Magnesium in PDB 6eac: Pseudomonas Syringae Selo
Protein crystallography data
The structure of Pseudomonas Syringae Selo, PDB code: 6eac
was solved by
D.R.Tomchick,
V.S.Tagliabracci,
A.Sreelatha,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.14 /
2.27
|
Space group
|
I 2 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
136.174,
158.056,
227.248,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.2 /
21.2
|
Other elements in 6eac:
The structure of Pseudomonas Syringae Selo also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Pseudomonas Syringae Selo
(pdb code 6eac). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Pseudomonas Syringae Selo, PDB code: 6eac:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6eac
Go back to
Magnesium Binding Sites List in 6eac
Magnesium binding site 1 out
of 4 in the Pseudomonas Syringae Selo
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Pseudomonas Syringae Selo within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg501
b:10.8
occ:1.00
|
O1G
|
A:ANP506
|
2.1
|
17.9
|
1.0
|
OD1
|
A:ASN253
|
2.1
|
27.4
|
1.0
|
O
|
A:HOH656
|
2.2
|
30.5
|
1.0
|
OD2
|
A:ASP262
|
2.2
|
21.8
|
1.0
|
O1A
|
A:ANP506
|
2.2
|
25.6
|
1.0
|
O3A
|
A:ANP506
|
2.3
|
31.6
|
1.0
|
PA
|
A:ANP506
|
2.8
|
33.7
|
1.0
|
CG
|
A:ASN253
|
3.1
|
27.8
|
1.0
|
HD21
|
A:ASN253
|
3.1
|
37.1
|
1.0
|
CG
|
A:ASP262
|
3.3
|
23.1
|
1.0
|
HH12
|
A:ARG183
|
3.3
|
37.8
|
1.0
|
PG
|
A:ANP506
|
3.5
|
25.9
|
1.0
|
HB2
|
A:ASP262
|
3.5
|
28.5
|
1.0
|
ND2
|
A:ASN253
|
3.5
|
30.9
|
1.0
|
PB
|
A:ANP506
|
3.5
|
29.1
|
1.0
|
O2A
|
A:ANP506
|
3.8
|
31.5
|
1.0
|
CB
|
A:ASP262
|
3.9
|
23.8
|
1.0
|
OD2
|
A:ASP252
|
3.9
|
23.0
|
1.0
|
N3B
|
A:ANP506
|
4.0
|
29.4
|
1.0
|
H3'
|
A:ANP506
|
4.0
|
30.2
|
1.0
|
O2G
|
A:ANP506
|
4.0
|
29.7
|
1.0
|
O5'
|
A:ANP506
|
4.0
|
33.6
|
1.0
|
O2B
|
A:ANP506
|
4.1
|
26.9
|
1.0
|
HB3
|
A:ASP262
|
4.1
|
28.5
|
1.0
|
H5'2
|
A:ANP506
|
4.1
|
35.7
|
1.0
|
NH1
|
A:ARG183
|
4.1
|
31.5
|
1.0
|
HNB1
|
A:ANP506
|
4.2
|
35.3
|
1.0
|
HH11
|
A:ARG183
|
4.2
|
37.8
|
1.0
|
O
|
A:HOH652
|
4.3
|
25.8
|
1.0
|
CA
|
A:CA502
|
4.3
|
25.1
|
1.0
|
HA
|
A:ASN253
|
4.3
|
26.5
|
1.0
|
OD1
|
A:ASP262
|
4.4
|
27.5
|
1.0
|
HD22
|
A:ASN253
|
4.4
|
37.1
|
1.0
|
CB
|
A:ASN253
|
4.5
|
21.4
|
1.0
|
OH
|
A:TYR77
|
4.6
|
27.7
|
1.0
|
C5'
|
A:ANP506
|
4.6
|
29.8
|
1.0
|
O3G
|
A:ANP506
|
4.7
|
29.7
|
1.0
|
O
|
A:ASP252
|
4.7
|
21.4
|
1.0
|
O1B
|
A:ANP506
|
4.8
|
30.9
|
1.0
|
HH
|
A:TYR77
|
4.8
|
33.3
|
1.0
|
CA
|
A:ASN253
|
4.8
|
22.1
|
1.0
|
HB3
|
A:ASN253
|
4.8
|
25.7
|
1.0
|
H2'
|
A:ANP506
|
4.8
|
34.3
|
1.0
|
C3'
|
A:ANP506
|
4.9
|
25.1
|
1.0
|
HH22
|
A:ARG183
|
4.9
|
25.7
|
1.0
|
CG
|
A:ASP252
|
4.9
|
25.2
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6eac
Go back to
Magnesium Binding Sites List in 6eac
Magnesium binding site 2 out
of 4 in the Pseudomonas Syringae Selo
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Pseudomonas Syringae Selo within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg501
b:13.1
occ:1.00
|
OD1
|
B:ASN253
|
2.1
|
29.8
|
1.0
|
O2A
|
B:ANP507
|
2.1
|
24.5
|
1.0
|
O2G
|
B:ANP507
|
2.1
|
16.5
|
1.0
|
O
|
B:HOH618
|
2.2
|
18.9
|
1.0
|
OD2
|
B:ASP262
|
2.3
|
24.9
|
1.0
|
O3A
|
B:ANP507
|
2.3
|
29.3
|
1.0
|
PA
|
B:ANP507
|
2.8
|
33.4
|
1.0
|
CG
|
B:ASN253
|
3.1
|
28.3
|
1.0
|
HD21
|
B:ASN253
|
3.2
|
33.4
|
1.0
|
CG
|
B:ASP262
|
3.3
|
29.8
|
1.0
|
HH12
|
B:ARG183
|
3.4
|
35.4
|
1.0
|
HB2
|
B:ASP262
|
3.5
|
34.2
|
1.0
|
PG
|
B:ANP507
|
3.6
|
26.8
|
1.0
|
ND2
|
B:ASN253
|
3.6
|
27.8
|
1.0
|
PB
|
B:ANP507
|
3.6
|
29.1
|
1.0
|
O1A
|
B:ANP507
|
3.8
|
30.8
|
1.0
|
CB
|
B:ASP262
|
3.9
|
28.5
|
1.0
|
OD2
|
B:ASP252
|
3.9
|
28.9
|
1.0
|
H5'2
|
B:ANP507
|
4.0
|
39.3
|
1.0
|
H3'
|
B:ANP507
|
4.0
|
33.7
|
1.0
|
O5'
|
B:ANP507
|
4.0
|
35.0
|
1.0
|
HB3
|
B:ASP262
|
4.0
|
34.2
|
1.0
|
N3B
|
B:ANP507
|
4.1
|
30.5
|
1.0
|
NH1
|
B:ARG183
|
4.1
|
29.4
|
1.0
|
O1B
|
B:ANP507
|
4.1
|
22.3
|
1.0
|
O
|
B:HOH683
|
4.1
|
31.0
|
1.0
|
O1G
|
B:ANP507
|
4.2
|
28.1
|
1.0
|
HH11
|
B:ARG183
|
4.3
|
35.4
|
1.0
|
HA
|
B:ASN253
|
4.3
|
30.6
|
1.0
|
HNB1
|
B:ANP507
|
4.3
|
36.6
|
1.0
|
CA
|
B:CA502
|
4.3
|
28.8
|
1.0
|
OD1
|
B:ASP262
|
4.4
|
30.4
|
1.0
|
HD22
|
B:ASN253
|
4.4
|
33.4
|
1.0
|
CB
|
B:ASN253
|
4.5
|
24.3
|
1.0
|
C5'
|
B:ANP507
|
4.5
|
32.7
|
1.0
|
OH
|
B:TYR77
|
4.6
|
27.7
|
1.0
|
O
|
B:ASP252
|
4.7
|
20.4
|
1.0
|
O3G
|
B:ANP507
|
4.7
|
29.4
|
1.0
|
CA
|
B:ASN253
|
4.8
|
25.5
|
1.0
|
HB3
|
B:ASN253
|
4.8
|
29.1
|
1.0
|
H2'
|
B:ANP507
|
4.8
|
33.8
|
1.0
|
HH
|
B:TYR77
|
4.9
|
33.3
|
1.0
|
O2B
|
B:ANP507
|
4.9
|
33.1
|
1.0
|
C3'
|
B:ANP507
|
4.9
|
28.0
|
1.0
|
CG
|
B:ASP252
|
4.9
|
29.0
|
1.0
|
HH22
|
B:ARG183
|
5.0
|
28.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6eac
Go back to
Magnesium Binding Sites List in 6eac
Magnesium binding site 3 out
of 4 in the Pseudomonas Syringae Selo
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Pseudomonas Syringae Selo within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg501
b:20.2
occ:1.00
|
OD1
|
C:ASN253
|
2.0
|
34.2
|
1.0
|
O2G
|
C:ANP506
|
2.1
|
22.9
|
1.0
|
OD2
|
C:ASP262
|
2.1
|
26.7
|
1.0
|
O
|
C:HOH642
|
2.1
|
26.1
|
1.0
|
O1A
|
C:ANP506
|
2.2
|
30.9
|
1.0
|
O3A
|
C:ANP506
|
2.2
|
31.8
|
1.0
|
PA
|
C:ANP506
|
2.7
|
36.5
|
1.0
|
CG
|
C:ASN253
|
3.1
|
30.6
|
1.0
|
HD21
|
C:ASN253
|
3.1
|
41.3
|
1.0
|
CG
|
C:ASP262
|
3.2
|
29.1
|
1.0
|
HB2
|
C:ASP262
|
3.4
|
33.7
|
1.0
|
HH12
|
C:ARG183
|
3.4
|
40.5
|
1.0
|
ND2
|
C:ASN253
|
3.5
|
34.4
|
1.0
|
PG
|
C:ANP506
|
3.5
|
29.0
|
1.0
|
PB
|
C:ANP506
|
3.5
|
29.4
|
1.0
|
O2A
|
C:ANP506
|
3.7
|
26.2
|
1.0
|
CB
|
C:ASP262
|
3.8
|
28.1
|
1.0
|
H5'2
|
C:ANP506
|
3.9
|
45.4
|
1.0
|
O5'
|
C:ANP506
|
3.9
|
37.2
|
1.0
|
OD2
|
C:ASP252
|
4.0
|
32.0
|
1.0
|
N3B
|
C:ANP506
|
4.0
|
33.7
|
1.0
|
HB3
|
C:ASP262
|
4.0
|
33.7
|
1.0
|
O1B
|
C:ANP506
|
4.0
|
24.5
|
1.0
|
H3'
|
C:ANP506
|
4.1
|
47.5
|
1.0
|
NH1
|
C:ARG183
|
4.1
|
33.7
|
1.0
|
O3G
|
C:ANP506
|
4.1
|
26.1
|
1.0
|
O
|
C:HOH616
|
4.2
|
31.3
|
1.0
|
HH11
|
C:ARG183
|
4.2
|
40.5
|
1.0
|
OD1
|
C:ASP262
|
4.3
|
26.3
|
1.0
|
HNB1
|
C:ANP506
|
4.3
|
40.5
|
1.0
|
CA
|
C:CA502
|
4.3
|
30.9
|
1.0
|
HA
|
C:ASN253
|
4.3
|
33.3
|
1.0
|
HD22
|
C:ASN253
|
4.3
|
41.3
|
1.0
|
CB
|
C:ASN253
|
4.4
|
25.6
|
1.0
|
C5'
|
C:ANP506
|
4.4
|
37.8
|
1.0
|
OH
|
C:TYR77
|
4.6
|
37.1
|
1.0
|
O1G
|
C:ANP506
|
4.6
|
33.4
|
1.0
|
O
|
C:ASP252
|
4.7
|
31.8
|
1.0
|
O2B
|
C:ANP506
|
4.7
|
29.1
|
1.0
|
H2'
|
C:ANP506
|
4.7
|
46.8
|
1.0
|
HB3
|
C:ASN253
|
4.8
|
30.8
|
1.0
|
CA
|
C:ASN253
|
4.8
|
27.7
|
1.0
|
HH
|
C:TYR77
|
4.9
|
44.6
|
1.0
|
CG
|
C:ASP252
|
4.9
|
31.5
|
1.0
|
C3'
|
C:ANP506
|
5.0
|
39.6
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6eac
Go back to
Magnesium Binding Sites List in 6eac
Magnesium binding site 4 out
of 4 in the Pseudomonas Syringae Selo
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Pseudomonas Syringae Selo within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg501
b:17.1
occ:1.00
|
O1G
|
D:ANP506
|
2.0
|
19.6
|
1.0
|
O
|
D:HOH617
|
2.0
|
25.1
|
1.0
|
OD2
|
D:ASP262
|
2.0
|
29.9
|
1.0
|
OD1
|
D:ASN253
|
2.1
|
33.4
|
1.0
|
O3A
|
D:ANP506
|
2.2
|
32.1
|
1.0
|
O2A
|
D:ANP506
|
2.2
|
34.2
|
1.0
|
PA
|
D:ANP506
|
2.8
|
37.5
|
1.0
|
CG
|
D:ASN253
|
3.0
|
31.6
|
1.0
|
HD21
|
D:ASN253
|
3.1
|
40.6
|
1.0
|
CG
|
D:ASP262
|
3.2
|
29.7
|
1.0
|
HH12
|
D:ARG183
|
3.4
|
36.7
|
1.0
|
HB2
|
D:ASP262
|
3.4
|
31.1
|
1.0
|
PG
|
D:ANP506
|
3.4
|
28.4
|
1.0
|
ND2
|
D:ASN253
|
3.4
|
33.8
|
1.0
|
PB
|
D:ANP506
|
3.5
|
32.3
|
1.0
|
O1A
|
D:ANP506
|
3.7
|
29.6
|
1.0
|
CB
|
D:ASP262
|
3.8
|
26.0
|
1.0
|
O2B
|
D:ANP506
|
3.9
|
25.2
|
1.0
|
H5'2
|
D:ANP506
|
3.9
|
39.9
|
1.0
|
N3B
|
D:ANP506
|
3.9
|
31.6
|
1.0
|
OD2
|
D:ASP252
|
3.9
|
29.2
|
1.0
|
O5'
|
D:ANP506
|
4.0
|
35.6
|
1.0
|
HB3
|
D:ASP262
|
4.0
|
31.1
|
1.0
|
O2G
|
D:ANP506
|
4.0
|
27.3
|
1.0
|
H3'
|
D:ANP506
|
4.1
|
42.6
|
1.0
|
NH1
|
D:ARG183
|
4.1
|
30.6
|
1.0
|
OD1
|
D:ASP262
|
4.2
|
26.2
|
1.0
|
HH11
|
D:ARG183
|
4.2
|
36.7
|
1.0
|
CA
|
D:CA502
|
4.3
|
31.2
|
1.0
|
HD22
|
D:ASN253
|
4.3
|
40.6
|
1.0
|
HA
|
D:ASN253
|
4.3
|
31.6
|
1.0
|
CB
|
D:ASN253
|
4.4
|
26.2
|
1.0
|
O
|
D:HOH641
|
4.5
|
24.8
|
1.0
|
C5'
|
D:ANP506
|
4.5
|
33.2
|
1.0
|
OH
|
D:TYR77
|
4.5
|
35.0
|
1.0
|
O3G
|
D:ANP506
|
4.6
|
33.6
|
1.0
|
HB3
|
D:ASN253
|
4.7
|
31.5
|
1.0
|
O
|
D:ASP252
|
4.7
|
31.8
|
1.0
|
HNB1
|
D:ANP506
|
4.7
|
37.9
|
1.0
|
O1B
|
D:ANP506
|
4.8
|
33.9
|
1.0
|
HH
|
D:TYR77
|
4.8
|
42.0
|
1.0
|
H2'
|
D:ANP506
|
4.8
|
44.6
|
1.0
|
CA
|
D:ASN253
|
4.8
|
26.3
|
1.0
|
CG
|
D:ASP252
|
5.0
|
31.7
|
1.0
|
C3'
|
D:ANP506
|
5.0
|
35.5
|
1.0
|
|
Reference:
A.Sreelatha,
S.S.Yee,
V.A.Lopez,
B.C.Park,
L.N.Kinch,
S.Pilch,
K.A.Servage,
J.Zhang,
J.Jiou,
M.Karasiewicz-Urbanska,
M.Lobocka,
N.V.Grishin,
K.Orth,
R.Kucharczyk,
K.Pawlowski,
D.R.Tomchick,
V.S.Tagliabracci.
Protein Ampylation By An Evolutionarily Conserved Pseudokinase. Cell V. 175 809 2018.
ISSN: ISSN 1097-4172
PubMed: 30270044
DOI: 10.1016/J.CELL.2018.08.046
Page generated: Mon Sep 30 23:52:22 2024
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