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Magnesium in PDB 8un3: Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)

Enzymatic activity of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)

All present enzymatic activity of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One):
3.6.5.2;

Protein crystallography data

The structure of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One), PDB code: 8un3 was solved by M.H.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.69 / 2.07
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 69.217, 69.217, 166.92, 90, 90, 120
R / Rfree (%) 16.2 / 19.1

Other elements in 8un3:

The structure of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Fluorine (F) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) (pdb code 8un3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One), PDB code: 8un3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 8un3

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Magnesium binding site 1 out of 5 in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:39.1
occ:1.00
 O A:HOH332 2.0 39.9 1.0
OG A:SER17 2.0 32.2 1.0
O A:HOH348 2.1 40.7 1.0
O A:HOH319 2.1 37.2 1.0
O2B A:GDP202 2.3 34.2 1.0
CB A:SER17 3.2 33.3 1.0
PB A:GDP202 3.5 29.1 1.0
O1B A:GDP202 3.6 31.9 1.0
O1A A:GDP202 3.8 43.7 1.0
OD2 A:ASP57 3.9 36.4 1.0
N A:SER17 3.9 33.9 1.0
CA A:SER17 4.1 30.1 1.0
O A:ASP33 4.1 37.9 1.0
CA A:PRO34 4.3 38.1 1.0
OD1 A:ASP57 4.3 31.2 1.0
O A:PRO34 4.3 39.9 1.0
O3A A:GDP202 4.4 34.6 1.0
CG A:ASP57 4.5 33.5 1.0
PA A:GDP202 4.5 35.6 1.0
O A:ILE36 4.5 35.7 1.0
CD2 A:TYR32 4.6 35.8 1.0
O2A A:GDP202 4.6 28.3 1.0
O3B A:GDP202 4.6 31.3 1.0
C A:PRO34 4.6 38.4 1.0
CB A:ALA59 4.6 36.6 1.0
O A:THR58 4.8 31.3 1.0
C A:ASP33 4.9 38.9 1.0

Magnesium binding site 2 out of 5 in 8un3

Go back to Magnesium Binding Sites List in 8un3
Magnesium binding site 2 out of 5 in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:33.7
occ:1.00
 O B:HOH305 2.0 33.3 1.0
O B:HOH335 2.0 34.5 1.0
O B:HOH302 2.1 33.3 1.0
O B:HOH303 2.1 33.3 1.0
OG B:SER17 2.1 34.8 1.0
O B:ASP33 2.4 43.8 1.0
O2B B:GDP202 2.9 38.2 1.0
CB B:SER17 3.3 36.2 1.0
CD2 B:TYR32 3.4 40.6 1.0
C B:ASP33 3.5 38.5 1.0
CA B:PRO34 3.6 40.3 1.0
N B:PRO34 4.0 37.0 1.0
CE2 B:TYR32 4.0 39.7 1.0
C B:PRO34 4.0 40.8 1.0
PB B:GDP202 4.1 31.9 1.0
O1A B:GDP202 4.1 39.9 1.0
O1B B:GDP202 4.1 42.9 1.0
O B:PRO34 4.1 41.5 1.0
O B:ILE36 4.2 30.8 1.0
OD2 B:ASP57 4.3 37.0 1.0
CG B:TYR32 4.5 39.7 1.0
CA B:SER17 4.6 29.9 1.0
O B:TYR32 4.7 43.7 1.0
N B:ASP33 4.7 42.2 1.0
CA B:ASP33 4.7 40.1 1.0
C B:TYR32 4.7 43.0 1.0
N B:SER17 4.7 35.2 1.0
CB B:TYR32 4.7 38.7 1.0
CB B:ALA59 4.7 36.5 1.0
O B:HOH314 4.8 40.7 1.0
N B:THR35 4.8 36.3 1.0
CB B:PRO34 4.8 48.8 1.0
PA B:GDP202 4.9 35.8 1.0
O3A B:GDP202 5.0 36.1 1.0

Magnesium binding site 3 out of 5 in 8un3

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Magnesium binding site 3 out of 5 in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:37.6
occ:1.00
 O B:HOH337 2.1 36.4 1.0
O B:HOH311 2.3 32.5 1.0
O B:HOH343 2.3 36.8 1.0
OD1 B:ASN26 2.3 53.1 1.0
OD1 B:ASP153 2.4 42.2 1.0
O B:LEU23 2.8 33.5 1.0
CG B:ASP153 3.4 36.8 1.0
NZ B:LYS42 3.5 37.1 1.0
CG B:ASN26 3.6 43.6 1.0
C B:LEU23 3.6 36.2 1.0
CA B:LEU23 3.7 35.8 1.0
OD2 B:ASP153 3.8 42.9 1.0
O B:GLN22 3.8 42.2 1.0
O B:HOH348 4.1 39.6 1.0
CD1 B:LEU23 4.3 29.1 1.0
ND2 B:ASN26 4.3 44.5 1.0
CG B:LEU23 4.5 28.6 1.0
CB B:LEU23 4.6 32.7 1.0
CB B:ASN26 4.7 43.4 1.0
C B:GLN22 4.7 36.0 1.0
N B:LEU23 4.7 33.6 1.0
CB B:ASP153 4.8 34.8 1.0
CA B:ASN26 4.8 41.1 1.0
N B:ILE24 4.9 38.3 1.0
CE B:LYS42 4.9 39.9 1.0

Magnesium binding site 4 out of 5 in 8un3

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Magnesium binding site 4 out of 5 in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg204

b:34.4
occ:1.00
 O C:HOH336 2.0 33.5 1.0
OG C:SER17 2.1 31.8 1.0
O C:HOH340 2.1 34.1 1.0
O2B C:GDP202 2.2 33.1 1.0
O C:HOH345 2.3 39.6 1.0
CB C:SER17 3.1 32.0 1.0
PB C:GDP202 3.5 25.4 1.0
OD2 C:ASP57 3.8 36.4 1.0
O3B C:GDP202 3.8 27.7 1.0
N C:SER17 3.9 33.3 1.0
O2A C:GDP202 3.9 42.2 1.0
CA C:SER17 4.1 27.4 1.0
O C:ASP33 4.2 41.2 1.0
OD1 C:ASP57 4.3 33.7 1.0
O3A C:GDP202 4.4 36.7 1.0
CD2 C:TYR32 4.4 36.0 1.0
CG C:ASP57 4.4 33.0 1.0
O C:ILE36 4.5 34.1 1.0
O1B C:GDP202 4.5 30.1 1.0
PA C:GDP202 4.5 34.5 1.0
CA C:PRO34 4.5 42.0 1.0
O C:PRO34 4.6 42.8 1.0
O1A C:GDP202 4.6 25.9 1.0
CB C:ALA59 4.7 37.1 1.0
O C:THR58 4.7 35.5 1.0
C C:PRO34 4.9 41.8 1.0
CE2 C:TYR32 5.0 38.1 1.0
C C:LYS16 5.0 24.5 1.0

Magnesium binding site 5 out of 5 in 8un3

Go back to Magnesium Binding Sites List in 8un3
Magnesium binding site 5 out of 5 in the Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kras-G13D-Gdp in Complex with CPD5 (1-((S)-10-(6-Amino-4-Methyl-3- (Trifluoromethyl)Pyridin-2-Yl)-11-Chloro-7-(((2S,4R)-4-Fluoro-1- Methylpyrrolidin-2-Yl)Methoxy)-3,4,13,13A-Tetrahydropyrazino[2',1':3, 4][1,4]Oxazepino[5,6,7-De]Quinazolin-2(1H)-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:34.2
occ:1.00
 O D:HOH309 1.8 32.2 1.0
O D:HOH320 1.9 33.4 1.0
O D:HOH306 2.1 28.4 1.0
O D:HOH302 2.1 38.5 1.0
OG D:SER17 2.4 35.3 1.0
O D:ASP33 2.6 41.4 1.0
O2B D:GDP202 2.6 38.0 1.0
CB D:SER17 3.3 32.6 1.0
C D:ASP33 3.5 36.7 1.0
CA D:PRO34 3.5 43.9 1.0
CD2 D:TYR32 3.6 36.4 1.0
PB D:GDP202 3.9 34.1 1.0
N D:PRO34 3.9 38.4 1.0
O3B D:GDP202 4.0 36.9 1.0
C D:PRO34 4.0 40.6 1.0
O2A D:GDP202 4.0 31.4 1.0
O D:PRO34 4.1 43.3 1.0
O D:ILE36 4.2 33.4 1.0
OD2 D:ASP57 4.2 34.8 1.0
CE2 D:TYR32 4.2 38.1 1.0
CA D:SER17 4.6 31.9 1.0
N D:ASP33 4.7 38.5 1.0
CG D:TYR32 4.7 38.8 1.0
N D:SER17 4.7 32.8 1.0
CA D:ASP33 4.7 41.1 1.0
CB D:ALA59 4.7 35.8 1.0
C D:TYR32 4.7 39.6 1.0
O D:TYR32 4.8 39.1 1.0
CB D:TYR32 4.8 40.6 1.0
CB D:PRO34 4.8 50.7 1.0
O1B D:GDP202 4.8 31.4 1.0
PA D:GDP202 4.8 31.8 1.0
N D:THR35 4.8 32.2 1.0
O3A D:GDP202 4.9 38.3 1.0
O1A D:GDP202 5.0 31.6 1.0

Reference:

C.Nilewski, M.H.Ultsch. N/A N/A.
Page generated: Thu Dec 28 10:35:32 2023

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