Iron in PDB 4jea: Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
Protein crystallography data
The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea
was solved by
F.A.Tezcan,
A.M.Medina-Morales,
A.Perez,
J.D.Brodin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.94 /
1.22
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.850,
64.788,
74.177,
90.00,
98.18,
90.00
|
R / Rfree (%)
|
13.1 /
17.9
|
Other elements in 4jea:
The structure of Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
(pdb code 4jea). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds, PDB code: 4jea:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 4jea
Go back to
Iron Binding Sites List in 4jea
Iron binding site 1 out
of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe201
b:12.8
occ:1.00
|
FE
|
A:HEM201
|
0.0
|
12.8
|
1.0
|
NA
|
A:HEM201
|
2.0
|
13.4
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
13.4
|
1.0
|
NC
|
A:HEM201
|
2.0
|
12.6
|
1.0
|
ND
|
A:HEM201
|
2.1
|
12.8
|
1.0
|
NB
|
A:HEM201
|
2.1
|
12.2
|
1.0
|
SD
|
A:MET7
|
2.4
|
13.5
|
1.0
|
CE1
|
A:HIS102
|
3.0
|
13.4
|
1.0
|
CD2
|
A:HIS102
|
3.1
|
13.7
|
1.0
|
C4A
|
A:HEM201
|
3.1
|
13.4
|
1.0
|
C4B
|
A:HEM201
|
3.1
|
12.4
|
1.0
|
C1A
|
A:HEM201
|
3.1
|
14.3
|
1.0
|
C1D
|
A:HEM201
|
3.1
|
14.0
|
1.0
|
C4D
|
A:HEM201
|
3.1
|
14.2
|
1.0
|
C1C
|
A:HEM201
|
3.1
|
12.1
|
1.0
|
C1B
|
A:HEM201
|
3.1
|
13.8
|
1.0
|
C4C
|
A:HEM201
|
3.1
|
12.4
|
1.0
|
CE
|
A:MET7
|
3.4
|
16.0
|
1.0
|
CG
|
A:MET7
|
3.5
|
15.1
|
1.0
|
CHC
|
A:HEM201
|
3.5
|
13.8
|
1.0
|
CHA
|
A:HEM201
|
3.5
|
15.0
|
1.0
|
CHB
|
A:HEM201
|
3.5
|
13.2
|
1.0
|
CHD
|
A:HEM201
|
3.5
|
13.4
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
13.3
|
1.0
|
CB
|
A:MET7
|
4.2
|
13.9
|
1.0
|
CG
|
A:HIS102
|
4.2
|
13.5
|
1.0
|
C3A
|
A:HEM201
|
4.3
|
14.8
|
1.0
|
C2A
|
A:HEM201
|
4.4
|
15.0
|
1.0
|
C3B
|
A:HEM201
|
4.4
|
13.6
|
1.0
|
C3C
|
A:HEM201
|
4.4
|
13.0
|
1.0
|
C2C
|
A:HEM201
|
4.4
|
12.1
|
1.0
|
C3D
|
A:HEM201
|
4.4
|
14.9
|
1.0
|
C2B
|
A:HEM201
|
4.4
|
13.6
|
1.0
|
C2D
|
A:HEM201
|
4.4
|
15.8
|
1.0
|
|
Iron binding site 2 out
of 4 in 4jea
Go back to
Iron Binding Sites List in 4jea
Iron binding site 2 out
of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe201
b:17.9
occ:1.00
|
FE
|
B:HEM201
|
0.0
|
17.9
|
1.0
|
NA
|
B:HEM201
|
2.0
|
19.1
|
1.0
|
NC
|
B:HEM201
|
2.0
|
17.3
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
19.5
|
1.0
|
NB
|
B:HEM201
|
2.1
|
15.8
|
1.0
|
ND
|
B:HEM201
|
2.1
|
18.3
|
1.0
|
SD
|
B:MET7
|
2.4
|
18.6
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
18.9
|
1.0
|
CE1
|
B:HIS102
|
3.1
|
18.9
|
1.0
|
C4B
|
B:HEM201
|
3.1
|
15.8
|
1.0
|
C1D
|
B:HEM201
|
3.1
|
19.4
|
1.0
|
C1C
|
B:HEM201
|
3.1
|
15.5
|
1.0
|
C1A
|
B:HEM201
|
3.1
|
20.2
|
1.0
|
C4D
|
B:HEM201
|
3.1
|
22.6
|
1.0
|
C1B
|
B:HEM201
|
3.1
|
17.0
|
1.0
|
C4A
|
B:HEM201
|
3.1
|
20.3
|
1.0
|
C4C
|
B:HEM201
|
3.2
|
16.9
|
1.0
|
CE
|
B:MET7
|
3.4
|
20.2
|
1.0
|
CHC
|
B:HEM201
|
3.5
|
15.6
|
1.0
|
CHD
|
B:HEM201
|
3.5
|
18.0
|
1.0
|
CG
|
B:MET7
|
3.5
|
20.1
|
1.0
|
CHA
|
B:HEM201
|
3.5
|
21.7
|
1.0
|
CHB
|
B:HEM201
|
3.5
|
17.9
|
1.0
|
ND1
|
B:HIS102
|
4.2
|
19.9
|
1.0
|
CG
|
B:HIS102
|
4.2
|
20.2
|
1.0
|
CB
|
B:MET7
|
4.3
|
20.1
|
1.0
|
C3B
|
B:HEM201
|
4.4
|
16.2
|
1.0
|
C2D
|
B:HEM201
|
4.4
|
21.3
|
1.0
|
C2C
|
B:HEM201
|
4.4
|
15.5
|
1.0
|
C3A
|
B:HEM201
|
4.4
|
21.7
|
1.0
|
C3D
|
B:HEM201
|
4.4
|
22.6
|
1.0
|
C2A
|
B:HEM201
|
4.4
|
23.3
|
1.0
|
C3C
|
B:HEM201
|
4.4
|
17.4
|
1.0
|
C2B
|
B:HEM201
|
4.4
|
17.0
|
1.0
|
|
Iron binding site 3 out
of 4 in 4jea
Go back to
Iron Binding Sites List in 4jea
Iron binding site 3 out
of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:14.0
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
14.0
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
15.4
|
1.0
|
NC
|
C:HEM201
|
2.0
|
13.7
|
1.0
|
NA
|
C:HEM201
|
2.0
|
14.8
|
1.0
|
ND
|
C:HEM201
|
2.1
|
14.2
|
1.0
|
NB
|
C:HEM201
|
2.1
|
13.5
|
1.0
|
SD
|
C:MET7
|
2.4
|
15.0
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
15.2
|
1.0
|
CD2
|
C:HIS102
|
3.1
|
14.0
|
1.0
|
C1D
|
C:HEM201
|
3.1
|
15.4
|
1.0
|
C1A
|
C:HEM201
|
3.1
|
16.4
|
1.0
|
C4C
|
C:HEM201
|
3.1
|
13.4
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
12.8
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
14.6
|
1.0
|
C4D
|
C:HEM201
|
3.1
|
15.2
|
1.0
|
C4B
|
C:HEM201
|
3.1
|
12.9
|
1.0
|
C4A
|
C:HEM201
|
3.2
|
16.8
|
1.0
|
CE
|
C:MET7
|
3.4
|
17.3
|
1.0
|
CHA
|
C:HEM201
|
3.4
|
16.3
|
1.0
|
CHC
|
C:HEM201
|
3.5
|
13.9
|
1.0
|
CHB
|
C:HEM201
|
3.5
|
16.5
|
1.0
|
CHD
|
C:HEM201
|
3.5
|
15.2
|
1.0
|
CG
|
C:MET7
|
3.5
|
15.5
|
1.0
|
ND1
|
C:HIS102
|
4.2
|
16.5
|
1.0
|
CG
|
C:HIS102
|
4.2
|
14.7
|
1.0
|
CB
|
C:MET7
|
4.2
|
15.8
|
1.0
|
C2A
|
C:HEM201
|
4.3
|
18.1
|
1.0
|
C3B
|
C:HEM201
|
4.4
|
14.0
|
1.0
|
C2C
|
C:HEM201
|
4.4
|
12.8
|
1.0
|
C3D
|
C:HEM201
|
4.4
|
16.2
|
1.0
|
C2B
|
C:HEM201
|
4.4
|
15.2
|
1.0
|
C3C
|
C:HEM201
|
4.4
|
14.0
|
1.0
|
C3A
|
C:HEM201
|
4.4
|
17.0
|
1.0
|
C2D
|
C:HEM201
|
4.4
|
14.8
|
1.0
|
NH2
|
C:ARG106
|
4.9
|
28.1
|
1.0
|
|
Iron binding site 4 out
of 4 in 4jea
Go back to
Iron Binding Sites List in 4jea
Iron binding site 4 out
of 4 in the Crystal Structure of An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds
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 An Engineered Zn-RIDC1 Construct with Four Interfacial Disulfide Bonds within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:19.6
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
19.6
|
1.0
|
NC
|
D:HEM201
|
2.0
|
17.5
|
1.0
|
NA
|
D:HEM201
|
2.0
|
22.3
|
1.0
|
NB
|
D:HEM201
|
2.1
|
20.3
|
1.0
|
NE2
|
D:HIS102
|
2.1
|
20.7
|
1.0
|
ND
|
D:HEM201
|
2.1
|
19.8
|
1.0
|
SD
|
D:MET7
|
2.3
|
20.2
|
1.0
|
CE1
|
D:HIS102
|
3.0
|
19.8
|
1.0
|
CD2
|
D:HIS102
|
3.1
|
19.0
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
16.6
|
1.0
|
C1D
|
D:HEM201
|
3.1
|
18.4
|
1.0
|
C4D
|
D:HEM201
|
3.1
|
21.3
|
1.0
|
C4B
|
D:HEM201
|
3.1
|
16.3
|
1.0
|
C1A
|
D:HEM201
|
3.1
|
22.8
|
1.0
|
C4A
|
D:HEM201
|
3.1
|
23.7
|
1.0
|
C4C
|
D:HEM201
|
3.1
|
17.0
|
1.0
|
C1B
|
D:HEM201
|
3.1
|
18.8
|
1.0
|
CE
|
D:MET7
|
3.4
|
21.8
|
1.0
|
CHC
|
D:HEM201
|
3.5
|
17.7
|
1.0
|
CHA
|
D:HEM201
|
3.5
|
23.2
|
1.0
|
CHD
|
D:HEM201
|
3.5
|
17.2
|
1.0
|
CG
|
D:MET7
|
3.5
|
22.8
|
1.0
|
CHB
|
D:HEM201
|
3.5
|
22.4
|
1.0
|
ND1
|
D:HIS102
|
4.2
|
20.9
|
1.0
|
CG
|
D:HIS102
|
4.3
|
19.2
|
1.0
|
CB
|
D:MET7
|
4.3
|
26.7
|
1.0
|
C2C
|
D:HEM201
|
4.4
|
15.9
|
1.0
|
C3C
|
D:HEM201
|
4.4
|
15.8
|
1.0
|
C3A
|
D:HEM201
|
4.4
|
25.6
|
1.0
|
C2A
|
D:HEM201
|
4.4
|
28.0
|
1.0
|
C3B
|
D:HEM201
|
4.4
|
17.3
|
1.0
|
C3D
|
D:HEM201
|
4.4
|
24.4
|
1.0
|
C2D
|
D:HEM201
|
4.4
|
21.6
|
1.0
|
C2B
|
D:HEM201
|
4.4
|
19.9
|
1.0
|
NH2
|
D:ARG106
|
4.8
|
36.8
|
1.0
|
|
Reference:
A.Medina-Morales,
A.Perez,
J.D.Brodin,
F.A.Tezcan.
In Vitro and Cellular Self-Assembly of A Zn-Binding Protein Cryptand Via Templated Disulfide Bonds. J.Am.Chem.Soc. V. 135 12013 2013.
ISSN: ISSN 0002-7863
PubMed: 23905754
DOI: 10.1021/JA405318D
Page generated: Mon Aug 5 04:37:14 2024
|