Iron in PDB 3hnj: Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
Protein crystallography data
The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2, PDB code: 3hnj
was solved by
E.N.Salgado,
R.A.Lewis,
J.Brodin,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.70 /
2.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.448,
65.316,
70.773,
90.00,
104.70,
90.00
|
R / Rfree (%)
|
22.4 /
27.2
|
Other elements in 3hnj:
The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
(pdb code 3hnj). 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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2, PDB code: 3hnj:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3hnj
Go back to
Iron Binding Sites List in 3hnj
Iron binding site 1 out
of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:16.1
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
16.1
|
1.0
|
NA
|
A:HEM150
|
2.0
|
16.8
|
1.0
|
NB
|
A:HEM150
|
2.0
|
16.2
|
1.0
|
NE2
|
A:HIS102
|
2.1
|
17.3
|
1.0
|
NC
|
A:HEM150
|
2.1
|
15.2
|
1.0
|
ND
|
A:HEM150
|
2.1
|
16.8
|
1.0
|
SD
|
A:MET7
|
2.3
|
21.6
|
1.0
|
C4A
|
A:HEM150
|
3.0
|
16.5
|
1.0
|
C1B
|
A:HEM150
|
3.0
|
16.4
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
17.1
|
1.0
|
CD2
|
A:HIS102
|
3.1
|
19.8
|
1.0
|
C4B
|
A:HEM150
|
3.1
|
14.7
|
1.0
|
CE1
|
A:HIS102
|
3.1
|
19.2
|
1.0
|
C1C
|
A:HEM150
|
3.1
|
14.6
|
1.0
|
C4D
|
A:HEM150
|
3.1
|
17.8
|
1.0
|
C4C
|
A:HEM150
|
3.1
|
15.8
|
1.0
|
C1D
|
A:HEM150
|
3.2
|
18.5
|
1.0
|
CHB
|
A:HEM150
|
3.3
|
16.4
|
1.0
|
CE
|
A:MET7
|
3.5
|
21.0
|
1.0
|
CHA
|
A:HEM150
|
3.5
|
17.0
|
1.0
|
CG
|
A:MET7
|
3.5
|
21.4
|
1.0
|
CHC
|
A:HEM150
|
3.5
|
15.9
|
1.0
|
CHD
|
A:HEM150
|
3.5
|
16.4
|
1.0
|
ND1
|
A:HIS102
|
4.2
|
19.1
|
1.0
|
C3A
|
A:HEM150
|
4.2
|
16.7
|
1.0
|
CB
|
A:MET7
|
4.2
|
22.1
|
1.0
|
CG
|
A:HIS102
|
4.2
|
21.1
|
1.0
|
C2B
|
A:HEM150
|
4.2
|
15.4
|
1.0
|
C2A
|
A:HEM150
|
4.2
|
17.4
|
1.0
|
C3B
|
A:HEM150
|
4.3
|
15.5
|
1.0
|
C2C
|
A:HEM150
|
4.3
|
15.1
|
1.0
|
C3C
|
A:HEM150
|
4.4
|
14.2
|
1.0
|
C3D
|
A:HEM150
|
4.4
|
17.6
|
1.0
|
C2D
|
A:HEM150
|
4.4
|
18.1
|
1.0
|
CA
|
A:MET7
|
5.0
|
22.5
|
1.0
|
|
Iron binding site 2 out
of 4 in 3hnj
Go back to
Iron Binding Sites List in 3hnj
Iron binding site 2 out
of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:21.4
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
21.4
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
20.5
|
1.0
|
NA
|
B:HEM150
|
2.0
|
22.9
|
1.0
|
NC
|
B:HEM150
|
2.1
|
21.9
|
1.0
|
ND
|
B:HEM150
|
2.1
|
22.1
|
1.0
|
NB
|
B:HEM150
|
2.1
|
21.9
|
1.0
|
SD
|
B:MET7
|
2.4
|
22.1
|
1.0
|
CE1
|
B:HIS102
|
2.9
|
21.4
|
1.0
|
CD2
|
B:HIS102
|
3.0
|
22.1
|
1.0
|
C1A
|
B:HEM150
|
3.0
|
22.2
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
22.6
|
1.0
|
C4A
|
B:HEM150
|
3.1
|
22.6
|
1.0
|
C4C
|
B:HEM150
|
3.1
|
21.0
|
1.0
|
C4B
|
B:HEM150
|
3.1
|
21.1
|
1.0
|
C1C
|
B:HEM150
|
3.1
|
21.1
|
1.0
|
C1B
|
B:HEM150
|
3.1
|
22.4
|
1.0
|
C1D
|
B:HEM150
|
3.1
|
22.3
|
1.0
|
CHA
|
B:HEM150
|
3.4
|
22.5
|
1.0
|
CE
|
B:MET7
|
3.4
|
23.6
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
21.6
|
1.0
|
CHB
|
B:HEM150
|
3.5
|
23.1
|
1.0
|
CHD
|
B:HEM150
|
3.5
|
22.0
|
1.0
|
CG
|
B:MET7
|
3.5
|
23.1
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
21.4
|
1.0
|
CG
|
B:HIS102
|
4.1
|
22.4
|
1.0
|
CB
|
B:MET7
|
4.2
|
22.4
|
1.0
|
C2A
|
B:HEM150
|
4.3
|
23.4
|
1.0
|
C3A
|
B:HEM150
|
4.3
|
22.0
|
1.0
|
C2B
|
B:HEM150
|
4.3
|
21.6
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
21.1
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
23.6
|
1.0
|
C3B
|
B:HEM150
|
4.3
|
21.9
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
20.6
|
1.0
|
C2D
|
B:HEM150
|
4.4
|
22.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 3hnj
Go back to
Iron Binding Sites List in 3hnj
Iron binding site 3 out
of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:21.0
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
21.0
|
1.0
|
NA
|
C:HEM150
|
2.0
|
20.6
|
1.0
|
NE2
|
C:HIS102
|
2.0
|
21.9
|
1.0
|
NC
|
C:HEM150
|
2.1
|
19.7
|
1.0
|
NB
|
C:HEM150
|
2.1
|
20.0
|
1.0
|
ND
|
C:HEM150
|
2.1
|
19.9
|
1.0
|
SD
|
C:MET7
|
2.4
|
20.8
|
1.0
|
C1A
|
C:HEM150
|
2.9
|
21.4
|
1.0
|
CD2
|
C:HIS102
|
3.0
|
21.6
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
20.8
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
20.8
|
1.0
|
C4A
|
C:HEM150
|
3.0
|
21.6
|
1.0
|
C1C
|
C:HEM150
|
3.1
|
19.2
|
1.0
|
C4B
|
C:HEM150
|
3.1
|
18.6
|
1.0
|
C1B
|
C:HEM150
|
3.1
|
20.6
|
1.0
|
C4C
|
C:HEM150
|
3.1
|
20.1
|
1.0
|
C1D
|
C:HEM150
|
3.2
|
20.9
|
1.0
|
CHA
|
C:HEM150
|
3.3
|
20.6
|
1.0
|
CHC
|
C:HEM150
|
3.4
|
20.1
|
1.0
|
CE
|
C:MET7
|
3.4
|
21.1
|
1.0
|
CHB
|
C:HEM150
|
3.5
|
22.5
|
1.0
|
CG
|
C:MET7
|
3.5
|
21.8
|
1.0
|
CHD
|
C:HEM150
|
3.6
|
20.7
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
21.4
|
1.0
|
CG
|
C:HIS102
|
4.2
|
21.4
|
1.0
|
CB
|
C:MET7
|
4.2
|
22.2
|
1.0
|
C2A
|
C:HEM150
|
4.2
|
22.5
|
1.0
|
C3A
|
C:HEM150
|
4.2
|
22.5
|
1.0
|
C2C
|
C:HEM150
|
4.3
|
19.6
|
1.0
|
C3B
|
C:HEM150
|
4.3
|
20.4
|
1.0
|
C3D
|
C:HEM150
|
4.3
|
21.5
|
1.0
|
C2B
|
C:HEM150
|
4.3
|
19.9
|
1.0
|
C3C
|
C:HEM150
|
4.3
|
19.6
|
1.0
|
C2D
|
C:HEM150
|
4.4
|
20.2
|
1.0
|
CA
|
C:MET7
|
5.0
|
22.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 3hnj
Go back to
Iron Binding Sites List in 3hnj
Iron binding site 4 out
of 4 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2
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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:25.1
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
25.1
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
22.2
|
1.0
|
ND
|
D:HEM150
|
2.0
|
25.4
|
1.0
|
NA
|
D:HEM150
|
2.0
|
26.3
|
1.0
|
NC
|
D:HEM150
|
2.1
|
24.9
|
1.0
|
NB
|
D:HEM150
|
2.1
|
26.2
|
1.0
|
SD
|
D:MET7
|
2.4
|
27.1
|
1.0
|
CD2
|
D:HIS102
|
2.9
|
21.7
|
1.0
|
CE1
|
D:HIS102
|
3.0
|
20.8
|
1.0
|
C1D
|
D:HEM150
|
3.0
|
24.4
|
1.0
|
C1A
|
D:HEM150
|
3.1
|
25.7
|
1.0
|
C4D
|
D:HEM150
|
3.1
|
25.1
|
1.0
|
C4C
|
D:HEM150
|
3.1
|
24.7
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
26.2
|
1.0
|
C1C
|
D:HEM150
|
3.1
|
24.6
|
1.0
|
C4B
|
D:HEM150
|
3.1
|
25.4
|
1.0
|
C1B
|
D:HEM150
|
3.1
|
26.6
|
1.0
|
CHD
|
D:HEM150
|
3.4
|
24.5
|
1.0
|
CHA
|
D:HEM150
|
3.4
|
24.9
|
1.0
|
CE
|
D:MET7
|
3.5
|
25.2
|
1.0
|
CHC
|
D:HEM150
|
3.5
|
25.6
|
1.0
|
CHB
|
D:HEM150
|
3.5
|
26.3
|
1.0
|
CG
|
D:MET7
|
3.6
|
23.8
|
1.0
|
CG
|
D:HIS102
|
4.0
|
21.9
|
1.0
|
ND1
|
D:HIS102
|
4.1
|
20.1
|
1.0
|
C2D
|
D:HEM150
|
4.3
|
23.6
|
1.0
|
C2A
|
D:HEM150
|
4.3
|
26.1
|
1.0
|
C3C
|
D:HEM150
|
4.3
|
24.6
|
1.0
|
C3D
|
D:HEM150
|
4.3
|
24.2
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
25.5
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
25.6
|
1.0
|
C2B
|
D:HEM150
|
4.3
|
26.4
|
1.0
|
C3B
|
D:HEM150
|
4.4
|
26.2
|
1.0
|
CB
|
D:MET7
|
4.4
|
22.8
|
1.0
|
|
Reference:
E.N.Salgado,
X.I.Ambroggio,
J.D.Brodin,
R.A.Lewis,
B.Kuhlman,
F.A.Tezcan.
Metal Templated Design of Protein Interfaces. Proc.Natl.Acad.Sci.Usa V. 107 1827 2010.
ISSN: ISSN 0027-8424
PubMed: 20080561
DOI: 10.1073/PNAS.0906852107
Page generated: Sun Aug 4 11:42:54 2024
|