Sodium in PDB 6oqq: Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Protein crystallography data
The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq
was solved by
D.R.Tomchick,
V.S.Tagliabracci,
M.Black,
A.Osinski,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.83 /
2.10
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.490,
104.749,
107.770,
90.00,
103.97,
90.00
|
R / Rfree (%)
|
20.2 /
23.4
|
Other elements in 6oqq:
The structure of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
(pdb code 6oqq). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex, PDB code: 6oqq:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 6oqq
Go back to
Sodium Binding Sites List in 6oqq
Sodium binding site 1 out
of 2 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na907
b:40.0
occ:1.00
|
H
|
A:ASN733
|
2.1
|
43.5
|
1.0
|
HE
|
A:ARG522
|
2.4
|
57.5
|
1.0
|
O
|
A:HOH1043
|
2.7
|
26.6
|
1.0
|
N
|
A:ASN733
|
3.0
|
36.2
|
1.0
|
HA
|
A:ASN733
|
3.1
|
24.1
|
1.0
|
HH21
|
A:ARG522
|
3.1
|
54.0
|
1.0
|
NE
|
A:ARG522
|
3.2
|
47.9
|
1.0
|
HD1
|
A:TYR732
|
3.3
|
48.1
|
1.0
|
HB3
|
A:ARG522
|
3.4
|
15.7
|
1.0
|
HA
|
A:TYR732
|
3.4
|
22.9
|
1.0
|
HE2
|
A:HIS492
|
3.4
|
21.7
|
1.0
|
CA
|
A:ASN733
|
3.6
|
20.1
|
1.0
|
NE2
|
A:HIS492
|
3.8
|
18.1
|
1.0
|
NH2
|
A:ARG522
|
3.8
|
45.0
|
1.0
|
HD3
|
A:ARG522
|
3.9
|
17.6
|
1.0
|
CD1
|
A:TYR732
|
3.9
|
40.1
|
1.0
|
HB
|
A:THR493
|
3.9
|
27.9
|
1.0
|
HG1
|
A:THR493
|
3.9
|
65.5
|
1.0
|
CZ
|
A:ARG522
|
3.9
|
18.7
|
1.0
|
H
|
A:ARG734
|
4.0
|
22.5
|
1.0
|
HE1
|
A:TYR732
|
4.0
|
38.7
|
1.0
|
C
|
A:TYR732
|
4.0
|
41.7
|
1.0
|
HB2
|
A:ARG522
|
4.1
|
15.7
|
1.0
|
CD
|
A:ARG522
|
4.1
|
14.8
|
1.0
|
CB
|
A:ARG522
|
4.1
|
13.2
|
1.0
|
CA
|
A:TYR732
|
4.2
|
19.2
|
1.0
|
CE1
|
A:TYR732
|
4.2
|
32.2
|
1.0
|
MG
|
A:MG906
|
4.2
|
76.9
|
1.0
|
CE1
|
A:HIS492
|
4.2
|
17.4
|
1.0
|
O
|
A:HIS492
|
4.3
|
33.0
|
1.0
|
HE1
|
A:HIS492
|
4.3
|
20.9
|
1.0
|
OG1
|
A:THR493
|
4.3
|
54.5
|
1.0
|
O
|
A:GLY731
|
4.4
|
17.0
|
1.0
|
OD1
|
A:ASN733
|
4.5
|
0.4
|
1.0
|
CD2
|
A:HIS492
|
4.5
|
16.3
|
1.0
|
HE2
|
A:PHE495
|
4.5
|
91.2
|
1.0
|
O2P
|
A:AMP901
|
4.5
|
75.3
|
1.0
|
N
|
A:ARG734
|
4.5
|
18.7
|
1.0
|
C
|
A:ASN733
|
4.5
|
26.7
|
1.0
|
HH22
|
A:ARG522
|
4.6
|
54.0
|
1.0
|
CB
|
A:THR493
|
4.6
|
23.2
|
1.0
|
CB
|
A:ASN733
|
4.7
|
26.6
|
1.0
|
HD2
|
A:HIS492
|
4.7
|
19.6
|
1.0
|
CG
|
A:ASN733
|
4.7
|
33.0
|
1.0
|
H
|
A:ARG522
|
4.7
|
14.2
|
1.0
|
CG
|
A:ARG522
|
4.7
|
13.7
|
1.0
|
HD2
|
A:PHE495
|
4.7
|
0.7
|
1.0
|
CG
|
A:TYR732
|
4.8
|
55.2
|
1.0
|
HD2
|
A:ARG522
|
4.9
|
17.6
|
1.0
|
HB2
|
A:ASN733
|
5.0
|
32.0
|
1.0
|
|
Sodium binding site 2 out
of 2 in 6oqq
Go back to
Sodium Binding Sites List in 6oqq
Sodium binding site 2 out
of 2 in the Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Legionella Pneumophila Sidj/Saccharomyces Cerevisiae Calmodulin Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na203
b:49.3
occ:1.00
|
HD21
|
B:ASN24
|
2.2
|
71.2
|
1.0
|
O
|
B:HOH330
|
2.4
|
34.4
|
1.0
|
OD1
|
B:ASN24
|
2.5
|
29.5
|
1.0
|
ND2
|
B:ASN24
|
2.5
|
59.3
|
1.0
|
O
|
B:ASP21
|
2.5
|
28.3
|
1.0
|
O
|
B:ALA18
|
2.6
|
19.0
|
1.0
|
CG
|
B:ASN24
|
2.7
|
76.2
|
1.0
|
O
|
B:HOH313
|
3.1
|
37.1
|
1.0
|
HB3
|
B:ASP21
|
3.1
|
31.9
|
1.0
|
O
|
B:HOH323
|
3.2
|
44.9
|
1.0
|
HD22
|
B:ASN24
|
3.2
|
71.2
|
1.0
|
HA
|
B:ASN24
|
3.5
|
32.9
|
1.0
|
C
|
B:ASP21
|
3.6
|
28.1
|
1.0
|
C
|
B:ALA18
|
3.7
|
18.8
|
1.0
|
O
|
B:HOH306
|
3.8
|
29.4
|
1.0
|
CB
|
B:ASP21
|
3.9
|
26.7
|
1.0
|
CB
|
B:ASN24
|
3.9
|
46.2
|
1.0
|
HA
|
B:ALA18
|
4.0
|
27.3
|
1.0
|
H
|
B:ASP21
|
4.1
|
33.6
|
1.0
|
CA
|
B:ASN24
|
4.1
|
27.4
|
1.0
|
H
|
B:ASN24
|
4.1
|
42.1
|
1.0
|
HB1
|
B:ALA18
|
4.2
|
23.3
|
1.0
|
CA
|
B:ASP21
|
4.2
|
27.4
|
1.0
|
CG
|
B:ASP21
|
4.2
|
26.2
|
1.0
|
OD2
|
B:ASP21
|
4.3
|
25.9
|
1.0
|
CA
|
B:ALA18
|
4.4
|
22.7
|
1.0
|
HA
|
B:LEU19
|
4.4
|
22.8
|
1.0
|
N
|
B:ASN24
|
4.4
|
35.0
|
1.0
|
O
|
B:LYS22
|
4.4
|
48.4
|
1.0
|
HB3
|
B:ASN24
|
4.5
|
55.5
|
1.0
|
N
|
B:ASP21
|
4.5
|
28.2
|
1.0
|
HB2
|
B:ASN24
|
4.5
|
55.5
|
1.0
|
HA
|
B:LYS22
|
4.7
|
42.4
|
1.0
|
N
|
B:LEU19
|
4.7
|
18.5
|
1.0
|
HH22
|
A:ARG479
|
4.7
|
42.6
|
1.0
|
HB2
|
B:ASP21
|
4.7
|
31.9
|
1.0
|
O
|
B:LEU19
|
4.7
|
18.9
|
1.0
|
N
|
B:LYS22
|
4.7
|
66.0
|
1.0
|
CB
|
B:ALA18
|
4.8
|
19.5
|
1.0
|
C
|
B:LYS22
|
4.8
|
39.6
|
1.0
|
CA
|
B:LEU19
|
4.8
|
18.9
|
1.0
|
C
|
B:LEU19
|
4.9
|
28.5
|
1.0
|
OD1
|
B:ASP21
|
4.9
|
26.5
|
1.0
|
CA
|
B:LYS22
|
5.0
|
35.3
|
1.0
|
|
Reference:
M.H.Black,
A.Osinski,
M.Gradowski,
K.A.Servage,
K.Pawlowski,
D.R.Tomchick,
V.S.Tagliabracci.
Bacterial Pseudokinase Catalyzes Protein Polyglutamylation to Inhibit the Side-Family Ubiquitin Ligases. Science V. 364 787 2019.
ISSN: ESSN 1095-9203
PubMed: 31123136
DOI: 10.1126/SCIENCE.AAW7446
Page generated: Tue Oct 8 12:36:45 2024
|