Iron in PDB 5ee4: The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
Protein crystallography data
The structure of The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin, PDB code: 5ee4
was solved by
C.T.Wong,
S.A.Hare,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
123.07 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
54.790,
87.210,
124.320,
90.00,
98.13,
90.00
|
R / Rfree (%)
|
20.2 /
24.4
|
Iron Binding Sites:
The binding sites of Iron atom in the The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
(pdb code 5ee4). This binding sites where shown within
5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the
The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin, PDB code: 5ee4:
Jump to Iron binding site number:
1;
2;
3;
4;
Iron binding site 1 out
of 4 in 5ee4
Go back to
Iron Binding Sites List in 5ee4
Iron binding site 1 out
of 4 in the The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 1 of The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Fe201
b:23.5
occ:1.00
|
FE
|
C:HEM201
|
0.0
|
23.5
|
1.0
|
ND
|
C:HEM201
|
1.9
|
25.2
|
1.0
|
NA
|
C:HEM201
|
2.0
|
24.8
|
1.0
|
NC
|
C:HEM201
|
2.1
|
21.1
|
1.0
|
O1
|
C:OXY202
|
2.1
|
42.7
|
1.0
|
NB
|
C:HEM201
|
2.1
|
22.6
|
1.0
|
NE2
|
C:HIS87
|
2.3
|
24.8
|
1.0
|
C4D
|
C:HEM201
|
2.9
|
26.8
|
1.0
|
C1D
|
C:HEM201
|
2.9
|
24.4
|
1.0
|
O2
|
C:OXY202
|
3.0
|
43.7
|
1.0
|
C4A
|
C:HEM201
|
3.0
|
24.5
|
1.0
|
C1A
|
C:HEM201
|
3.0
|
26.4
|
1.0
|
C4B
|
C:HEM201
|
3.0
|
21.4
|
1.0
|
C4C
|
C:HEM201
|
3.0
|
22.2
|
1.0
|
C1C
|
C:HEM201
|
3.1
|
20.8
|
1.0
|
C1B
|
C:HEM201
|
3.1
|
22.1
|
1.0
|
CD2
|
C:HIS87
|
3.2
|
23.7
|
1.0
|
CE1
|
C:HIS87
|
3.3
|
25.1
|
1.0
|
CHA
|
C:HEM201
|
3.4
|
24.9
|
1.0
|
CHC
|
C:HEM201
|
3.4
|
20.9
|
1.0
|
CHD
|
C:HEM201
|
3.4
|
23.4
|
1.0
|
CHB
|
C:HEM201
|
3.4
|
23.9
|
1.0
|
C3A
|
C:HEM201
|
4.2
|
27.4
|
1.0
|
C3D
|
C:HEM201
|
4.2
|
28.2
|
1.0
|
C2D
|
C:HEM201
|
4.2
|
27.3
|
1.0
|
C2A
|
C:HEM201
|
4.2
|
30.1
|
1.0
|
C3C
|
C:HEM201
|
4.2
|
20.1
|
1.0
|
C2C
|
C:HEM201
|
4.3
|
19.8
|
1.0
|
C3B
|
C:HEM201
|
4.3
|
21.6
|
1.0
|
C2B
|
C:HEM201
|
4.3
|
21.1
|
1.0
|
NE2
|
C:HIS58
|
4.4
|
45.1
|
1.0
|
CG
|
C:HIS87
|
4.4
|
24.0
|
1.0
|
ND1
|
C:HIS87
|
4.4
|
22.8
|
1.0
|
CE1
|
C:HIS58
|
4.9
|
45.7
|
1.0
|
|
Iron binding site 2 out
of 4 in 5ee4
Go back to
Iron Binding Sites List in 5ee4
Iron binding site 2 out
of 4 in the The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 2 of The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Fe201
b:24.9
occ:1.00
|
FE
|
D:HEM201
|
0.0
|
24.9
|
1.0
|
O1
|
D:OXY202
|
1.8
|
50.3
|
1.0
|
ND
|
D:HEM201
|
1.9
|
28.0
|
1.0
|
NA
|
D:HEM201
|
2.0
|
27.7
|
1.0
|
NB
|
D:HEM201
|
2.1
|
24.5
|
1.0
|
NC
|
D:HEM201
|
2.1
|
23.3
|
1.0
|
NE2
|
D:HIS92
|
2.2
|
25.6
|
1.0
|
O2
|
D:OXY202
|
2.7
|
54.8
|
1.0
|
C1D
|
D:HEM201
|
2.9
|
28.3
|
1.0
|
C4D
|
D:HEM201
|
2.9
|
28.8
|
1.0
|
C4B
|
D:HEM201
|
3.0
|
24.7
|
1.0
|
C1A
|
D:HEM201
|
3.0
|
29.2
|
1.0
|
C4A
|
D:HEM201
|
3.0
|
27.9
|
1.0
|
C1B
|
D:HEM201
|
3.1
|
25.6
|
1.0
|
C4C
|
D:HEM201
|
3.1
|
24.1
|
1.0
|
C1C
|
D:HEM201
|
3.1
|
23.0
|
1.0
|
CE1
|
D:HIS92
|
3.1
|
25.7
|
1.0
|
CD2
|
D:HIS92
|
3.1
|
24.0
|
1.0
|
CHA
|
D:HEM201
|
3.4
|
29.3
|
1.0
|
CHD
|
D:HEM201
|
3.4
|
26.7
|
1.0
|
CHC
|
D:HEM201
|
3.4
|
22.6
|
1.0
|
CHB
|
D:HEM201
|
3.5
|
27.2
|
1.0
|
C2D
|
D:HEM201
|
4.2
|
29.7
|
1.0
|
C3D
|
D:HEM201
|
4.2
|
31.9
|
1.0
|
C2A
|
D:HEM201
|
4.2
|
30.4
|
1.0
|
C3A
|
D:HEM201
|
4.2
|
29.4
|
1.0
|
ND1
|
D:HIS92
|
4.2
|
23.5
|
1.0
|
C3B
|
D:HEM201
|
4.3
|
25.4
|
1.0
|
C2B
|
D:HEM201
|
4.3
|
25.6
|
1.0
|
CG
|
D:HIS92
|
4.3
|
24.5
|
1.0
|
C3C
|
D:HEM201
|
4.3
|
24.0
|
1.0
|
C2C
|
D:HEM201
|
4.3
|
22.2
|
1.0
|
NE2
|
D:HIS63
|
4.3
|
33.2
|
1.0
|
CE1
|
D:HIS63
|
5.0
|
32.6
|
1.0
|
|
Iron binding site 3 out
of 4 in 5ee4
Go back to
Iron Binding Sites List in 5ee4
Iron binding site 3 out
of 4 in the The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 3 of The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Fe201
b:21.6
occ:1.00
|
FE
|
E:HEM201
|
0.0
|
21.6
|
1.0
|
ND
|
E:HEM201
|
1.9
|
22.4
|
1.0
|
NA
|
E:HEM201
|
2.0
|
26.2
|
1.0
|
NB
|
E:HEM201
|
2.1
|
22.8
|
1.0
|
NC
|
E:HEM201
|
2.1
|
22.1
|
1.0
|
O1
|
E:OXY202
|
2.1
|
64.1
|
1.0
|
NE2
|
E:HIS87
|
2.3
|
20.3
|
1.0
|
C4D
|
E:HEM201
|
2.9
|
25.6
|
1.0
|
O2
|
E:OXY202
|
2.9
|
67.9
|
1.0
|
C1D
|
E:HEM201
|
2.9
|
23.1
|
1.0
|
C1B
|
E:HEM201
|
3.0
|
24.1
|
1.0
|
C4A
|
E:HEM201
|
3.0
|
25.6
|
1.0
|
C4B
|
E:HEM201
|
3.0
|
23.4
|
1.0
|
C1A
|
E:HEM201
|
3.0
|
25.8
|
1.0
|
C4C
|
E:HEM201
|
3.0
|
21.8
|
1.0
|
C1C
|
E:HEM201
|
3.1
|
21.4
|
1.0
|
CD2
|
E:HIS87
|
3.2
|
20.6
|
1.0
|
CHA
|
E:HEM201
|
3.4
|
25.8
|
1.0
|
CE1
|
E:HIS87
|
3.4
|
22.6
|
1.0
|
CHB
|
E:HEM201
|
3.4
|
24.6
|
1.0
|
CHC
|
E:HEM201
|
3.4
|
21.9
|
1.0
|
CHD
|
E:HEM201
|
3.4
|
21.8
|
1.0
|
C3D
|
E:HEM201
|
4.2
|
27.3
|
1.0
|
C2D
|
E:HEM201
|
4.2
|
23.6
|
1.0
|
C3A
|
E:HEM201
|
4.2
|
27.9
|
1.0
|
C2A
|
E:HEM201
|
4.2
|
29.2
|
1.0
|
C3C
|
E:HEM201
|
4.2
|
22.4
|
1.0
|
C2B
|
E:HEM201
|
4.2
|
24.6
|
1.0
|
C2C
|
E:HEM201
|
4.2
|
22.1
|
1.0
|
C3B
|
E:HEM201
|
4.3
|
24.0
|
1.0
|
NE2
|
E:HIS58
|
4.4
|
44.1
|
1.0
|
CG
|
E:HIS87
|
4.4
|
21.5
|
1.0
|
ND1
|
E:HIS87
|
4.5
|
20.5
|
1.0
|
CE1
|
E:HIS58
|
4.6
|
47.8
|
1.0
|
|
Iron binding site 4 out
of 4 in 5ee4
Go back to
Iron Binding Sites List in 5ee4
Iron binding site 4 out
of 4 in the The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin
Mono view
Stereo pair view
|
A full contact list of Iron with other atoms in the Fe binding
site number 4 of The Crystal Structure of Hpua From Kingella Denitrificans in Complex with Human Haemoglobin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Fe201
b:24.4
occ:1.00
|
FE
|
F:HEM201
|
0.0
|
24.4
|
1.0
|
O2
|
F:OXY202
|
1.9
|
27.0
|
1.0
|
ND
|
F:HEM201
|
1.9
|
24.9
|
1.0
|
NA
|
F:HEM201
|
2.0
|
26.1
|
1.0
|
NB
|
F:HEM201
|
2.1
|
23.5
|
1.0
|
NC
|
F:HEM201
|
2.1
|
21.3
|
1.0
|
NE2
|
F:HIS92
|
2.2
|
21.9
|
1.0
|
O1
|
F:OXY202
|
2.9
|
39.3
|
1.0
|
C4D
|
F:HEM201
|
2.9
|
27.0
|
1.0
|
C1D
|
F:HEM201
|
3.0
|
26.8
|
1.0
|
C1A
|
F:HEM201
|
3.0
|
26.8
|
1.0
|
C4B
|
F:HEM201
|
3.0
|
23.8
|
1.0
|
C4A
|
F:HEM201
|
3.1
|
24.4
|
1.0
|
C1C
|
F:HEM201
|
3.1
|
22.1
|
1.0
|
C4C
|
F:HEM201
|
3.1
|
23.4
|
1.0
|
C1B
|
F:HEM201
|
3.1
|
25.7
|
1.0
|
CD2
|
F:HIS92
|
3.2
|
22.1
|
1.0
|
CE1
|
F:HIS92
|
3.2
|
21.7
|
1.0
|
CHA
|
F:HEM201
|
3.4
|
25.9
|
1.0
|
CHD
|
F:HEM201
|
3.4
|
25.8
|
1.0
|
CHC
|
F:HEM201
|
3.5
|
21.0
|
1.0
|
CHB
|
F:HEM201
|
3.5
|
23.3
|
1.0
|
C3D
|
F:HEM201
|
4.2
|
32.7
|
1.0
|
C2D
|
F:HEM201
|
4.2
|
29.6
|
1.0
|
C2A
|
F:HEM201
|
4.2
|
29.7
|
1.0
|
C3A
|
F:HEM201
|
4.2
|
26.0
|
1.0
|
NE2
|
F:HIS63
|
4.3
|
42.8
|
1.0
|
C3C
|
F:HEM201
|
4.3
|
23.3
|
1.0
|
C2C
|
F:HEM201
|
4.3
|
21.3
|
1.0
|
C3B
|
F:HEM201
|
4.3
|
25.6
|
1.0
|
C2B
|
F:HEM201
|
4.3
|
25.3
|
1.0
|
ND1
|
F:HIS92
|
4.3
|
22.9
|
1.0
|
CG
|
F:HIS92
|
4.4
|
22.6
|
1.0
|
CG2
|
F:VAL67
|
4.6
|
26.5
|
1.0
|
CE1
|
F:HIS63
|
4.9
|
40.9
|
1.0
|
|
Reference:
C.T.Wong,
Y.Xu,
A.Gupta,
J.A.Garnett,
S.J.Matthews,
S.A.Hare.
Structural Analysis of Haemoglobin Binding By Hpua From the Neisseriaceae Family. Nat Commun V. 6 10172 2015.
ISSN: ESSN 2041-1723
PubMed: 26671256
DOI: 10.1038/NCOMMS10172
Page generated: Tue Aug 6 00:27:24 2024
|