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Magnesium in PDB 5iuj: Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm)

Enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm)

All present enzymatic activity of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm):
2.7.13.3;

Protein crystallography data

The structure of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm), PDB code: 5iuj 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) 66.70 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.820, 114.619, 91.597, 90.00, 116.44, 90.00
R / Rfree (%) 18.7 / 24

Other elements in 5iuj:

The structure of Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm) 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 Low MG2+ (20 Mm) (pdb code 5iuj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 Mm), PDB code: 5iuj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5iuj

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Magnesium binding site 1 out of 4 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 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 Low MG2+ (20 Mm) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:0.2
occ:0.70
 O1G A:ACP401 1.9 0.2 1.0
O A:HOH501 2.0 79.6 1.0
O2A A:ACP401 2.0 0.4 1.0
OD1 A:ASN293 2.1 98.8 1.0
O2B A:ACP401 2.3 0.2 1.0
OE2 A:GLU289 2.3 0.0 1.0
CG A:ASN293 3.1 0.9 1.0
PA A:ACP401 3.2 0.6 1.0
PG A:ACP401 3.2 0.7 1.0
PB A:ACP401 3.4 0.4 1.0
O3A A:ACP401 3.4 0.9 1.0
CD A:GLU289 3.4 0.3 1.0
O2G A:ACP401 3.5 0.1 1.0
ND2 A:ASN293 3.5 95.2 1.0
OE1 A:GLU289 3.8 0.3 1.0
C3B A:ACP401 3.9 0.1 1.0
NE2 A:HIS297 4.1 0.2 1.0
O5' A:ACP401 4.2 0.8 1.0
O1A A:ACP401 4.3 0.7 1.0
CA A:GLY336 4.4 0.7 1.0
N A:GLY336 4.4 0.4 1.0
O3G A:ACP401 4.4 1.0 1.0
CB A:ASN293 4.5 86.8 1.0
O1B A:ACP401 4.7 0.4 1.0
CG A:GLU289 4.7 93.6 1.0
CD2 A:HIS297 4.7 0.8 1.0
CA A:ASN293 4.9 88.9 1.0
CD1 A:LEU337 4.9 0.8 1.0

Magnesium binding site 2 out of 4 in 5iuj

Go back to Magnesium Binding Sites List in 5iuj
Magnesium binding site 2 out of 4 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 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 Low MG2+ (20 Mm) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:93.4
occ:1.00
 OE2 B:GLU289 2.0 0.2 1.0
O1B B:ACP401 2.0 92.2 1.0
OD1 B:ASN293 2.0 85.8 1.0
O1G B:ACP401 2.1 94.3 1.0
O B:HOH501 2.3 61.6 1.0
O2A B:ACP401 2.4 96.6 1.0
CG B:ASN293 3.0 92.8 1.0
CD B:GLU289 3.1 0.9 1.0
PB B:ACP401 3.2 96.5 1.0
ND2 B:ASN293 3.4 81.3 1.0
PG B:ACP401 3.4 94.1 1.0
PA B:ACP401 3.4 0.1 1.0
O3A B:ACP401 3.4 98.4 1.0
OE1 B:GLU289 3.6 0.1 1.0
C3B B:ACP401 3.8 96.0 1.0
O2G B:ACP401 3.9 92.5 1.0
CA B:GLY336 4.1 94.9 1.0
O5' B:ACP401 4.2 0.0 1.0
NE2 B:HIS297 4.2 0.7 1.0
N B:GLY336 4.3 98.9 1.0
CG B:GLU289 4.3 82.2 1.0
O2B B:ACP401 4.4 0.4 1.0
CB B:ASN293 4.4 83.8 1.0
CE B:LYS296 4.4 0.9 1.0
NZ B:LYS296 4.5 0.1 1.0
O3G B:ACP401 4.6 95.3 1.0
O1A B:ACP401 4.7 99.4 1.0
CA B:ASN293 4.8 86.1 1.0
O B:GLU289 4.8 75.3 1.0
CD2 B:HIS297 4.8 0.8 1.0
N B:ASN293 5.0 83.5 1.0
C B:GLY336 5.0 97.5 1.0

Magnesium binding site 3 out of 4 in 5iuj

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Magnesium binding site 3 out of 4 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 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 Low MG2+ (20 Mm) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:0.9
occ:0.50
 O2A D:ACP401 2.0 1.0 1.0
O D:HOH501 2.1 0.4 1.0
O1G D:ACP401 2.1 0.2 1.0
OD1 D:ASN293 2.1 91.5 1.0
O2B D:ACP401 2.2 0.3 1.0
OE2 D:GLU289 2.2 0.4 1.0
CG D:ASN293 3.2 0.5 1.0
CD D:GLU289 3.2 0.3 1.0
PA D:ACP401 3.2 0.2 1.0
PG D:ACP401 3.3 0.2 1.0
PB D:ACP401 3.3 0.4 1.0
O2G D:ACP401 3.4 0.7 1.0
O3A D:ACP401 3.4 0.5 1.0
OE1 D:GLU289 3.5 0.7 1.0
ND2 D:ASN293 3.6 0.5 1.0
C3B D:ACP401 3.8 0.0 1.0
NE2 D:HIS297 4.2 0.1 1.0
O5' D:ACP401 4.2 0.7 1.0
O1A D:ACP401 4.4 0.6 1.0
CA D:GLY336 4.4 0.7 1.0
N D:GLY336 4.4 0.6 1.0
CB D:ASN293 4.5 88.8 1.0
CG D:GLU289 4.5 93.5 1.0
O1B D:ACP401 4.6 0.0 1.0
O3G D:ACP401 4.6 0.4 1.0
CA D:ASN293 4.8 92.2 1.0
CD2 D:HIS297 4.8 0.4 1.0
O D:GLU289 5.0 80.7 1.0

Magnesium binding site 4 out of 4 in 5iuj

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Magnesium binding site 4 out of 4 in the Crystal Structure of the Desk-Desr Complex in the Phosphotransfer State with Low MG2+ (20 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 Low MG2+ (20 Mm) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg402

b:95.1
occ:0.90
 OE2 E:GLU289 1.9 87.9 1.0
O1B E:ACP401 2.0 88.4 1.0
O1G E:ACP401 2.1 93.3 1.0
OD1 E:ASN293 2.2 92.6 1.0
O E:HOH501 2.2 47.9 1.0
O1A E:ACP401 2.3 84.5 1.0
CD E:GLU289 3.0 0.7 1.0
PB E:ACP401 3.0 92.9 1.0
CG E:ASN293 3.1 92.6 1.0
PG E:ACP401 3.2 95.0 1.0
O3A E:ACP401 3.3 93.1 1.0
PA E:ACP401 3.4 90.2 1.0
ND2 E:ASN293 3.4 79.8 1.0
OE1 E:GLU289 3.5 83.1 1.0
O2G E:ACP401 3.6 93.7 1.0
C3B E:ACP401 3.6 95.9 1.0
CA E:GLY336 4.1 86.4 1.0
N E:GLY336 4.2 91.3 1.0
O5' E:ACP401 4.3 93.7 1.0
CG E:GLU289 4.3 82.1 1.0
O2B E:ACP401 4.3 97.1 1.0
NE2 E:HIS297 4.4 88.6 1.0
CB E:ASN293 4.5 77.1 1.0
O3G E:ACP401 4.5 96.3 1.0
O2A E:ACP401 4.6 89.3 1.0
O E:GLU289 4.9 73.5 1.0
CA E:ASN293 4.9 78.8 1.0
C E:GLY336 4.9 88.6 1.0
N E:LEU337 5.0 85.2 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 16:56:41 2024

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