Iron in PDB 3qvz: Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
Protein crystallography data
The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II), PDB code: 3qvz
was solved by
E.N.Salgado,
F.A.Tezcan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.86 /
2.64
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
52.525,
52.525,
255.717,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
26.1 /
30.6
|
Other elements in 3qvz:
The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II) also contains other interesting chemical elements:
Iron Binding Sites:
The binding sites of Iron atom in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
(pdb code 3qvz). 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-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II), PDB code: 3qvz:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 3qvz
Go back to
Iron Binding Sites List in 3qvz
Iron binding site 1 out
of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
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-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe150
b:12.6
occ:1.00
|
FE
|
A:HEM150
|
0.0
|
12.6
|
1.0
|
NB
|
A:HEM150
|
1.9
|
11.4
|
1.0
|
NC
|
A:HEM150
|
2.0
|
12.2
|
1.0
|
ND
|
A:HEM150
|
2.0
|
9.9
|
1.0
|
NE2
|
A:HIS102
|
2.0
|
14.4
|
1.0
|
NA
|
A:HEM150
|
2.0
|
10.4
|
1.0
|
SD
|
A:MET7
|
2.3
|
16.4
|
1.0
|
C1D
|
A:HEM150
|
2.9
|
10.5
|
1.0
|
CD2
|
A:HIS102
|
2.9
|
14.9
|
1.0
|
C1B
|
A:HEM150
|
3.0
|
9.9
|
1.0
|
C4C
|
A:HEM150
|
3.0
|
11.7
|
1.0
|
C4B
|
A:HEM150
|
3.0
|
13.1
|
1.0
|
C4D
|
A:HEM150
|
3.0
|
11.1
|
1.0
|
C1C
|
A:HEM150
|
3.0
|
14.1
|
1.0
|
CE1
|
A:HIS102
|
3.0
|
14.9
|
1.0
|
C4A
|
A:HEM150
|
3.1
|
11.0
|
1.0
|
C1A
|
A:HEM150
|
3.1
|
12.8
|
1.0
|
CE
|
A:MET7
|
3.3
|
14.6
|
1.0
|
CHD
|
A:HEM150
|
3.3
|
12.1
|
1.0
|
CG
|
A:MET7
|
3.4
|
18.1
|
1.0
|
CHB
|
A:HEM150
|
3.4
|
9.0
|
1.0
|
CHC
|
A:HEM150
|
3.4
|
14.7
|
1.0
|
CHA
|
A:HEM150
|
3.4
|
12.5
|
1.0
|
CG
|
A:HIS102
|
4.1
|
17.3
|
1.0
|
ND1
|
A:HIS102
|
4.1
|
15.3
|
1.0
|
CB
|
A:MET7
|
4.2
|
19.9
|
1.0
|
C2B
|
A:HEM150
|
4.2
|
8.4
|
1.0
|
C2D
|
A:HEM150
|
4.2
|
10.8
|
1.0
|
C3B
|
A:HEM150
|
4.2
|
12.2
|
1.0
|
C3C
|
A:HEM150
|
4.2
|
12.5
|
1.0
|
C3D
|
A:HEM150
|
4.2
|
12.4
|
1.0
|
C2C
|
A:HEM150
|
4.2
|
13.7
|
1.0
|
C3A
|
A:HEM150
|
4.3
|
13.0
|
1.0
|
C2A
|
A:HEM150
|
4.3
|
14.9
|
1.0
|
NH1
|
A:ARG106
|
4.9
|
26.9
|
1.0
|
CA
|
A:MET7
|
5.0
|
20.3
|
1.0
|
|
Iron binding site 2 out
of 4 in 3qvz
Go back to
Iron Binding Sites List in 3qvz
Iron binding site 2 out
of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
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-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe150
b:17.5
occ:1.00
|
FE
|
B:HEM150
|
0.0
|
17.5
|
1.0
|
NE2
|
B:HIS102
|
2.0
|
14.6
|
1.0
|
NB
|
B:HEM150
|
2.0
|
12.5
|
1.0
|
NC
|
B:HEM150
|
2.0
|
13.1
|
1.0
|
ND
|
B:HEM150
|
2.0
|
15.6
|
1.0
|
NA
|
B:HEM150
|
2.2
|
15.9
|
1.0
|
SD
|
B:MET7
|
2.3
|
17.2
|
1.0
|
CD2
|
B:HIS102
|
2.9
|
15.0
|
1.0
|
C1D
|
B:HEM150
|
3.0
|
15.6
|
1.0
|
C4B
|
B:HEM150
|
3.0
|
14.1
|
1.0
|
C4C
|
B:HEM150
|
3.0
|
13.9
|
1.0
|
C1B
|
B:HEM150
|
3.0
|
12.6
|
1.0
|
CE1
|
B:HIS102
|
3.0
|
14.8
|
1.0
|
C1C
|
B:HEM150
|
3.1
|
12.6
|
1.0
|
C4D
|
B:HEM150
|
3.1
|
18.2
|
1.0
|
CE
|
B:MET7
|
3.1
|
15.0
|
1.0
|
C4A
|
B:HEM150
|
3.2
|
15.9
|
1.0
|
C1A
|
B:HEM150
|
3.2
|
18.8
|
1.0
|
CG
|
B:MET7
|
3.3
|
18.1
|
1.0
|
CHD
|
B:HEM150
|
3.3
|
17.3
|
1.0
|
CHB
|
B:HEM150
|
3.4
|
14.4
|
1.0
|
CHC
|
B:HEM150
|
3.4
|
11.1
|
1.0
|
CHA
|
B:HEM150
|
3.5
|
17.6
|
1.0
|
CG
|
B:HIS102
|
4.0
|
17.6
|
1.0
|
ND1
|
B:HIS102
|
4.1
|
15.7
|
1.0
|
CB
|
B:MET7
|
4.2
|
20.1
|
1.0
|
C2D
|
B:HEM150
|
4.2
|
16.4
|
1.0
|
C2B
|
B:HEM150
|
4.2
|
9.5
|
1.0
|
C3B
|
B:HEM150
|
4.2
|
13.2
|
1.0
|
C3C
|
B:HEM150
|
4.3
|
11.4
|
1.0
|
C2C
|
B:HEM150
|
4.3
|
11.3
|
1.0
|
C3D
|
B:HEM150
|
4.3
|
18.8
|
1.0
|
C3A
|
B:HEM150
|
4.4
|
18.2
|
1.0
|
C2A
|
B:HEM150
|
4.5
|
20.4
|
1.0
|
|
Iron binding site 3 out
of 4 in 3qvz
Go back to
Iron Binding Sites List in 3qvz
Iron binding site 3 out
of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
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-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe150
b:12.7
occ:1.00
|
FE
|
C:HEM150
|
0.0
|
12.7
|
1.0
|
NC
|
C:HEM150
|
1.9
|
13.3
|
1.0
|
NE2
|
C:HIS102
|
1.9
|
14.4
|
1.0
|
ND
|
C:HEM150
|
1.9
|
11.8
|
1.0
|
NB
|
C:HEM150
|
2.0
|
16.0
|
1.0
|
NA
|
C:HEM150
|
2.1
|
12.0
|
1.0
|
SD
|
C:MET7
|
2.3
|
16.6
|
1.0
|
CD2
|
C:HIS102
|
2.9
|
14.9
|
1.0
|
C1C
|
C:HEM150
|
2.9
|
15.1
|
1.0
|
C4D
|
C:HEM150
|
3.0
|
11.9
|
1.0
|
CE1
|
C:HIS102
|
3.0
|
15.0
|
1.0
|
C1D
|
C:HEM150
|
3.0
|
10.6
|
1.0
|
C4B
|
C:HEM150
|
3.0
|
16.3
|
1.0
|
C1B
|
C:HEM150
|
3.0
|
16.2
|
1.0
|
C4C
|
C:HEM150
|
3.0
|
12.1
|
1.0
|
C1A
|
C:HEM150
|
3.1
|
12.5
|
1.0
|
C4A
|
C:HEM150
|
3.1
|
12.4
|
1.0
|
CE
|
C:MET7
|
3.2
|
14.6
|
1.0
|
CHC
|
C:HEM150
|
3.3
|
16.3
|
1.0
|
CG
|
C:MET7
|
3.4
|
18.2
|
1.0
|
CHD
|
C:HEM150
|
3.4
|
9.5
|
1.0
|
CHA
|
C:HEM150
|
3.4
|
11.5
|
1.0
|
CHB
|
C:HEM150
|
3.4
|
14.5
|
1.0
|
ND1
|
C:HIS102
|
4.1
|
15.7
|
1.0
|
CG
|
C:HIS102
|
4.1
|
17.5
|
1.0
|
C2C
|
C:HEM150
|
4.2
|
12.2
|
1.0
|
C2D
|
C:HEM150
|
4.2
|
9.6
|
1.0
|
C3D
|
C:HEM150
|
4.2
|
11.0
|
1.0
|
C2B
|
C:HEM150
|
4.2
|
17.0
|
1.0
|
C3C
|
C:HEM150
|
4.2
|
11.3
|
1.0
|
C3B
|
C:HEM150
|
4.2
|
17.5
|
1.0
|
CB
|
C:MET7
|
4.3
|
20.0
|
1.0
|
C2A
|
C:HEM150
|
4.3
|
14.2
|
1.0
|
C3A
|
C:HEM150
|
4.4
|
12.3
|
1.0
|
NH2
|
C:ARG106
|
4.9
|
23.4
|
1.0
|
|
Iron binding site 4 out
of 4 in 3qvz
Go back to
Iron Binding Sites List in 3qvz
Iron binding site 4 out
of 4 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II)
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-RIDC1 Complex Stabilized By Bmoe Crosslinks Cocrystallized in the Presence of Cu(II) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe150
b:18.9
occ:1.00
|
FE
|
D:HEM150
|
0.0
|
18.9
|
1.0
|
NE2
|
D:HIS102
|
2.0
|
14.9
|
1.0
|
NC
|
D:HEM150
|
2.0
|
15.7
|
1.0
|
ND
|
D:HEM150
|
2.0
|
17.8
|
1.0
|
NB
|
D:HEM150
|
2.0
|
16.4
|
1.0
|
NA
|
D:HEM150
|
2.1
|
16.8
|
1.0
|
SD
|
D:MET7
|
2.4
|
17.2
|
1.0
|
CD2
|
D:HIS102
|
2.9
|
14.9
|
1.0
|
C1D
|
D:HEM150
|
3.0
|
18.4
|
1.0
|
C4C
|
D:HEM150
|
3.0
|
16.7
|
1.0
|
CE1
|
D:HIS102
|
3.0
|
14.8
|
1.0
|
C1B
|
D:HEM150
|
3.0
|
17.7
|
1.0
|
C1C
|
D:HEM150
|
3.0
|
15.9
|
1.0
|
C4B
|
D:HEM150
|
3.0
|
16.3
|
1.0
|
C4D
|
D:HEM150
|
3.1
|
19.5
|
1.0
|
C4A
|
D:HEM150
|
3.1
|
17.9
|
1.0
|
CE
|
D:MET7
|
3.1
|
14.9
|
1.0
|
C1A
|
D:HEM150
|
3.2
|
19.4
|
1.0
|
CHD
|
D:HEM150
|
3.3
|
17.0
|
1.0
|
CG
|
D:MET7
|
3.4
|
18.1
|
1.0
|
CHB
|
D:HEM150
|
3.4
|
17.3
|
1.0
|
CHC
|
D:HEM150
|
3.4
|
17.0
|
1.0
|
CHA
|
D:HEM150
|
3.5
|
19.2
|
1.0
|
CG
|
D:HIS102
|
4.1
|
17.5
|
1.0
|
ND1
|
D:HIS102
|
4.1
|
15.6
|
1.0
|
C2D
|
D:HEM150
|
4.2
|
18.6
|
1.0
|
C3C
|
D:HEM150
|
4.2
|
15.3
|
1.0
|
C2B
|
D:HEM150
|
4.2
|
17.0
|
1.0
|
C2C
|
D:HEM150
|
4.3
|
14.5
|
1.0
|
C3B
|
D:HEM150
|
4.3
|
15.2
|
1.0
|
C3D
|
D:HEM150
|
4.3
|
18.6
|
1.0
|
CB
|
D:MET7
|
4.3
|
20.1
|
1.0
|
C3A
|
D:HEM150
|
4.3
|
17.9
|
1.0
|
C2A
|
D:HEM150
|
4.4
|
20.4
|
1.0
|
|
Reference:
E.N.Salgado,
J.D.Brodin,
M.M.To,
F.A.Tezcan.
Templated Construction of A Zn-Selective Protein Dimerization Motif. Inorg.Chem. V. 50 6323 2011.
ISSN: ISSN 0020-1669
PubMed: 21648390
DOI: 10.1021/IC200746M
Page generated: Sun Aug 4 18:55:47 2024
|