyg:
Jump to Iron binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Iron binding site 1 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 1 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:56.9
occ:0.40
|
OE1
|
A:GLU62
|
2.5
|
77.7
|
1.0
|
OE1
|
A:GLU27
|
2.5
|
67.3
|
1.0
|
FE
|
A:FE202
|
2.8
|
46.6
|
0.2
|
OE2
|
A:GLU62
|
3.0
|
77.5
|
1.0
|
CD
|
A:GLU62
|
3.1
|
61.8
|
1.0
|
OE2
|
A:GLU27
|
3.1
|
60.3
|
1.0
|
CD
|
A:GLU27
|
3.1
|
59.4
|
1.0
|
ND1
|
A:HIS65
|
3.2
|
71.7
|
1.0
|
NE2
|
A:GLN141
|
3.3
|
71.8
|
1.0
|
CE1
|
A:HIS65
|
4.0
|
71.5
|
1.0
|
OE1
|
A:GLN141
|
4.0
|
75.5
|
1.0
|
CD
|
A:GLN141
|
4.1
|
63.8
|
1.0
|
CG
|
A:HIS65
|
4.2
|
61.6
|
1.0
|
CG1
|
A:VAL110
|
4.3
|
61.0
|
1.0
|
OE2
|
A:GLU107
|
4.3
|
63.3
|
1.0
|
CB
|
A:HIS65
|
4.4
|
54.2
|
1.0
|
CG
|
A:GLU62
|
4.6
|
49.9
|
1.0
|
CG
|
A:GLU27
|
4.6
|
46.2
|
1.0
|
CD2
|
A:TYR137
|
4.7
|
52.9
|
1.0
|
CE2
|
A:TYR137
|
5.0
|
50.3
|
1.0
|
OE1
|
A:GLU107
|
5.0
|
75.9
|
1.0
|
|
Iron binding site 2 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 2 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe202
b:46.6
occ:0.25
|
OE1
|
A:GLU107
|
2.5
|
75.9
|
1.0
|
OE2
|
A:GLU62
|
2.5
|
77.5
|
1.0
|
OE1
|
A:GLU62
|
2.8
|
77.7
|
1.0
|
FE
|
A:FE201
|
2.8
|
56.9
|
0.4
|
CD
|
A:GLU62
|
2.9
|
61.8
|
1.0
|
OE2
|
A:GLU107
|
3.0
|
63.3
|
1.0
|
CD
|
A:GLU107
|
3.1
|
60.8
|
1.0
|
OE1
|
A:GLN141
|
3.4
|
75.5
|
1.0
|
NE2
|
A:GLN141
|
3.9
|
71.8
|
1.0
|
CD
|
A:GLN141
|
4.0
|
63.8
|
1.0
|
CG
|
A:GLU62
|
4.2
|
49.9
|
1.0
|
ND1
|
A:HIS65
|
4.4
|
71.7
|
1.0
|
CG
|
A:GLU107
|
4.6
|
49.5
|
1.0
|
CB
|
A:ALA144
|
4.6
|
39.0
|
1.0
|
CE1
|
A:HIS65
|
4.8
|
71.5
|
1.0
|
OE1
|
A:GLU27
|
4.8
|
67.3
|
1.0
|
|
Iron binding site 3 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 3 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe203
b:71.3
occ:1.00
|
NE2
|
D:HIS173
|
2.9
|
50.6
|
1.0
|
NE2
|
A:HIS173
|
3.1
|
52.1
|
1.0
|
NE2
|
C:HIS173
|
3.1
|
48.2
|
1.0
|
NE2
|
B:HIS173
|
3.1
|
46.2
|
1.0
|
CE1
|
D:HIS173
|
3.8
|
56.9
|
1.0
|
CE1
|
C:HIS173
|
3.8
|
54.9
|
1.0
|
CE1
|
B:HIS173
|
3.8
|
42.7
|
1.0
|
CE1
|
A:HIS173
|
3.8
|
47.1
|
1.0
|
CD2
|
A:LEU169
|
3.9
|
40.3
|
1.0
|
CD2
|
D:LEU169
|
3.9
|
40.7
|
1.0
|
CD2
|
D:HIS173
|
4.0
|
47.2
|
1.0
|
CD2
|
B:LEU169
|
4.1
|
44.6
|
1.0
|
CD2
|
C:LEU169
|
4.1
|
44.5
|
1.0
|
CD2
|
A:HIS173
|
4.1
|
47.7
|
1.0
|
CD2
|
C:HIS173
|
4.2
|
47.5
|
1.0
|
CD2
|
B:HIS173
|
4.2
|
46.8
|
1.0
|
CD1
|
A:LEU169
|
4.8
|
41.5
|
1.0
|
CD1
|
C:LEU169
|
4.9
|
46.8
|
1.0
|
CG
|
A:LEU169
|
4.9
|
45.8
|
1.0
|
ND1
|
D:HIS173
|
4.9
|
55.8
|
1.0
|
ND1
|
C:HIS173
|
5.0
|
50.5
|
1.0
|
|
Iron binding site 4 out
of 9 in 6wyg
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Iron Binding Sites List in 6wyg
Iron binding site 4 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:67.6
occ:0.40
|
OE1
|
B:GLU62
|
2.3
|
65.5
|
1.0
|
OE2
|
B:GLU62
|
2.4
|
66.3
|
1.0
|
CD
|
B:GLU62
|
2.7
|
56.0
|
1.0
|
OE1
|
B:GLU27
|
2.7
|
60.8
|
1.0
|
ND1
|
B:HIS65
|
2.8
|
74.6
|
1.0
|
NE2
|
B:GLN141
|
3.0
|
62.3
|
1.0
|
FE
|
B:FE202
|
3.1
|
42.1
|
0.2
|
CE1
|
B:HIS65
|
3.5
|
76.2
|
1.0
|
CD
|
B:GLU27
|
3.7
|
59.2
|
1.0
|
CG
|
B:HIS65
|
3.8
|
67.9
|
1.0
|
OE2
|
B:GLU27
|
3.9
|
51.8
|
1.0
|
CG
|
B:GLU62
|
4.1
|
46.3
|
1.0
|
CB
|
B:HIS65
|
4.2
|
52.0
|
1.0
|
CD
|
B:GLN141
|
4.3
|
63.6
|
1.0
|
OE2
|
B:GLU107
|
4.4
|
64.6
|
1.0
|
CG1
|
B:VAL110
|
4.5
|
47.2
|
1.0
|
O
|
B:HOH306
|
4.6
|
53.3
|
1.0
|
NE2
|
B:HIS65
|
4.7
|
80.7
|
1.0
|
CA
|
B:GLU62
|
4.7
|
48.1
|
1.0
|
CB
|
B:GLU62
|
4.8
|
39.2
|
1.0
|
CD2
|
B:HIS65
|
4.8
|
77.9
|
1.0
|
OE1
|
B:GLU107
|
4.9
|
65.4
|
1.0
|
|
Iron binding site 5 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 5 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 5 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe202
b:42.1
occ:0.25
|
OE1
|
B:GLU62
|
2.3
|
65.5
|
1.0
|
O
|
B:HOH306
|
2.5
|
53.3
|
1.0
|
OE2
|
B:GLU107
|
2.6
|
64.6
|
1.0
|
OE1
|
B:GLU107
|
2.6
|
65.4
|
1.0
|
CD
|
B:GLU107
|
2.9
|
58.1
|
1.0
|
NE2
|
B:GLN141
|
3.0
|
62.3
|
1.0
|
FE
|
B:FE201
|
3.1
|
67.6
|
0.4
|
CD
|
B:GLU62
|
3.5
|
56.0
|
1.0
|
CB
|
B:ALA144
|
4.0
|
43.1
|
1.0
|
CD
|
B:GLN141
|
4.0
|
63.6
|
1.0
|
OE2
|
B:GLU61
|
4.1
|
86.5
|
1.0
|
OE2
|
B:GLU62
|
4.1
|
66.3
|
1.0
|
CG
|
B:GLU107
|
4.3
|
54.8
|
1.0
|
OE1
|
B:GLN141
|
4.4
|
71.7
|
1.0
|
CG
|
B:GLU62
|
4.5
|
46.3
|
1.0
|
CE1
|
B:HIS65
|
4.7
|
76.2
|
1.0
|
OE1
|
B:GLN58
|
4.7
|
77.3
|
1.0
|
ND1
|
B:HIS65
|
4.7
|
74.6
|
1.0
|
OH
|
B:TYR34
|
5.0
|
61.8
|
1.0
|
|
Iron binding site 6 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 6 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 6 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:83.0
occ:0.40
|
OE1
|
C:GLU27
|
2.4
|
66.2
|
1.0
|
FE
|
C:FE202
|
2.7
|
40.6
|
0.2
|
OE2
|
C:GLU62
|
2.7
|
64.4
|
1.0
|
OE1
|
C:GLU62
|
2.9
|
75.4
|
1.0
|
OE1
|
C:GLN141
|
3.1
|
69.9
|
1.0
|
CD
|
C:GLU62
|
3.2
|
62.7
|
1.0
|
CD
|
C:GLU27
|
3.3
|
66.0
|
1.0
|
OE2
|
C:GLU27
|
3.4
|
69.0
|
1.0
|
ND1
|
C:HIS65
|
3.8
|
73.2
|
1.0
|
CB
|
C:HIS65
|
4.1
|
51.7
|
1.0
|
CG1
|
C:VAL110
|
4.2
|
54.2
|
1.0
|
CG
|
C:HIS65
|
4.2
|
67.1
|
1.0
|
CD
|
C:GLN141
|
4.2
|
65.0
|
1.0
|
O
|
C:HOH310
|
4.3
|
62.9
|
1.0
|
CD2
|
C:TYR137
|
4.5
|
64.3
|
1.0
|
CE2
|
C:TYR137
|
4.6
|
65.6
|
1.0
|
CG
|
C:GLU62
|
4.6
|
55.6
|
1.0
|
OE2
|
C:GLU107
|
4.6
|
66.7
|
1.0
|
CG
|
C:GLU27
|
4.7
|
54.5
|
1.0
|
CE1
|
C:HIS65
|
4.7
|
77.8
|
1.0
|
CG
|
C:GLN141
|
4.9
|
65.3
|
1.0
|
CA
|
C:GLU62
|
5.0
|
51.0
|
1.0
|
|
Iron binding site 7 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 7 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 7 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe202
b:40.6
occ:0.25
|
OE1
|
C:GLU62
|
2.1
|
75.4
|
1.0
|
OE1
|
C:GLN141
|
2.3
|
69.9
|
1.0
|
O
|
C:HOH310
|
2.4
|
62.9
|
1.0
|
OE2
|
C:GLU107
|
2.4
|
66.7
|
1.0
|
FE
|
C:FE201
|
2.7
|
83.0
|
0.4
|
OE1
|
C:GLU107
|
2.7
|
67.9
|
1.0
|
CD
|
C:GLU107
|
2.9
|
59.4
|
1.0
|
CD
|
C:GLU62
|
3.0
|
62.7
|
1.0
|
OE2
|
C:GLU62
|
3.3
|
64.4
|
1.0
|
CD
|
C:GLN141
|
3.4
|
65.0
|
1.0
|
NE2
|
C:GLN141
|
4.1
|
56.9
|
1.0
|
CG
|
C:GLU62
|
4.3
|
55.6
|
1.0
|
CG
|
C:GLU107
|
4.4
|
52.0
|
1.0
|
CG
|
C:GLN141
|
4.6
|
65.3
|
1.0
|
OE1
|
C:GLU27
|
4.7
|
66.2
|
1.0
|
CG1
|
C:VAL110
|
4.8
|
54.2
|
1.0
|
CB
|
C:ALA144
|
5.0
|
43.0
|
1.0
|
|
Iron binding site 8 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 8 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 8 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:71.1
occ:0.40
|
OE1
|
D:GLN141
|
2.3
|
84.7
|
1.0
|
FE
|
D:FE202
|
2.4
|
58.0
|
0.2
|
OE2
|
D:GLU62
|
2.4
|
64.7
|
1.0
|
OE1
|
D:GLU62
|
2.7
|
71.9
|
1.0
|
OE1
|
D:GLU27
|
2.8
|
73.5
|
1.0
|
CD
|
D:GLU62
|
2.9
|
64.7
|
1.0
|
ND1
|
D:HIS65
|
3.2
|
74.7
|
1.0
|
CD
|
D:GLN141
|
3.3
|
82.1
|
1.0
|
OE2
|
D:GLU27
|
3.4
|
71.3
|
1.0
|
CD
|
D:GLU27
|
3.5
|
71.5
|
1.0
|
CE1
|
D:HIS65
|
3.7
|
76.9
|
1.0
|
NE2
|
D:GLN141
|
3.8
|
77.1
|
1.0
|
OE2
|
D:GLU107
|
4.0
|
77.3
|
1.0
|
O
|
D:HOH312
|
4.2
|
63.1
|
1.0
|
OE1
|
D:GLU107
|
4.3
|
71.8
|
1.0
|
CG
|
D:HIS65
|
4.4
|
72.5
|
1.0
|
CG
|
D:GLU62
|
4.4
|
63.6
|
1.0
|
CG1
|
D:VAL110
|
4.4
|
57.1
|
1.0
|
CD
|
D:GLU107
|
4.6
|
71.3
|
1.0
|
CG
|
D:GLN141
|
4.6
|
78.8
|
1.0
|
CB
|
D:HIS65
|
4.8
|
67.6
|
1.0
|
NE2
|
D:HIS65
|
5.0
|
79.4
|
1.0
|
|
Iron binding site 9 out
of 9 in 6wyg
Go back to
Iron Binding Sites List in 6wyg
Iron binding site 9 out
of 9 in the Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 9 of Crystal Structure of Human H-Chain Ferritin Variant 157C Delta C-Star Modified with A Raft Agent within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe202
b:58.0
occ:0.25
|
O
|
D:HOH312
|
2.2
|
63.1
|
1.0
|
OE2
|
D:GLU107
|
2.4
|
77.3
|
1.0
|
FE
|
D:FE201
|
2.4
|
71.1
|
0.4
|
OE1
|
D:GLU62
|
2.4
|
71.9
|
1.0
|
OE1
|
D:GLN141
|
2.5
|
84.7
|
1.0
|
OE1
|
D:GLU107
|
2.7
|
71.8
|
1.0
|
CD
|
D:GLU107
|
2.8
|
71.3
|
1.0
|
CD
|
D:GLN141
|
3.2
|
82.1
|
1.0
|
CD
|
D:GLU62
|
3.3
|
64.7
|
1.0
|
NE2
|
D:GLN141
|
3.3
|
77.1
|
1.0
|
OE2
|
D:GLU62
|
3.5
|
64.7
|
1.0
|
CG
|
D:GLU107
|
4.2
|
69.8
|
1.0
|
CB
|
D:ALA144
|
4.5
|
51.4
|
1.0
|
CE1
|
D:HIS65
|
4.6
|
76.9
|
1.0
|
CG
|
D:GLN141
|
4.6
|
78.8
|
1.0
|
CG
|
D:GLU62
|
4.6
|
63.6
|
1.0
|
ND1
|
D:HIS65
|
4.7
|
74.7
|
1.0
|
|
Reference:
K.Han,
J.B.Bailey,
L.Zhang,
F.A.Tezcan.
Anisotropic Dynamics and Mechanics of Macromolecular Crystals Containing Lattice-Patterned Polymer Networks. J.Am.Chem.Soc. V. 142 19402 2020.
ISSN: ESSN 1520-5126
PubMed: 33124805
DOI: 10.1021/JACS.0C10065
Page generated: Wed Aug 7 14:30:52 2024
|