Magnesium in PDB 5iuk: Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
All present enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm):
2.7.13.3;
Protein crystallography data
The structure of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm), PDB code: 5iuk
was solved by
F.Trajtenberg,
J.A.Imelio,
N.Larrieux,
A.Buschiazzo,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.27 /
2.90
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
87.930,
115.610,
91.590,
90.00,
116.71,
90.00
|
R / Rfree (%)
|
19.5 /
23.9
|
Other elements in 5iuk:
The structure of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
(pdb code 5iuk). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the
Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm), PDB code: 5iuk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
Magnesium binding site 1 out
of 5 in 5iuk
Go back to
Magnesium Binding Sites List in 5iuk
Magnesium binding site 1 out
of 5 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg402
b:0.1
occ:1.00
|
O3G
|
A:ACP401
|
1.9
|
0.4
|
1.0
|
OD1
|
A:ASN293
|
2.0
|
0.8
|
1.0
|
OE2
|
A:GLU289
|
2.1
|
0.1
|
1.0
|
O2B
|
A:ACP401
|
2.2
|
0.0
|
1.0
|
O1A
|
A:ACP401
|
2.3
|
0.5
|
1.0
|
CG
|
A:ASN293
|
3.1
|
0.3
|
1.0
|
CD
|
A:GLU289
|
3.1
|
0.5
|
1.0
|
PG
|
A:ACP401
|
3.2
|
0.4
|
1.0
|
PB
|
A:ACP401
|
3.3
|
0.7
|
1.0
|
O3A
|
A:ACP401
|
3.3
|
0.2
|
1.0
|
PA
|
A:ACP401
|
3.4
|
0.2
|
1.0
|
ND2
|
A:ASN293
|
3.4
|
0.1
|
1.0
|
OE1
|
A:GLU289
|
3.5
|
0.8
|
1.0
|
O2G
|
A:ACP401
|
3.7
|
0.6
|
1.0
|
C3B
|
A:ACP401
|
3.8
|
0.8
|
1.0
|
NE2
|
A:HIS297
|
4.2
|
0.8
|
1.0
|
CA
|
A:GLY336
|
4.4
|
0.1
|
1.0
|
CE
|
A:LYS296
|
4.4
|
0.3
|
1.0
|
O5'
|
A:ACP401
|
4.4
|
0.2
|
1.0
|
NZ
|
A:LYS296
|
4.4
|
0.8
|
1.0
|
CB
|
A:ASN293
|
4.4
|
0.7
|
1.0
|
CG
|
A:GLU289
|
4.4
|
0.1
|
1.0
|
O2A
|
A:ACP401
|
4.4
|
0.9
|
1.0
|
O1G
|
A:ACP401
|
4.4
|
0.2
|
1.0
|
N
|
A:GLY336
|
4.5
|
0.1
|
1.0
|
O1B
|
A:ACP401
|
4.6
|
0.6
|
1.0
|
CA
|
A:ASN293
|
4.8
|
0.0
|
1.0
|
O
|
A:GLU289
|
4.9
|
97.2
|
1.0
|
CD2
|
A:HIS297
|
4.9
|
0.6
|
1.0
|
N
|
A:ASN293
|
5.0
|
0.2
|
1.0
|
|
Magnesium binding site 2 out
of 5 in 5iuk
Go back to
Magnesium Binding Sites List in 5iuk
Magnesium binding site 2 out
of 5 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg402
b:99.6
occ:1.00
|
O2B
|
B:ACP401
|
2.0
|
0.8
|
1.0
|
OD1
|
B:ASN293
|
2.0
|
96.2
|
1.0
|
OE2
|
B:GLU289
|
2.0
|
94.5
|
1.0
|
O
|
B:HOH501
|
2.1
|
0.9
|
1.0
|
O3G
|
B:ACP401
|
2.2
|
0.2
|
1.0
|
O1A
|
B:ACP401
|
2.3
|
0.9
|
1.0
|
CG
|
B:ASN293
|
3.1
|
0.6
|
1.0
|
CD
|
B:GLU289
|
3.1
|
0.3
|
1.0
|
PB
|
B:ACP401
|
3.2
|
1.0
|
1.0
|
PG
|
B:ACP401
|
3.4
|
0.6
|
1.0
|
PA
|
B:ACP401
|
3.4
|
0.3
|
1.0
|
O3A
|
B:ACP401
|
3.4
|
0.6
|
1.0
|
ND2
|
B:ASN293
|
3.5
|
98.5
|
1.0
|
OE1
|
B:GLU289
|
3.5
|
0.1
|
1.0
|
O2G
|
B:ACP401
|
3.7
|
0.5
|
1.0
|
C3B
|
B:ACP401
|
3.8
|
0.6
|
1.0
|
CA
|
B:GLY336
|
4.2
|
0.2
|
1.0
|
NE2
|
B:HIS297
|
4.2
|
0.6
|
1.0
|
O5'
|
B:ACP401
|
4.3
|
0.7
|
1.0
|
N
|
B:GLY336
|
4.4
|
0.0
|
1.0
|
O1B
|
B:ACP401
|
4.4
|
0.1
|
1.0
|
CG
|
B:GLU289
|
4.4
|
92.1
|
1.0
|
NZ
|
B:LYS296
|
4.4
|
0.7
|
1.0
|
CE
|
B:LYS296
|
4.4
|
0.3
|
1.0
|
CB
|
B:ASN293
|
4.4
|
95.4
|
1.0
|
O2A
|
B:ACP401
|
4.6
|
0.2
|
1.0
|
O1G
|
B:ACP401
|
4.6
|
0.8
|
1.0
|
CA
|
B:ASN293
|
4.8
|
96.5
|
1.0
|
O
|
B:GLU289
|
4.9
|
90.3
|
1.0
|
CD2
|
B:HIS297
|
4.9
|
0.2
|
1.0
|
N
|
B:ASN293
|
5.0
|
94.6
|
1.0
|
|
Magnesium binding site 3 out
of 5 in 5iuk
Go back to
Magnesium Binding Sites List in 5iuk
Magnesium binding site 3 out
of 5 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg402
b:0.1
occ:1.00
|
OD1
|
D:ASN293
|
2.1
|
0.7
|
1.0
|
O
|
D:HOH501
|
2.1
|
0.8
|
1.0
|
O2B
|
D:ACP401
|
2.1
|
0.3
|
1.0
|
OE2
|
D:GLU289
|
2.1
|
0.7
|
1.0
|
O1A
|
D:ACP401
|
2.2
|
0.6
|
1.0
|
O3G
|
D:ACP401
|
2.2
|
0.8
|
1.0
|
CG
|
D:ASN293
|
3.1
|
0.3
|
1.0
|
CD
|
D:GLU289
|
3.1
|
0.6
|
1.0
|
PB
|
D:ACP401
|
3.2
|
0.5
|
1.0
|
PA
|
D:ACP401
|
3.3
|
0.7
|
1.0
|
O3A
|
D:ACP401
|
3.3
|
0.9
|
1.0
|
OE1
|
D:GLU289
|
3.5
|
0.4
|
1.0
|
PG
|
D:ACP401
|
3.5
|
0.5
|
1.0
|
ND2
|
D:ASN293
|
3.6
|
0.8
|
1.0
|
C3B
|
D:ACP401
|
3.9
|
0.0
|
1.0
|
O2G
|
D:ACP401
|
4.0
|
0.8
|
1.0
|
NE2
|
D:HIS297
|
4.2
|
0.4
|
1.0
|
NZ
|
D:LYS296
|
4.3
|
1.0
|
1.0
|
CE
|
D:LYS296
|
4.3
|
0.6
|
1.0
|
O2A
|
D:ACP401
|
4.4
|
0.5
|
1.0
|
CA
|
D:GLY336
|
4.4
|
0.1
|
1.0
|
O5'
|
D:ACP401
|
4.4
|
0.0
|
1.0
|
CB
|
D:ASN293
|
4.5
|
0.3
|
1.0
|
CG
|
D:GLU289
|
4.5
|
0.7
|
1.0
|
N
|
D:GLY336
|
4.5
|
1.0
|
1.0
|
O1B
|
D:ACP401
|
4.5
|
0.6
|
1.0
|
O1G
|
D:ACP401
|
4.7
|
0.5
|
1.0
|
CA
|
D:ASN293
|
4.8
|
0.9
|
1.0
|
O
|
D:GLU289
|
4.9
|
91.5
|
1.0
|
CD2
|
D:HIS297
|
4.9
|
0.5
|
1.0
|
N
|
D:ASN293
|
5.0
|
0.3
|
1.0
|
|
Magnesium binding site 4 out
of 5 in 5iuk
Go back to
Magnesium Binding Sites List in 5iuk
Magnesium binding site 4 out
of 5 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg402
b:0.8
occ:1.00
|
O3G
|
E:ACP401
|
1.9
|
99.2
|
1.0
|
O
|
E:HOH501
|
2.0
|
82.1
|
1.0
|
O2B
|
E:ACP401
|
2.1
|
0.9
|
1.0
|
OE2
|
E:GLU289
|
2.1
|
91.0
|
1.0
|
O1A
|
E:ACP401
|
2.1
|
99.6
|
1.0
|
OD1
|
E:ASN293
|
2.2
|
88.2
|
1.0
|
CD
|
E:GLU289
|
3.1
|
0.5
|
1.0
|
CG
|
E:ASN293
|
3.1
|
97.4
|
1.0
|
PG
|
E:ACP401
|
3.2
|
0.4
|
1.0
|
PB
|
E:ACP401
|
3.2
|
0.7
|
1.0
|
PA
|
E:ACP401
|
3.3
|
0.0
|
1.0
|
O3A
|
E:ACP401
|
3.5
|
0.6
|
1.0
|
ND2
|
E:ASN293
|
3.5
|
83.5
|
1.0
|
OE1
|
E:GLU289
|
3.5
|
0.3
|
1.0
|
O2G
|
E:ACP401
|
3.7
|
0.3
|
1.0
|
C3B
|
E:ACP401
|
3.7
|
0.3
|
1.0
|
CA
|
E:GLY336
|
4.2
|
0.8
|
1.0
|
NE2
|
E:HIS297
|
4.2
|
0.2
|
1.0
|
O5'
|
E:ACP401
|
4.2
|
0.0
|
1.0
|
NZ
|
E:LYS296
|
4.3
|
0.8
|
1.0
|
N
|
E:GLY336
|
4.4
|
0.1
|
1.0
|
CE
|
E:LYS296
|
4.4
|
0.7
|
1.0
|
CG
|
E:GLU289
|
4.4
|
91.9
|
1.0
|
O1G
|
E:ACP401
|
4.4
|
0.7
|
1.0
|
O2A
|
E:ACP401
|
4.5
|
0.4
|
1.0
|
O1B
|
E:ACP401
|
4.5
|
0.1
|
1.0
|
CB
|
E:ASN293
|
4.5
|
94.2
|
1.0
|
CA
|
E:ASN293
|
4.9
|
97.2
|
1.0
|
CD2
|
E:HIS297
|
4.9
|
0.1
|
1.0
|
O
|
E:GLU289
|
5.0
|
87.6
|
1.0
|
|
Magnesium binding site 5 out
of 5 in 5iuk
Go back to
Magnesium Binding Sites List in 5iuk
Magnesium binding site 5 out
of 5 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm)
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg201
b:62.1
occ:0.50
|
O
|
C:GLU56
|
2.2
|
0.6
|
1.0
|
OD2
|
C:ASP54
|
2.3
|
0.5
|
1.0
|
O
|
C:HOH301
|
2.3
|
61.6
|
1.0
|
OD1
|
C:ASP9
|
2.3
|
0.4
|
1.0
|
CG
|
C:ASP54
|
3.2
|
86.6
|
1.0
|
C
|
C:GLU56
|
3.4
|
0.9
|
1.0
|
CG
|
C:ASP9
|
3.4
|
0.8
|
1.0
|
OD1
|
C:ASP54
|
3.4
|
79.7
|
1.0
|
OD2
|
C:ASP9
|
3.7
|
0.9
|
1.0
|
OE2
|
C:GLU8
|
4.1
|
89.5
|
1.0
|
CA
|
C:GLU56
|
4.2
|
98.5
|
1.0
|
NZ
|
C:LYS102
|
4.2
|
0.7
|
1.0
|
CB
|
C:GLU56
|
4.4
|
0.1
|
1.0
|
N
|
C:GLU56
|
4.4
|
94.1
|
1.0
|
N
|
C:MET57
|
4.4
|
0.2
|
1.0
|
CB
|
C:ASP54
|
4.6
|
83.3
|
1.0
|
CG
|
C:MET57
|
4.6
|
0.3
|
1.0
|
CB
|
C:ASP9
|
4.7
|
96.9
|
1.0
|
CA
|
C:MET57
|
4.7
|
0.2
|
1.0
|
CG
|
C:GLN10
|
4.8
|
0.8
|
1.0
|
CD
|
C:GLU8
|
4.8
|
99.4
|
1.0
|
OE1
|
C:GLU8
|
4.9
|
99.2
|
1.0
|
N
|
C:ASP9
|
4.9
|
88.1
|
1.0
|
|
Reference:
F.Trajtenberg,
J.A.Imelio,
M.R.Machado,
N.Larrieux,
M.A.Marti,
G.Obal,
A.E.Mechaly,
A.Buschiazzo.
Regulation of Signaling Directionality Revealed By 3D Snapshots of A Kinase:Regulator Complex in Action. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27938660
DOI: 10.7554/ELIFE.21422
Page generated: Sun Sep 29 16:56:48 2024
|