Magnesium in PDB 5iun: Crystal Structure of the Desk-Desr Complex in the Phosphatase State

Enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphatase State

All present enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphatase State:
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of the Desk-Desr Complex in the Phosphatase State, PDB code: 5iun 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) 48.35 / 2.79
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.330, 94.330, 239.910, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 24.8

Other elements in 5iun:

The structure of Crystal Structure of the Desk-Desr Complex in the Phosphatase State also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State (pdb code 5iun). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State, PDB code: 5iun:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5iun

Go back to Magnesium Binding Sites List in 5iun
Magnesium binding site 1 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


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 Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.7
occ:1.00
O A:HOH501 2.0 89.0 1.0
OE2 A:GLU289 2.0 0.9 1.0
O3G A:ACP401 2.1 0.2 1.0
O1A A:ACP401 2.1 0.7 1.0
O2B A:ACP401 2.1 0.5 1.0
OD1 A:ASN293 2.1 0.3 1.0
CD A:GLU289 3.1 0.3 1.0
CG A:ASN293 3.1 0.7 1.0
PB A:ACP401 3.2 0.9 1.0
PA A:ACP401 3.2 0.5 1.0
PG A:ACP401 3.3 0.2 1.0
O3A A:ACP401 3.3 1.0 1.0
ND2 A:ASN293 3.5 0.7 1.0
OE1 A:GLU289 3.5 0.4 1.0
O1G A:ACP401 3.6 0.2 1.0
C3B A:ACP401 3.7 0.1 1.0
O5' A:ACP401 4.2 0.1 1.0
CA A:GLY336 4.2 0.8 1.0
N A:GLY336 4.3 0.9 1.0
NE2 A:HIS297 4.3 0.9 1.0
O2A A:ACP401 4.3 0.8 1.0
CG A:GLU289 4.4 0.3 1.0
NZ A:LYS296 4.4 0.6 1.0
CE A:LYS296 4.4 0.7 1.0
CB A:ASN293 4.5 0.5 1.0
O1B A:ACP401 4.5 0.2 1.0
O2G A:ACP401 4.5 0.6 1.0
CA A:ASN293 4.8 0.9 1.0
O A:GLU289 4.9 0.2 1.0
CD2 A:HIS297 5.0 0.2 1.0

Magnesium binding site 2 out of 6 in 5iun

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


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 Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.1
occ:1.00
O B:HOH501 2.0 82.5 1.0
OE2 B:GLU289 2.0 0.9 1.0
O3G B:ACP401 2.0 0.0 1.0
O1B B:ACP401 2.1 98.9 1.0
O2A B:ACP401 2.1 99.2 1.0
OD1 B:ASN293 2.1 0.8 1.0
CD B:GLU289 3.1 0.5 1.0
CG B:ASN293 3.1 0.2 1.0
PB B:ACP401 3.2 97.2 1.0
PA B:ACP401 3.2 98.8 1.0
PG B:ACP401 3.2 0.7 1.0
O3A B:ACP401 3.3 98.9 1.0
ND2 B:ASN293 3.5 86.4 1.0
OE1 B:GLU289 3.5 0.1 1.0
O2G B:ACP401 3.6 0.6 1.0
C3B B:ACP401 3.7 0.5 1.0
O5' B:ACP401 4.2 98.3 1.0
CA B:GLY336 4.2 98.8 1.0
N B:GLY336 4.3 0.5 1.0
NE2 B:HIS297 4.3 98.0 1.0
O1A B:ACP401 4.3 97.0 1.0
CG B:GLU289 4.4 98.2 1.0
CE B:LYS296 4.4 0.6 1.0
NZ B:LYS296 4.4 0.7 1.0
CB B:ASN293 4.5 89.0 1.0
O2B B:ACP401 4.5 93.3 1.0
O1G B:ACP401 4.5 0.4 1.0
CA B:ASN293 4.9 90.0 1.0
O B:GLU289 4.9 92.7 1.0
CD2 B:HIS297 5.0 99.9 1.0

Magnesium binding site 3 out of 6 in 5iun

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


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 Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:0.8
occ:1.00
O C:HOH301 1.9 70.2 1.0
O C:HOH303 1.9 84.5 1.0
F3 C:BEF202 1.9 82.3 1.0
OD2 C:ASP54 2.0 98.3 1.0
O C:GLU56 2.1 85.4 1.0
OD1 C:ASP9 2.1 90.5 1.0
CG C:ASP54 3.0 88.7 1.0
CG C:ASP9 3.2 93.9 1.0
BE C:BEF202 3.2 82.1 1.0
C C:GLU56 3.3 88.1 1.0
OD1 C:ASP54 3.3 86.2 1.0
OD2 C:ASP9 3.7 0.4 1.0
OE2 C:GLU8 3.9 0.2 1.0
CA C:GLU56 4.1 86.5 1.0
CB C:GLU56 4.2 88.8 1.0
F2 C:BEF202 4.2 78.9 1.0
N C:MET57 4.3 86.3 1.0
NE2 A:GLN193 4.3 0.7 1.0
N C:GLU56 4.3 84.4 1.0
CB C:ASP54 4.3 83.7 1.0
CG C:MET57 4.3 87.3 1.0
CB C:ASP9 4.4 83.7 1.0
OE1 A:GLN193 4.4 95.9 1.0
F1 C:BEF202 4.4 88.4 1.0
N C:ASP9 4.5 77.7 1.0
CD C:GLU8 4.5 0.3 1.0
CA C:MET57 4.5 86.6 1.0
CD A:GLN193 4.5 0.6 1.0
OE1 C:GLU8 4.6 0.7 1.0
NZ C:LYS102 4.6 80.9 1.0
CG C:GLN10 4.8 86.2 1.0
CA C:ASP9 5.0 79.5 1.0

Magnesium binding site 4 out of 6 in 5iun

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


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 Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:0.3
occ:1.00
O D:HOH302 1.9 98.6 1.0
O D:HOH301 1.9 1.0 1.0
OD1 D:ASP9 2.0 0.4 1.0
F3 D:BEF202 2.1 0.7 1.0
O D:GLU56 2.1 0.3 1.0
OD2 D:ASP54 2.1 0.2 1.0
CG D:ASP54 3.1 0.3 1.0
BE D:BEF202 3.1 0.2 1.0
CG D:ASP9 3.1 0.7 1.0
C D:GLU56 3.3 0.0 1.0
OD1 D:ASP54 3.4 0.9 1.0
OD2 D:ASP9 3.6 0.3 1.0
OE2 D:GLU8 3.9 0.6 1.0
NZ D:LYS102 4.0 0.2 1.0
CA D:GLU56 4.1 0.9 1.0
F1 D:BEF202 4.2 0.1 1.0
CB D:GLU56 4.2 0.2 1.0
NE2 B:GLN193 4.3 0.6 1.0
N D:MET57 4.3 0.1 1.0
N D:GLU56 4.3 0.8 1.0
F2 D:BEF202 4.4 0.3 1.0
CG D:MET57 4.4 0.7 1.0
CB D:ASP9 4.4 0.2 1.0
OE1 B:GLN193 4.4 0.0 1.0
CB D:ASP54 4.4 0.5 1.0
CD B:GLN193 4.5 0.4 1.0
CA D:MET57 4.5 0.7 1.0
N D:ASP9 4.6 0.3 1.0
CD D:GLU8 4.6 0.3 1.0
OE1 D:GLU8 4.6 0.7 1.0
CG D:GLN10 4.8 0.7 1.0
CA D:ASP9 5.0 0.6 1.0

Magnesium binding site 5 out of 6 in 5iun

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


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 Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:99.1
occ:1.00
OE2 E:GLU289 2.0 0.9 1.0
O3G E:ACP401 2.1 0.4 1.0
O1B E:ACP401 2.1 0.3 1.0
O2A E:ACP401 2.1 94.9 1.0
O E:HOH502 2.1 85.9 1.0
OD1 E:ASN293 2.1 89.1 1.0
CD E:GLU289 3.1 0.2 1.0
CG E:ASN293 3.1 93.9 1.0
PB E:ACP401 3.2 1.0 1.0
PA E:ACP401 3.2 95.6 1.0
PG E:ACP401 3.2 1.0 1.0
O3A E:ACP401 3.3 0.3 1.0
ND2 E:ASN293 3.5 78.8 1.0
OE1 E:GLU289 3.5 0.0 1.0
O2G E:ACP401 3.6 0.7 1.0
C3B E:ACP401 3.7 1.0 1.0
O5' E:ACP401 4.2 90.9 1.0
CA E:GLY336 4.3 0.5 1.0
N E:GLY336 4.3 0.4 1.0
NE2 E:HIS297 4.3 0.1 1.0
O1A E:ACP401 4.3 95.6 1.0
CG E:GLU289 4.4 91.8 1.0
NZ E:LYS296 4.4 0.7 1.0
CE E:LYS296 4.4 0.8 1.0
CB E:ASN293 4.5 84.1 1.0
O2B E:ACP401 4.5 1.0 1.0
O1G E:ACP401 4.5 0.8 1.0
CA E:ASN293 4.9 83.9 1.0
O E:GLU289 4.9 84.9 1.0
CD2 E:HIS297 5.0 0.1 1.0

Magnesium binding site 6 out of 6 in 5iun

Go back to Magnesium Binding Sites List in 5iun
Magnesium binding site 6 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphatase State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Desk-Desr Complex in the Phosphatase State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:79.3
occ:1.00
O F:GLU56 1.9 78.0 1.0
O E:HOH501 2.0 64.4 1.0
OD2 F:ASP54 2.0 72.3 1.0
O F:HOH302 2.0 88.9 1.0
F3 F:BEF202 2.1 82.0 1.0
OD1 F:ASP9 2.1 81.7 1.0
CG F:ASP54 3.0 73.8 1.0
C F:GLU56 3.1 83.8 1.0
CG F:ASP9 3.1 80.7 1.0
BE F:BEF202 3.2 81.5 1.0
OD1 F:ASP54 3.4 75.0 1.0
OD2 F:ASP9 3.6 86.9 1.0
OE2 F:GLU8 3.9 0.6 1.0
CA F:GLU56 4.0 84.2 1.0
CB F:GLU56 4.1 85.5 1.0
N F:MET57 4.2 82.3 1.0
N F:GLU56 4.2 83.4 1.0
F2 F:BEF202 4.3 79.1 1.0
OE1 E:GLN193 4.3 75.0 1.0
CG F:MET57 4.3 82.2 1.0
CB F:ASP54 4.4 72.0 1.0
CB F:ASP9 4.4 72.5 1.0
NE2 E:GLN193 4.4 76.5 1.0
F1 F:BEF202 4.4 89.2 1.0
CA F:MET57 4.5 80.7 1.0
NZ F:LYS102 4.5 78.4 1.0
CD E:GLN193 4.5 74.6 1.0
N F:ASP9 4.6 68.9 1.0
CD F:GLU8 4.6 0.3 1.0
OE1 F:GLU8 4.7 0.6 1.0
CG F:GLN10 4.8 73.8 1.0
CA F:ASP9 5.0 69.1 1.0
CB F:MET57 5.0 82.2 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: Mon Dec 14 20:31:15 2020

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