Sodium in PDB 1qhu: Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
Protein crystallography data
The structure of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem, PDB code: 1qhu
was solved by
M.Paoli,
H.M.Baker,
W.T.Morgan,
A.Smith,
E.N.Baker,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.30
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
44.680,
61.950,
83.290,
90.00,
93.21,
90.00
|
R / Rfree (%)
|
20.7 /
28.9
|
Other elements in 1qhu:
The structure of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
(pdb code 1qhu). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem, PDB code: 1qhu:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 1qhu
Go back to
Sodium Binding Sites List in 1qhu
Sodium binding site 1 out
of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na436
b:33.2
occ:1.00
|
O
|
A:ASP34
|
2.3
|
30.7
|
1.0
|
O
|
A:ASP121
|
2.4
|
40.4
|
1.0
|
O
|
A:THR166
|
2.4
|
32.5
|
1.0
|
O
|
A:HOH526
|
2.5
|
33.7
|
1.0
|
O
|
A:ASP75
|
2.6
|
28.7
|
1.0
|
C
|
A:THR166
|
3.4
|
32.3
|
1.0
|
C
|
A:ASP121
|
3.4
|
38.7
|
1.0
|
C
|
A:ASP34
|
3.5
|
30.1
|
1.0
|
C
|
A:ASP75
|
3.7
|
30.2
|
1.0
|
CA
|
A:ASP121
|
4.1
|
39.3
|
1.0
|
CA
|
A:ASP34
|
4.2
|
29.2
|
1.0
|
CA
|
A:THR166
|
4.2
|
31.8
|
1.0
|
N
|
A:SER167
|
4.3
|
30.8
|
1.0
|
CA
|
A:ASP75
|
4.4
|
32.5
|
1.0
|
N
|
A:ALA122
|
4.4
|
36.7
|
1.0
|
CA
|
A:SER167
|
4.5
|
30.0
|
1.0
|
N
|
A:ALA35
|
4.5
|
30.4
|
1.0
|
O
|
A:HOH598
|
4.5
|
38.3
|
1.0
|
CA
|
A:ALA35
|
4.6
|
30.2
|
1.0
|
CA
|
A:ALA122
|
4.6
|
35.4
|
1.0
|
CB
|
A:ALA35
|
4.7
|
29.7
|
1.0
|
N
|
A:ALA76
|
4.8
|
28.4
|
1.0
|
CB
|
A:SER167
|
4.8
|
29.3
|
1.0
|
O
|
A:VAL74
|
4.8
|
36.8
|
1.0
|
O
|
A:LEU120
|
4.9
|
36.6
|
1.0
|
CB
|
A:ASP121
|
4.9
|
40.6
|
1.0
|
CB
|
A:ASP34
|
4.9
|
28.7
|
1.0
|
CB
|
A:ALA122
|
5.0
|
34.0
|
1.0
|
CA
|
A:ALA76
|
5.0
|
27.1
|
1.0
|
|
Sodium binding site 2 out
of 4 in 1qhu
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Sodium Binding Sites List in 1qhu
Sodium binding site 2 out
of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na437
b:32.4
occ:1.00
|
O
|
A:ALA168
|
2.2
|
23.7
|
1.0
|
O
|
A:ALA123
|
2.4
|
30.4
|
1.0
|
O
|
A:THR36
|
2.4
|
28.8
|
1.0
|
O
|
A:ALA77
|
2.5
|
26.3
|
1.0
|
O
|
A:HOH502
|
2.6
|
23.5
|
1.0
|
CL
|
A:CL435
|
3.1
|
26.7
|
1.0
|
C
|
A:ALA168
|
3.4
|
23.7
|
1.0
|
C
|
A:THR36
|
3.6
|
27.0
|
1.0
|
C
|
A:ALA77
|
3.6
|
26.7
|
1.0
|
C
|
A:ALA123
|
3.6
|
31.4
|
1.0
|
OG1
|
A:THR36
|
4.0
|
23.2
|
1.0
|
N
|
A:ALA168
|
4.2
|
28.0
|
1.0
|
CA
|
A:ALA168
|
4.2
|
25.6
|
1.0
|
N
|
A:LEU169
|
4.2
|
25.1
|
1.0
|
N
|
A:THR36
|
4.3
|
27.6
|
1.0
|
CA
|
A:LEU169
|
4.3
|
23.5
|
1.0
|
CB
|
A:ALA168
|
4.4
|
25.1
|
1.0
|
N
|
A:ALA123
|
4.4
|
32.9
|
1.0
|
CA
|
A:VAL124
|
4.4
|
30.3
|
1.0
|
CA
|
A:PHE78
|
4.4
|
30.5
|
1.0
|
N
|
A:ALA77
|
4.5
|
25.1
|
1.0
|
CA
|
A:THR36
|
4.5
|
27.2
|
1.0
|
N
|
A:VAL124
|
4.5
|
29.5
|
1.0
|
N
|
A:PHE78
|
4.5
|
29.6
|
1.0
|
N
|
A:THR37
|
4.5
|
26.1
|
1.0
|
CG1
|
A:VAL124
|
4.5
|
29.1
|
1.0
|
CB
|
A:PHE78
|
4.5
|
31.0
|
1.0
|
CA
|
A:ALA77
|
4.6
|
25.2
|
1.0
|
CB
|
A:THR37
|
4.6
|
25.1
|
1.0
|
CA
|
A:THR37
|
4.6
|
25.8
|
1.0
|
CA
|
A:ALA123
|
4.6
|
31.9
|
1.0
|
CB
|
A:LEU169
|
4.6
|
23.1
|
1.0
|
CB
|
A:THR36
|
4.8
|
26.3
|
1.0
|
CB
|
A:ALA77
|
4.9
|
22.9
|
1.0
|
CB
|
A:VAL124
|
4.9
|
28.6
|
1.0
|
|
Sodium binding site 3 out
of 4 in 1qhu
Go back to
Sodium Binding Sites List in 1qhu
Sodium binding site 3 out
of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na438
b:26.0
occ:1.00
|
O
|
A:ALA283
|
2.2
|
22.5
|
1.0
|
O
|
A:ALA378
|
2.3
|
19.9
|
1.0
|
O
|
A:MET238
|
2.4
|
23.1
|
1.0
|
O
|
A:ALA335
|
2.4
|
18.6
|
1.0
|
CL
|
A:CL439
|
2.9
|
20.4
|
1.0
|
O4
|
A:PO4441
|
2.9
|
19.7
|
0.5
|
O2
|
A:PO4441
|
3.2
|
20.9
|
0.5
|
C
|
A:ALA283
|
3.4
|
23.0
|
1.0
|
C
|
A:ALA378
|
3.4
|
18.1
|
1.0
|
C
|
A:MET238
|
3.5
|
22.1
|
1.0
|
C
|
A:ALA335
|
3.6
|
20.1
|
1.0
|
P
|
A:PO4441
|
3.8
|
20.9
|
0.5
|
N
|
A:MET238
|
3.9
|
22.6
|
1.0
|
N
|
A:ALA378
|
4.1
|
15.6
|
1.0
|
N
|
A:ALA283
|
4.2
|
22.4
|
1.0
|
CA
|
A:MET238
|
4.2
|
22.2
|
1.0
|
CA
|
A:ALA378
|
4.2
|
17.2
|
1.0
|
CA
|
A:ALA283
|
4.3
|
23.1
|
1.0
|
N
|
A:LEU379
|
4.3
|
19.0
|
1.0
|
N
|
A:PHE284
|
4.4
|
22.0
|
1.0
|
N
|
A:VAL239
|
4.4
|
22.0
|
1.0
|
N
|
A:ALA335
|
4.4
|
20.6
|
1.0
|
CA
|
A:LEU379
|
4.4
|
21.1
|
1.0
|
CB
|
A:MET238
|
4.4
|
22.5
|
1.0
|
CA
|
A:ALA335
|
4.5
|
21.0
|
1.0
|
N
|
A:PHE336
|
4.5
|
21.9
|
1.0
|
CA
|
A:PHE284
|
4.5
|
20.0
|
1.0
|
CB
|
A:ALA378
|
4.6
|
12.8
|
1.0
|
O3
|
A:PO4441
|
4.6
|
20.0
|
0.5
|
CA
|
A:PHE336
|
4.6
|
21.5
|
1.0
|
CA
|
A:VAL239
|
4.7
|
22.8
|
1.0
|
CB
|
A:ALA283
|
4.8
|
22.5
|
1.0
|
CG
|
A:MET238
|
4.8
|
24.3
|
1.0
|
CB
|
A:LEU379
|
4.8
|
23.9
|
1.0
|
CB
|
A:PHE284
|
4.9
|
19.0
|
1.0
|
CB
|
A:ALA335
|
4.9
|
22.3
|
1.0
|
O1
|
A:PO4441
|
5.0
|
18.3
|
0.5
|
CD1
|
A:LEU379
|
5.0
|
21.5
|
1.0
|
|
Sodium binding site 4 out
of 4 in 1qhu
Go back to
Sodium Binding Sites List in 1qhu
Sodium binding site 4 out
of 4 in the Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Mammalian Blood Serum Haemopexin Deglycosylated and in Complex with Its Ligand Haem within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na440
b:27.7
occ:1.00
|
O
|
A:SER236
|
2.2
|
20.6
|
1.0
|
O
|
A:ASP333
|
2.3
|
22.4
|
1.0
|
O
|
A:ASP376
|
2.3
|
21.2
|
1.0
|
O
|
A:HOH619
|
2.3
|
34.6
|
1.0
|
O
|
A:ASP281
|
2.3
|
26.4
|
1.0
|
C
|
A:SER236
|
3.2
|
20.4
|
1.0
|
C
|
A:ASP376
|
3.3
|
22.3
|
1.0
|
C
|
A:ASP333
|
3.3
|
23.9
|
1.0
|
C
|
A:ASP281
|
3.3
|
25.5
|
1.0
|
CA
|
A:SER236
|
3.8
|
20.8
|
1.0
|
CA
|
A:ASP333
|
3.9
|
25.4
|
1.0
|
CA
|
A:ASP281
|
4.0
|
23.8
|
1.0
|
CA
|
A:ASP376
|
4.1
|
22.3
|
1.0
|
N
|
A:GLY377
|
4.2
|
21.6
|
1.0
|
N
|
A:ALA237
|
4.2
|
21.6
|
1.0
|
CB
|
A:SER236
|
4.2
|
19.6
|
1.0
|
CA
|
A:GLY377
|
4.3
|
19.1
|
1.0
|
N
|
A:ALA334
|
4.3
|
22.4
|
1.0
|
N
|
A:ALA282
|
4.3
|
25.3
|
1.0
|
CA
|
A:ALA237
|
4.5
|
21.3
|
1.0
|
CA
|
A:ALA282
|
4.6
|
23.0
|
1.0
|
CA
|
A:ALA334
|
4.6
|
21.2
|
1.0
|
CB
|
A:ASP333
|
4.7
|
22.7
|
1.0
|
CB
|
A:ALA282
|
4.7
|
20.5
|
1.0
|
CB
|
A:ALA237
|
4.8
|
24.4
|
1.0
|
CB
|
A:ASP281
|
4.8
|
24.2
|
1.0
|
O
|
A:VAL280
|
4.9
|
21.3
|
1.0
|
CB
|
A:ASP376
|
5.0
|
20.9
|
1.0
|
|
Reference:
M.Paoli,
B.F.Anderson,
H.M.Baker,
W.T.Morgan,
A.Smith,
E.N.Baker.
Crystal Structure of Hemopexin Reveals A Novel High-Affinity Heme Site Formed Between Two Beta-Propeller Domains. Nat.Struct.Biol. V. 6 926 1999.
ISSN: ISSN 1072-8368
PubMed: 10504726
DOI: 10.1038/13294
Page generated: Sun Oct 6 21:26:19 2024
|