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Magnesium in PDB 4jsv: Mtor Kinase Structure, Mechanism and Regulation.

Enzymatic activity of Mtor Kinase Structure, Mechanism and Regulation.

All present enzymatic activity of Mtor Kinase Structure, Mechanism and Regulation.:
2.7.11.1;

Protein crystallography data

The structure of Mtor Kinase Structure, Mechanism and Regulation., PDB code: 4jsv was solved by N.P.Pavletich, H.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 3.50
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 139.400, 163.200, 207.800, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 25.1

Other elements in 4jsv:

The structure of Mtor Kinase Structure, Mechanism and Regulation. also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mtor Kinase Structure, Mechanism and Regulation. (pdb code 4jsv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Mtor Kinase Structure, Mechanism and Regulation., PDB code: 4jsv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 1 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2602

b:57.2
occ:1.00
 O1A B:ADP2601 2.1 60.8 1.0
F1 B:MGF2604 2.2 57.7 1.0
O3B B:ADP2601 2.2 59.9 1.0
OD1 B:ASN2343 2.4 53.1 1.0
OD2 B:ASP2357 3.1 54.6 1.0
MG B:MGF2604 3.1 60.3 1.0
PB B:ADP2601 3.2 62.1 1.0
PA B:ADP2601 3.4 62.2 1.0
CG B:ASN2343 3.5 47.8 1.0
O2B B:ADP2601 3.5 62.1 1.0
O3A B:ADP2601 3.6 62.7 1.0
F2 B:MGF2604 3.8 59.9 1.0
CG B:ASP2357 3.9 51.9 1.0
O B:SER2342 4.0 40.0 1.0
NE2 B:HIS2340 4.0 41.2 1.0
CE1 B:HIS2340 4.0 41.4 1.0
ND2 B:ASN2343 4.1 47.8 1.0
CB B:ASP2357 4.3 48.8 1.0
F3 B:MGF2604 4.4 59.8 1.0
O5' B:ADP2601 4.4 60.5 1.0
O2A B:ADP2601 4.4 60.8 1.0
C B:SER2342 4.5 39.9 1.0
C5' B:ADP2601 4.5 58.0 1.0
O1B B:ADP2601 4.6 60.2 1.0
CB B:ASN2343 4.7 45.0 1.0
MG B:MG2603 4.7 57.6 1.0
CB B:SER2342 4.7 38.4 1.0
CA B:ASN2343 4.8 42.6 1.0
OD1 B:ASP2357 4.8 54.4 1.0
N B:ASN2343 4.8 41.1 1.0
CD1 B:ILE2356 5.0 39.5 1.0

Magnesium binding site 2 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 2 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2603

b:57.6
occ:1.00
 F3 B:MGF2604 2.0 59.8 1.0
OD1 B:ASP2357 2.1 54.4 1.0
OD2 B:ASP2357 2.7 54.6 1.0
CG B:ASP2357 2.7 51.9 1.0
O3B B:ADP2601 3.3 59.9 1.0
MG B:MGF2604 3.3 60.3 1.0
F1 B:MGF2604 4.0 57.7 1.0
O1B B:ADP2601 4.1 60.2 1.0
OD2 B:ASP2338 4.2 41.3 1.0
CB B:ASP2357 4.2 48.8 1.0
PB B:ADP2601 4.3 62.1 1.0
ND2 B:ASN2343 4.6 47.8 1.0
MG B:MG2602 4.7 57.2 1.0
F2 B:MGF2604 4.7 59.9 1.0
O3A B:ADP2601 4.9 62.7 1.0

Magnesium binding site 3 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 3 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2604

b:60.3
occ:1.00
 MG B:MGF2604 0.0 60.3 1.0
F1 B:MGF2604 1.8 57.7 1.0
F3 B:MGF2604 1.8 59.8 1.0
F2 B:MGF2604 1.8 59.9 1.0
O3B B:ADP2601 2.6 59.9 1.0
MG B:MG2602 3.1 57.2 1.0
MG B:MG2603 3.3 57.6 1.0
NE2 B:HIS2340 3.6 41.2 1.0
OD2 B:ASP2357 3.9 54.6 1.0
PB B:ADP2601 3.9 62.1 1.0
OD2 B:ASP2338 4.0 41.3 1.0
CE1 B:HIS2340 4.2 41.4 1.0
OD1 B:ASN2343 4.3 53.1 1.0
ND2 B:ASN2343 4.4 47.8 1.0
CG B:ASP2357 4.5 51.9 1.0
O2B B:ADP2601 4.5 62.1 1.0
O1B B:ADP2601 4.5 60.2 1.0
OD1 B:ASP2357 4.6 54.4 1.0
CG B:ASN2343 4.7 47.8 1.0
CD2 B:HIS2340 4.7 41.0 1.0
CG B:ASP2338 4.9 41.2 1.0
O1A B:ADP2601 4.9 60.8 1.0

Magnesium binding site 4 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 4 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2602

b:74.5
occ:1.00
 O1A A:ADP2601 2.0 79.6 1.0
F1 A:MGF2604 2.2 75.1 1.0
OD1 A:ASN2343 2.4 68.2 1.0
O3B A:ADP2601 2.5 78.5 1.0
PA A:ADP2601 3.3 81.1 1.0
PB A:ADP2601 3.3 81.9 1.0
O2B A:ADP2601 3.3 81.5 1.0
OD2 A:ASP2357 3.3 69.3 1.0
MG A:MGF2604 3.3 78.7 1.0
O A:SER2342 3.5 49.4 1.0
O3A A:ADP2601 3.6 82.5 1.0
CG A:ASN2343 3.6 60.7 1.0
O2A A:ADP2601 4.1 79.0 1.0
C A:SER2342 4.1 49.9 1.0
CG A:ASP2357 4.1 65.8 1.0
F3 A:MGF2604 4.3 76.8 1.0
CD1 A:ILE2356 4.3 51.7 1.0
CB A:ASP2357 4.3 61.8 1.0
CE1 A:HIS2340 4.4 54.1 1.0
ND2 A:ASN2343 4.4 61.2 1.0
F2 A:MGF2604 4.5 79.3 1.0
NE2 A:HIS2340 4.5 53.6 1.0
CB A:SER2342 4.5 49.0 1.0
O5' A:ADP2601 4.5 76.6 1.0
CA A:ASN2343 4.5 52.5 1.0
N A:ASN2343 4.6 51.4 1.0
CB A:ASN2343 4.7 56.2 1.0
O1B A:ADP2601 4.7 78.6 1.0
C5' A:ADP2601 4.7 73.0 1.0
O3' A:ADP2601 4.8 70.7 1.0
C3' A:ADP2601 4.9 70.6 1.0
CA A:SER2342 5.0 49.3 1.0

Magnesium binding site 5 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 5 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2603

b:72.6
occ:1.00
 F3 A:MGF2604 1.9 76.8 1.0
OD1 A:ASP2357 2.1 69.0 1.0
CG A:ASP2357 2.8 65.8 1.0
OD2 A:ASP2357 3.0 69.3 1.0
MG A:MGF2604 3.6 78.7 1.0
OD2 A:ASP2338 3.7 52.3 1.0
O3B A:ADP2601 3.8 78.5 1.0
CB A:ASP2357 4.3 61.8 1.0
ND2 A:ASN2343 4.4 61.2 1.0
F2 A:MGF2604 4.5 79.3 1.0
CA A:GLY2359 4.9 57.4 1.0
N A:GLY2359 4.9 55.3 1.0
F1 A:MGF2604 4.9 75.1 1.0
CG A:ASP2338 4.9 52.4 1.0
O A:ASP2357 4.9 54.8 1.0
O1B A:ADP2601 4.9 78.6 1.0
PB A:ADP2601 5.0 81.9 1.0

Magnesium binding site 6 out of 6 in 4jsv

Go back to Magnesium Binding Sites List in 4jsv
Magnesium binding site 6 out of 6 in the Mtor Kinase Structure, Mechanism and Regulation.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mtor Kinase Structure, Mechanism and Regulation. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2604

b:78.7
occ:1.00
 MG A:MGF2604 0.0 78.7 1.0
F1 A:MGF2604 1.8 75.1 1.0
F2 A:MGF2604 1.8 79.3 1.0
F3 A:MGF2604 1.8 76.8 1.0
O3B A:ADP2601 2.6 78.5 1.0
MG A:MG2602 3.3 74.5 1.0
PB A:ADP2601 3.5 81.9 1.0
MG A:MG2603 3.6 72.6 1.0
OD2 A:ASP2357 3.6 69.3 1.0
O2B A:ADP2601 3.7 81.5 1.0
NE2 A:HIS2340 3.7 53.6 1.0
OD1 A:ASN2343 4.1 68.2 1.0
O1B A:ADP2601 4.1 78.6 1.0
CE1 A:HIS2340 4.2 54.1 1.0
CG A:ASP2357 4.3 65.8 1.0
ND2 A:ASN2343 4.5 61.2 1.0
OD1 A:ASP2357 4.6 69.0 1.0
OD2 A:ASP2338 4.6 52.3 1.0
CG A:ASN2343 4.7 60.7 1.0
O3A A:ADP2601 4.9 82.5 1.0
O1A A:ADP2601 4.9 79.6 1.0
CD2 A:HIS2340 5.0 53.2 1.0

Reference:

H.Yang, D.G.Rudge, J.D.Koos, B.Vaidialingam, H.J.Yang, N.P.Pavletich. Mtor Kinase Structure, Mechanism and Regulation. Nature V. 497 217 2013.
ISSN: ISSN 0028-0836
PubMed: 23636326
DOI: 10.1038/NATURE12122
Page generated: Sat Aug 17 03:15:38 2024

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