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Magnesium in PDB 5iul: Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3

Enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3

All present enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3:
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) and BEF3, PDB code: 5iul 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) 38.59 / 3.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 88.186, 116.680, 91.877, 90.00, 117.10, 90.00
R / Rfree (%) 19 / 23.1

Other elements in 5iul:

The structure of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3 also contains other interesting chemical elements:

Potassium (K) 2 atoms

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) and BEF3 (pdb code 5iul). 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 Phosphotransfer State with High MG2+ (150 Mm) and BEF3, PDB code: 5iul:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5iul

Go back to Magnesium Binding Sites List in 5iul
Magnesium binding site 1 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.9
occ:1.00
O A:HOH502 2.0 0.4 1.0
OE2 A:GLU289 2.0 0.0 1.0
O2B A:ACP401 2.1 0.8 1.0
O3G A:ACP401 2.1 0.3 1.0
O2A A:ACP401 2.1 0.9 1.0
OD1 A:ASN293 2.1 99.9 1.0
CG A:ASN293 3.1 0.2 1.0
CD A:GLU289 3.1 0.1 1.0
PB A:ACP401 3.2 0.9 1.0
PA A:ACP401 3.2 0.9 1.0
PG A:ACP401 3.3 0.4 1.0
O3A A:ACP401 3.4 0.3 1.0
ND2 A:ASN293 3.4 96.4 1.0
OE1 A:GLU289 3.5 0.1 1.0
O2G A:ACP401 3.6 0.4 1.0
C3B A:ACP401 3.8 0.7 1.0
CA A:GLY336 4.2 1.0 1.0
O5' A:ACP401 4.2 0.5 1.0
N A:GLY336 4.3 0.7 1.0
NE2 A:HIS297 4.3 0.7 1.0
O1A A:ACP401 4.4 0.9 1.0
CG A:GLU289 4.4 97.9 1.0
CE A:LYS296 4.4 0.5 1.0
NZ A:LYS296 4.4 1.0 1.0
CB A:ASN293 4.5 0.2 1.0
O1B A:ACP401 4.5 0.9 1.0
O1G A:ACP401 4.5 0.3 1.0
CA A:ASN293 4.9 0.9 1.0
O A:GLU289 4.9 85.0 1.0
CD2 A:HIS297 5.0 0.5 1.0

Magnesium binding site 2 out of 6 in 5iul

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:85.7
occ:1.00
OE2 B:GLU289 2.0 98.4 1.0
O B:HOH501 2.0 66.1 1.0
OD1 B:ASN293 2.0 0.8 1.0
O2A B:ACP401 2.1 85.5 1.0
O1G B:ACP401 2.1 96.7 1.0
O1B B:ACP401 2.1 89.8 1.0
CG B:ASN293 3.0 1.0 1.0
CD B:GLU289 3.1 0.1 1.0
PA B:ACP401 3.2 91.6 1.0
PB B:ACP401 3.2 95.0 1.0
PG B:ACP401 3.3 97.9 1.0
ND2 B:ASN293 3.4 0.1 1.0
O3A B:ACP401 3.4 93.7 1.0
OE1 B:GLU289 3.5 92.0 1.0
O2G B:ACP401 3.7 97.0 1.0
C3B B:ACP401 3.8 98.6 1.0
O5' B:ACP401 4.2 93.5 1.0
CA B:GLY336 4.2 87.1 1.0
N B:GLY336 4.3 90.8 1.0
NE2 B:HIS297 4.3 98.6 1.0
CG B:GLU289 4.3 77.1 1.0
O1A B:ACP401 4.4 93.3 1.0
CB B:ASN293 4.4 83.2 1.0
CE B:LYS296 4.5 0.5 1.0
NZ B:LYS296 4.5 0.0 1.0
O2B B:ACP401 4.5 0.3 1.0
O3G B:ACP401 4.6 99.0 1.0
CA B:ASN293 4.8 82.0 1.0
O B:GLU289 4.8 70.3 1.0
CD1 B:LEU337 5.0 94.6 1.0
CD2 B:HIS297 5.0 98.0 1.0

Magnesium binding site 3 out of 6 in 5iul

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:82.1
occ:1.00
O C:HOH304 2.0 77.3 1.0
O C:HOH306 2.1 61.4 1.0
O C:GLU56 2.2 77.3 1.0
OD2 C:ASP54 2.3 75.3 1.0
OD1 C:ASP9 2.3 67.5 1.0
O C:HOH302 2.5 78.3 1.0
CG C:ASP54 3.2 65.6 1.0
CG C:ASP9 3.4 72.3 1.0
OD1 C:ASP54 3.4 63.1 1.0
C C:GLU56 3.4 77.3 1.0
OD2 C:ASP9 3.8 77.1 1.0
OE2 C:GLU8 3.9 51.7 1.0
NZ C:LYS102 4.0 58.6 1.0
CA C:GLU56 4.2 74.3 1.0
CB C:GLU56 4.3 76.9 1.0
N C:GLU56 4.4 71.8 1.0
N C:MET57 4.5 72.7 1.0
CB C:ASP54 4.6 62.1 1.0
CB C:ASP9 4.6 71.0 1.0
CD C:GLU8 4.6 69.6 1.0
OE1 C:GLU8 4.7 72.2 1.0
CG C:MET57 4.7 72.4 1.0
CG C:GLN10 4.7 92.0 1.0
CA C:MET57 4.8 72.8 1.0
N C:ASP9 4.8 65.4 1.0

Magnesium binding site 4 out of 6 in 5iul

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:0.6
occ:1.00
OE2 D:GLU289 2.0 0.9 1.0
O D:HOH501 2.1 78.5 1.0
O2B D:ACP401 2.1 0.4 1.0
O2A D:ACP401 2.1 0.0 1.0
O1G D:ACP401 2.1 0.3 1.0
OD1 D:ASN293 2.1 97.2 1.0
CG D:ASN293 3.1 0.9 1.0
CD D:GLU289 3.1 0.2 1.0
PB D:ACP401 3.2 0.8 1.0
PA D:ACP401 3.2 0.8 1.0
PG D:ACP401 3.3 0.7 1.0
O3A D:ACP401 3.4 0.7 1.0
ND2 D:ASN293 3.4 93.5 1.0
OE1 D:GLU289 3.5 0.7 1.0
O2G D:ACP401 3.7 0.4 1.0
C3B D:ACP401 3.8 0.1 1.0
CA D:GLY336 4.2 0.9 1.0
O5' D:ACP401 4.2 0.3 1.0
N D:GLY336 4.3 0.6 1.0
NE2 D:HIS297 4.3 0.2 1.0
O1A D:ACP401 4.4 0.5 1.0
CG D:GLU289 4.4 85.3 1.0
CE D:LYS296 4.4 0.2 1.0
NZ D:LYS296 4.4 1.0 1.0
CB D:ASN293 4.5 87.3 1.0
O1B D:ACP401 4.5 0.8 1.0
O3G D:ACP401 4.6 1.0 1.0
CA D:ASN293 4.8 88.5 1.0
O D:GLU289 4.9 71.5 1.0
CD2 D:HIS297 5.0 0.4 1.0

Magnesium binding site 5 out of 6 in 5iul

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:72.2
occ:1.00
O1G E:ACP401 2.0 81.8 1.0
OE2 E:GLU289 2.0 0.7 1.0
O1B E:ACP401 2.1 87.5 1.0
O1A E:ACP401 2.1 90.9 1.0
OD1 E:ASN293 2.1 86.9 1.0
O E:HOH501 2.2 70.9 1.0
CD E:GLU289 3.1 97.3 1.0
CG E:ASN293 3.1 92.6 1.0
PB E:ACP401 3.2 94.1 1.0
PG E:ACP401 3.2 85.3 1.0
PA E:ACP401 3.2 94.8 1.0
O3A E:ACP401 3.4 96.2 1.0
ND2 E:ASN293 3.5 82.2 1.0
OE1 E:GLU289 3.5 72.8 1.0
O2G E:ACP401 3.6 81.3 1.0
C3B E:ACP401 3.7 92.2 1.0
CA E:GLY336 4.2 90.2 1.0
O5' E:ACP401 4.2 99.6 1.0
N E:GLY336 4.2 96.3 1.0
NE2 E:HIS297 4.3 90.6 1.0
O2A E:ACP401 4.4 93.4 1.0
CG E:GLU289 4.4 76.3 1.0
NZ E:LYS296 4.4 0.4 1.0
CE E:LYS296 4.4 0.3 1.0
O3G E:ACP401 4.5 88.9 1.0
CB E:ASN293 4.5 80.9 1.0
O2B E:ACP401 4.5 0.1 1.0
CA E:ASN293 4.9 84.2 1.0
O E:GLU289 4.9 77.7 1.0

Magnesium binding site 6 out of 6 in 5iul

Go back to Magnesium Binding Sites List in 5iul
Magnesium binding site 6 out of 6 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with High MG2+ (150 Mm) and BEF3


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 Phosphotransfer State with High MG2+ (150 Mm) and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg201

b:57.1
occ:1.00
O F:HOH303 2.0 80.1 1.0
OD1 F:ASP9 2.0 76.1 1.0
O F:HOH302 2.1 80.2 1.0
O F:GLU56 2.2 65.6 1.0
OD2 F:ASP54 2.3 74.3 1.0
O F:HOH304 2.4 49.1 1.0
CG F:ASP9 3.1 78.4 1.0
CG F:ASP54 3.3 67.3 1.0
C F:GLU56 3.4 65.7 1.0
OD2 F:ASP9 3.5 84.0 1.0
OD1 F:ASP54 3.6 65.8 1.0
OE2 F:GLU8 3.9 62.2 1.0
NZ F:LYS102 4.2 80.8 1.0
CA F:GLU56 4.3 67.6 1.0
CB F:ASP9 4.4 69.7 1.0
N F:MET57 4.4 60.3 1.0
CB F:GLU56 4.4 70.5 1.0
N F:GLU56 4.6 66.4 1.0
CG F:MET57 4.6 61.7 1.0
CG F:GLN10 4.6 99.1 1.0
N F:ASP9 4.6 62.2 1.0
CD F:GLU8 4.6 80.5 1.0
CA F:MET57 4.6 62.1 1.0
CB F:ASP54 4.7 61.7 1.0
OE1 F:GLU8 4.7 80.7 1.0
CA F:ASP9 5.0 66.2 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: Sun Sep 29 16:57:44 2024

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