Iron in PDB 6otx: Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0
Protein crystallography data
The structure of Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0, PDB code: 6otx
was solved by
D.Marchany-Rivera,
C.A.Smith,
J.D.Rodriguez-Perez,
J.Lopez-Garriga,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
33.56 /
2.54
|
Space group
|
P 42 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.736,
74.736,
152.571,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
24.9
|
Iron Binding Sites:
The binding sites of Iron atom in the Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0
(pdb code 6otx). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the
Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0, PDB code: 6otx:
Jump to Iron binding site number:
1;
2;
Iron binding site 1 out
of 2 in 6otx
Go back to
Iron Binding Sites List in 6otx
Iron binding site 1 out
of 2 in the Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Fe500
b:75.6
occ:1.00
|
FE
|
A:HEM500
|
0.0
|
75.6
|
1.0
|
O1
|
A:OXY501
|
1.9
|
0.3
|
1.0
|
ND
|
A:HEM500
|
2.0
|
70.6
|
1.0
|
NB
|
A:HEM500
|
2.0
|
70.1
|
1.0
|
NA
|
A:HEM500
|
2.1
|
69.0
|
1.0
|
NC
|
A:HEM500
|
2.1
|
70.1
|
1.0
|
NE2
|
A:HIS97
|
2.4
|
85.6
|
1.0
|
O2
|
A:OXY501
|
2.8
|
0.4
|
1.0
|
C4D
|
A:HEM500
|
3.0
|
66.1
|
1.0
|
C1D
|
A:HEM500
|
3.0
|
76.6
|
1.0
|
C4B
|
A:HEM500
|
3.1
|
68.5
|
1.0
|
C1A
|
A:HEM500
|
3.1
|
62.2
|
1.0
|
C1B
|
A:HEM500
|
3.1
|
74.3
|
1.0
|
C4C
|
A:HEM500
|
3.1
|
74.1
|
1.0
|
C4A
|
A:HEM500
|
3.1
|
71.5
|
1.0
|
C1C
|
A:HEM500
|
3.1
|
66.0
|
1.0
|
CD2
|
A:HIS97
|
3.3
|
81.9
|
1.0
|
CE1
|
A:HIS97
|
3.4
|
83.7
|
1.0
|
CHA
|
A:HEM500
|
3.4
|
59.4
|
1.0
|
CHD
|
A:HEM500
|
3.4
|
75.6
|
1.0
|
CHC
|
A:HEM500
|
3.4
|
64.9
|
1.0
|
CHB
|
A:HEM500
|
3.5
|
74.0
|
1.0
|
C2D
|
A:HEM500
|
4.2
|
76.5
|
1.0
|
C3D
|
A:HEM500
|
4.3
|
75.0
|
1.0
|
C3B
|
A:HEM500
|
4.3
|
75.4
|
1.0
|
C2B
|
A:HEM500
|
4.3
|
71.0
|
1.0
|
C2A
|
A:HEM500
|
4.3
|
63.7
|
1.0
|
C3A
|
A:HEM500
|
4.3
|
63.3
|
1.0
|
C3C
|
A:HEM500
|
4.3
|
78.6
|
1.0
|
C2C
|
A:HEM500
|
4.4
|
71.7
|
1.0
|
CG
|
A:HIS97
|
4.5
|
83.8
|
1.0
|
ND1
|
A:HIS97
|
4.5
|
87.0
|
1.0
|
CZ
|
A:PHE44
|
4.6
|
68.3
|
1.0
|
NE2
|
A:GLN65
|
4.6
|
74.8
|
1.0
|
OH
|
A:TYR30
|
4.6
|
81.9
|
1.0
|
|
Iron binding site 2 out
of 2 in 6otx
Go back to
Iron Binding Sites List in 6otx
Iron binding site 2 out
of 2 in the Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of Crystallographic Structure of (Hbii-Hbiii)-O2 From Lucina Pectinata at pH 7.0 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Fe500
b:71.9
occ:1.00
|
FE
|
B:HEM500
|
0.0
|
71.9
|
1.0
|
O1
|
B:OXY501
|
1.8
|
74.2
|
1.0
|
ND
|
B:HEM500
|
2.0
|
78.5
|
1.0
|
NA
|
B:HEM500
|
2.1
|
81.8
|
1.0
|
NC
|
B:HEM500
|
2.1
|
80.9
|
1.0
|
NB
|
B:HEM500
|
2.1
|
75.8
|
1.0
|
O2
|
B:OXY501
|
2.3
|
89.0
|
1.0
|
NE2
|
B:HIS98
|
2.3
|
79.1
|
1.0
|
C1D
|
B:HEM500
|
3.0
|
72.2
|
1.0
|
C4C
|
B:HEM500
|
3.1
|
70.9
|
1.0
|
C4D
|
B:HEM500
|
3.1
|
80.9
|
1.0
|
C4A
|
B:HEM500
|
3.1
|
77.2
|
1.0
|
C1B
|
B:HEM500
|
3.1
|
74.5
|
1.0
|
C1A
|
B:HEM500
|
3.1
|
81.6
|
1.0
|
CD2
|
B:HIS98
|
3.1
|
80.9
|
1.0
|
C1C
|
B:HEM500
|
3.1
|
79.3
|
1.0
|
C4B
|
B:HEM500
|
3.1
|
78.3
|
1.0
|
CHD
|
B:HEM500
|
3.4
|
63.8
|
1.0
|
CE1
|
B:HIS98
|
3.4
|
78.2
|
1.0
|
CHB
|
B:HEM500
|
3.4
|
74.2
|
1.0
|
CHA
|
B:HEM500
|
3.5
|
84.3
|
1.0
|
CHC
|
B:HEM500
|
3.5
|
79.6
|
1.0
|
OH
|
B:TYR31
|
4.0
|
63.7
|
1.0
|
C2D
|
B:HEM500
|
4.3
|
77.2
|
1.0
|
NE2
|
B:GLN66
|
4.3
|
57.8
|
1.0
|
C3D
|
B:HEM500
|
4.3
|
78.4
|
1.0
|
C3A
|
B:HEM500
|
4.3
|
72.0
|
1.0
|
C3C
|
B:HEM500
|
4.3
|
78.0
|
1.0
|
C2A
|
B:HEM500
|
4.3
|
75.2
|
1.0
|
C2B
|
B:HEM500
|
4.3
|
73.5
|
1.0
|
C2C
|
B:HEM500
|
4.3
|
76.4
|
1.0
|
C3B
|
B:HEM500
|
4.3
|
75.5
|
1.0
|
CG
|
B:HIS98
|
4.3
|
77.3
|
1.0
|
ND1
|
B:HIS98
|
4.4
|
75.6
|
1.0
|
CZ
|
B:PHE45
|
4.6
|
68.1
|
1.0
|
NH1
|
B:ARG101
|
4.9
|
64.1
|
1.0
|
|
Reference:
D.Marchany-Rivera,
C.A.Smith,
J.D.Rodriguez-Perez,
J.Lopez-Garriga.
Lucina Pectinata Oxyhemoglobin (II-III) Heterodimer pH Susceptibility J.Inorg.Biochem. V. 207 2020.
ISSN: ISSN 0162-0134
DOI: 10.1016/J.JINORGBIO.2020.111055
Page generated: Sun Dec 13 16:48:13 2020
|