Magnesium in PDB 8jmj: Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
Protein crystallography data
The structure of Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex, PDB code: 8jmj
was solved by
C.T.Wu,
C.H.Chu,
Y.J.Sun,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.57 /
2.57
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
75.178,
75.193,
81.116,
71.34,
71.46,
67.7
|
R / Rfree (%)
|
22.4 /
30.2
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
(pdb code 8jmj). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex, PDB code: 8jmj:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 8jmj
Go back to
Magnesium Binding Sites List in 8jmj
Magnesium binding site 1 out
of 4 in the Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:42.9
occ:1.00
|
OG1
|
A:THR18
|
2.1
|
32.2
|
1.0
|
O1G
|
A:ATP500
|
2.5
|
24.1
|
1.0
|
O1B
|
A:ATP500
|
2.6
|
25.9
|
1.0
|
CB
|
A:THR18
|
3.5
|
31.3
|
1.0
|
PG
|
A:ATP500
|
3.7
|
21.9
|
1.0
|
PB
|
A:ATP500
|
3.8
|
22.1
|
1.0
|
OD2
|
A:ASP130
|
3.8
|
25.1
|
1.0
|
OD1
|
A:ASP130
|
3.9
|
24.9
|
1.0
|
N
|
A:THR18
|
3.9
|
25.4
|
1.0
|
O3B
|
A:ATP500
|
4.0
|
21.2
|
1.0
|
CA
|
A:THR18
|
4.1
|
23.1
|
1.0
|
CG
|
A:ASP130
|
4.2
|
36.0
|
1.0
|
CB
|
A:LYS17
|
4.4
|
26.9
|
1.0
|
O2G
|
A:ATP500
|
4.4
|
21.9
|
1.0
|
O
|
A:SER131
|
4.4
|
39.2
|
1.0
|
CG2
|
A:THR18
|
4.5
|
25.6
|
1.0
|
CE
|
A:LYS17
|
4.6
|
23.1
|
1.0
|
O2B
|
A:ATP500
|
4.6
|
21.4
|
1.0
|
ND2
|
A:ASN45
|
4.6
|
23.3
|
1.0
|
CB
|
A:ALA41
|
4.7
|
26.2
|
1.0
|
CB
|
A:ASN45
|
4.7
|
23.6
|
1.0
|
C
|
A:LYS17
|
4.8
|
24.1
|
1.0
|
O3G
|
A:ATP500
|
4.9
|
31.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 8jmj
Go back to
Magnesium Binding Sites List in 8jmj
Magnesium binding site 2 out
of 4 in the Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:49.1
occ:1.00
|
OG1
|
B:THR18
|
2.1
|
24.1
|
1.0
|
O1G
|
B:ATP500
|
2.2
|
38.4
|
1.0
|
O1B
|
B:ATP500
|
2.3
|
40.2
|
1.0
|
CB
|
B:THR18
|
3.1
|
23.5
|
1.0
|
PG
|
B:ATP500
|
3.4
|
22.0
|
1.0
|
PB
|
B:ATP500
|
3.5
|
45.1
|
1.0
|
ND2
|
B:ASN45
|
3.6
|
29.9
|
1.0
|
O3B
|
B:ATP500
|
3.6
|
21.5
|
1.0
|
CB
|
B:ASN45
|
4.0
|
24.0
|
1.0
|
OD1
|
B:ASP130
|
4.1
|
25.2
|
1.0
|
CG2
|
B:THR18
|
4.1
|
24.1
|
1.0
|
N
|
B:THR18
|
4.1
|
25.4
|
1.0
|
O2G
|
B:ATP500
|
4.2
|
21.9
|
1.0
|
CA
|
B:THR18
|
4.2
|
23.7
|
1.0
|
O2A
|
B:ATP500
|
4.2
|
21.4
|
1.0
|
CG
|
B:ASN45
|
4.3
|
29.7
|
1.0
|
O2B
|
B:ATP500
|
4.5
|
21.7
|
1.0
|
O3A
|
B:ATP500
|
4.6
|
28.8
|
1.0
|
O3G
|
B:ATP500
|
4.6
|
29.6
|
1.0
|
OD2
|
B:ASP130
|
4.7
|
25.0
|
1.0
|
CG
|
B:ASP130
|
4.8
|
45.8
|
1.0
|
PA
|
B:ATP500
|
4.8
|
21.1
|
1.0
|
CB
|
B:LYS17
|
5.0
|
23.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 8jmj
Go back to
Magnesium Binding Sites List in 8jmj
Magnesium binding site 3 out
of 4 in the Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:41.3
occ:1.00
|
O1B
|
C:ATP500
|
2.2
|
30.5
|
1.0
|
O1G
|
C:ATP500
|
2.4
|
22.6
|
1.0
|
OG1
|
C:THR18
|
2.5
|
31.3
|
1.0
|
CB
|
C:THR18
|
3.4
|
33.4
|
1.0
|
PB
|
C:ATP500
|
3.5
|
21.4
|
1.0
|
PG
|
C:ATP500
|
3.6
|
22.3
|
1.0
|
O3B
|
C:ATP500
|
3.8
|
21.3
|
1.0
|
N
|
C:THR18
|
3.9
|
28.4
|
1.0
|
OD2
|
C:ASP130
|
4.1
|
25.1
|
1.0
|
O2G
|
C:ATP500
|
4.1
|
22.0
|
1.0
|
OD1
|
C:ASP130
|
4.2
|
25.4
|
1.0
|
CA
|
C:THR18
|
4.2
|
23.3
|
1.0
|
CE
|
C:LYS17
|
4.3
|
28.8
|
1.0
|
O2B
|
C:ATP500
|
4.3
|
21.6
|
1.0
|
ND2
|
C:ASN45
|
4.5
|
22.7
|
1.0
|
CB
|
C:LYS17
|
4.5
|
36.3
|
1.0
|
CG
|
C:ASP130
|
4.5
|
35.6
|
1.0
|
CG2
|
C:THR18
|
4.6
|
23.3
|
1.0
|
O2A
|
C:ATP500
|
4.7
|
20.7
|
1.0
|
O3A
|
C:ATP500
|
4.7
|
21.7
|
1.0
|
CB
|
C:ASN45
|
4.7
|
23.6
|
1.0
|
NZ
|
C:LYS17
|
4.8
|
22.6
|
1.0
|
O3G
|
C:ATP500
|
4.8
|
28.2
|
1.0
|
C
|
C:LYS17
|
4.8
|
23.2
|
1.0
|
O
|
C:SER131
|
4.8
|
38.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 8jmj
Go back to
Magnesium Binding Sites List in 8jmj
Magnesium binding site 4 out
of 4 in the Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Helicobacter Pylori Soj-Dna-SPO0J Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:40.1
occ:1.00
|
O1G
|
D:ATP500
|
2.1
|
28.6
|
1.0
|
O1B
|
D:ATP500
|
2.3
|
35.0
|
1.0
|
OG1
|
D:THR18
|
2.4
|
23.6
|
1.0
|
PG
|
D:ATP500
|
3.1
|
22.9
|
1.0
|
ND2
|
D:ASN45
|
3.2
|
26.4
|
1.0
|
CB
|
D:THR18
|
3.2
|
23.4
|
1.0
|
O3B
|
D:ATP500
|
3.4
|
21.5
|
1.0
|
PB
|
D:ATP500
|
3.4
|
32.1
|
1.0
|
O2A
|
D:ATP500
|
3.7
|
21.4
|
1.0
|
O2G
|
D:ATP500
|
3.7
|
22.0
|
1.0
|
CB
|
D:ASN45
|
3.7
|
24.1
|
1.0
|
CG
|
D:ASN45
|
3.9
|
28.7
|
1.0
|
CG2
|
D:THR18
|
4.1
|
23.9
|
1.0
|
N
|
D:THR18
|
4.3
|
23.1
|
1.0
|
CA
|
D:THR18
|
4.4
|
23.6
|
1.0
|
O3A
|
D:ATP500
|
4.4
|
34.2
|
1.0
|
O3G
|
D:ATP500
|
4.4
|
25.4
|
1.0
|
PA
|
D:ATP500
|
4.4
|
21.1
|
1.0
|
NZ
|
D:LYS17
|
4.5
|
52.1
|
1.0
|
OD2
|
D:ASP130
|
4.5
|
28.6
|
1.0
|
NZ
|
C:LYS12
|
4.5
|
37.4
|
1.0
|
O2B
|
D:ATP500
|
4.6
|
21.6
|
1.0
|
O1A
|
D:ATP500
|
4.9
|
29.4
|
1.0
|
|
Reference:
C.H.Chu,
C.T.Wu,
M.G.Lin,
C.Y.Yen,
Y.Z.Wu,
C.D.Hsiao,
Y.J.Sun.
Insights Into the Molecular Mechanism of Parabs System in Chromosome Partition By Hppara and Hpparb Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAE450
Page generated: Fri Oct 4 13:11:43 2024
|