Magnesium in PDB 5v71: Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder

Protein crystallography data

The structure of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder, PDB code: 5v71 was solved by K.Westover, J.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.39 / 2.23
Space group P 3
Cell size a, b, c (Å), α, β, γ (°) 84.933, 84.933, 130.785, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 22.8

Other elements in 5v71:

The structure of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder also contains other interesting chemical elements:

Fluorine (F) 6 atoms
Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder (pdb code 5v71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder, PDB code: 5v71:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 5v71

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Magnesium binding site 1 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:24.1
occ:1.00
 O A:HOH307 2.1 25.2 1.0
O A:HOH317 2.2 31.7 1.0
O A:HOH311 2.2 24.5 1.0
O3B A:GDP201 2.2 29.6 1.0
OG A:SER17 2.3 25.6 1.0
O A:HOH329 2.3 23.9 1.0
O1B A:GDP201 3.1 27.6 1.0
PB A:GDP201 3.2 24.7 1.0
CB A:SER17 3.3 25.1 1.0
O1A A:GDP201 3.9 22.1 1.0
N A:SER17 3.9 22.3 1.0
CA A:SER17 4.2 23.5 1.0
O3A A:GDP201 4.2 23.0 1.0
O2B A:GDP201 4.2 24.2 1.0
OD2 A:ASP57 4.3 25.8 1.0
OD1 A:ASP57 4.3 36.1 1.0
PA A:GDP201 4.4 29.2 1.0
CA A:PRO34 4.4 38.3 1.0
CD1 A:TYR32 4.4 39.0 1.0
O A:ASP33 4.5 32.7 1.0
O A:THR58 4.5 36.6 1.0
O2A A:GDP201 4.6 29.6 1.0
O A:TYR32 4.7 37.8 1.0
O01 A:8ZG203 4.7 40.7 1.0
CG A:ASP57 4.7 30.2 1.0
O A:PRO34 4.7 36.1 1.0
CB A:LYS16 4.8 20.6 1.0
CB A:ALA59 4.8 45.1 1.0
O A:HOH344 4.8 33.5 1.0
O A:ILE36 4.8 31.8 1.0
CE A:LYS16 4.8 21.7 1.0
C A:PRO34 4.9 35.7 1.0
C A:LYS16 5.0 22.6 1.0

Magnesium binding site 2 out of 6 in 5v71

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Magnesium binding site 2 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:18.2
occ:1.00
 O3B B:GDP201 2.0 17.8 1.0
O B:HOH316 2.0 21.3 1.0
O B:HOH311 2.1 18.9 1.0
OG B:SER17 2.2 26.2 1.0
O B:HOH315 2.2 19.4 1.0
O B:HOH308 2.2 20.0 1.0
CB B:SER17 3.2 26.9 1.0
PB B:GDP201 3.4 38.0 1.0
O1B B:GDP201 3.6 22.1 1.0
N B:SER17 3.9 26.3 1.0
CD1 B:TYR32 4.1 27.7 1.0
CA B:SER17 4.1 28.7 1.0
O1A B:GDP201 4.2 23.7 1.0
OD2 B:ASP57 4.2 25.9 1.0
CA B:PRO34 4.2 26.9 1.0
OD1 B:ASP57 4.2 33.8 1.0
O B:ASP33 4.3 27.9 1.0
O2B B:GDP201 4.3 21.8 1.0
O3A B:GDP201 4.4 21.7 1.0
CE1 B:TYR32 4.4 29.9 1.0
O B:ILE36 4.5 32.1 1.0
O B:PRO34 4.5 29.9 1.0
PA B:GDP201 4.6 27.4 1.0
O B:TYR32 4.6 39.4 1.0
CG B:ASP57 4.7 32.6 1.0
O2A B:GDP201 4.7 27.3 1.0
C B:PRO34 4.7 26.5 1.0
O B:THR58 4.7 30.6 1.0
CB B:LYS16 4.9 28.5 1.0
O B:HOH312 4.9 28.9 1.0
C B:ASP33 5.0 28.0 1.0

Magnesium binding site 3 out of 6 in 5v71

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Magnesium binding site 3 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:35.1
occ:1.00
 O2B C:GDP201 1.9 40.1 1.0
O C:HOH303 2.0 34.4 1.0
O C:HOH316 2.1 29.5 1.0
O C:HOH309 2.1 21.7 1.0
OG C:SER17 2.2 35.3 1.0
O C:HOH301 2.5 31.9 1.0
PB C:GDP201 3.2 31.0 1.0
CB C:SER17 3.4 34.3 1.0
O1B C:GDP201 3.4 46.0 1.0
O1A C:GDP201 3.9 31.7 1.0
N C:SER17 4.1 31.1 1.0
O3B C:GDP201 4.1 36.0 1.0
O C:ASP33 4.1 51.6 1.0
CA C:PRO34 4.2 48.8 1.0
O C:PRO34 4.2 49.1 1.0
OD2 C:ASP57 4.2 34.6 1.0
O3A C:GDP201 4.3 28.4 1.0
CA C:SER17 4.3 34.7 1.0
PA C:GDP201 4.4 27.2 1.0
C C:PRO34 4.5 46.2 1.0
OD1 C:ASP57 4.5 34.7 1.0
O2A C:GDP201 4.5 26.9 1.0
CD2 C:TYR32 4.6 43.4 1.0
O C:ILE36 4.7 42.0 1.0
O C:THR58 4.7 40.7 1.0
O01 C:8ZG203 4.8 42.6 1.0
CG C:ASP57 4.8 33.4 1.0
O C:TYR32 4.8 45.5 1.0
CE C:LYS16 4.8 33.6 1.0
CB C:ALA59 4.9 48.4 1.0
C C:ASP33 4.9 46.5 1.0
CB C:LYS16 4.9 30.2 1.0
N C:PRO34 5.0 46.7 1.0

Magnesium binding site 4 out of 6 in 5v71

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Magnesium binding site 4 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:23.5
occ:1.00
 O2B D:GDP201 2.1 30.4 1.0
OG D:SER17 2.2 23.9 1.0
O D:HOH318 2.2 38.8 1.0
O D:HOH303 2.2 19.0 1.0
O D:HOH322 2.2 30.5 1.0
O D:HOH308 2.3 19.7 1.0
O1B D:GDP201 3.2 28.4 1.0
PB D:GDP201 3.2 24.2 1.0
CB D:SER17 3.3 23.4 1.0
N D:SER17 3.9 21.2 1.0
O1A D:GDP201 4.0 22.5 1.0
CA D:SER17 4.2 22.2 1.0
OD2 D:ASP57 4.2 33.1 1.0
OD1 D:ASP57 4.2 43.0 1.0
O3B D:GDP201 4.2 27.4 1.0
CA D:PRO34 4.3 36.3 1.0
O3A D:GDP201 4.3 22.8 1.0
CD1 D:TYR32 4.3 35.9 1.0
O D:ASP33 4.4 33.2 1.0
PA D:GDP201 4.5 29.9 1.0
O D:THR58 4.5 36.4 1.0
CG D:ASP57 4.6 31.8 1.0
O2A D:GDP201 4.7 28.6 1.0
CB D:ALA59 4.7 37.8 1.0
CB D:LYS16 4.7 18.3 1.0
O D:TYR32 4.7 41.0 1.0
O D:PRO34 4.7 37.9 1.0
CE D:LYS16 4.8 22.1 1.0
O D:ILE36 4.8 30.5 1.0
C D:PRO34 4.9 38.1 1.0
NZ D:LYS16 4.9 21.1 1.0
O01 D:8ZG203 4.9 35.7 1.0
CE1 D:TYR32 4.9 34.6 1.0
C D:LYS16 5.0 25.8 1.0

Magnesium binding site 5 out of 6 in 5v71

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Magnesium binding site 5 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg202

b:26.2
occ:1.00
 OG E:SER17 2.0 33.7 1.0
O E:HOH314 2.0 22.0 1.0
O E:HOH315 2.0 31.3 1.0
O E:HOH301 2.1 38.6 1.0
O3B E:GDP201 2.1 25.0 1.0
O E:HOH316 2.2 31.6 1.0
CB E:SER17 3.2 30.8 1.0
PB E:GDP201 3.5 34.7 1.0
O1B E:GDP201 3.8 36.3 1.0
OD2 E:ASP57 3.9 38.0 1.0
N E:SER17 3.9 31.6 1.0
CA E:SER17 4.1 29.6 1.0
O1A E:GDP201 4.2 34.6 1.0
O E:ASP33 4.3 49.8 1.0
OD1 E:ASP57 4.3 33.3 1.0
O E:PRO34 4.3 47.9 1.0
CA E:PRO34 4.4 44.7 1.0
O E:ILE36 4.4 46.3 1.0
CG E:ASP57 4.5 33.2 1.0
O2B E:GDP201 4.5 37.5 1.0
CD2 E:TYR32 4.5 54.1 1.0
O3A E:GDP201 4.5 28.6 1.0
O E:THR58 4.6 39.4 1.0
O2A E:GDP201 4.6 24.9 1.0
PA E:GDP201 4.6 29.4 1.0
C E:PRO34 4.6 45.0 1.0
CB E:LYS16 4.8 28.4 1.0
CE E:LYS16 4.8 30.3 1.0
O01 E:8ZG203 4.8 43.7 1.0
C E:LYS16 5.0 33.8 1.0
CE2 E:TYR32 5.0 54.9 1.0

Magnesium binding site 6 out of 6 in 5v71

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Magnesium binding site 6 out of 6 in the Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Kras G12C in Bound to Quinazoline Based Switch II Pocket (Swiip) Binder within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg202

b:19.8
occ:1.00
 O3B F:GDP201 2.1 25.7 1.0
O F:HOH312 2.1 24.3 1.0
OG F:SER17 2.1 27.0 1.0
O F:HOH314 2.2 20.3 1.0
O F:HOH309 2.2 26.3 1.0
O F:HOH305 2.2 21.2 1.0
CB F:SER17 3.2 27.6 1.0
PB F:GDP201 3.4 23.9 1.0
O1B F:GDP201 3.5 23.8 1.0
N F:SER17 4.0 26.7 1.0
O1A F:GDP201 4.1 17.0 1.0
CA F:SER17 4.1 27.4 1.0
OD2 F:ASP57 4.1 26.5 1.0
CD1 F:TYR32 4.1 29.0 1.0
CA F:PRO34 4.2 28.6 1.0
O F:ASP33 4.2 29.0 1.0
OD1 F:ASP57 4.3 27.1 1.0
O2B F:GDP201 4.4 28.1 1.0
O3A F:GDP201 4.4 21.7 1.0
O F:PRO34 4.4 34.2 1.0
O F:TYR32 4.5 41.4 1.0
CE1 F:TYR32 4.6 30.0 1.0
O F:ILE36 4.6 30.4 1.0
PA F:GDP201 4.6 23.2 1.0
C F:PRO34 4.6 28.3 1.0
CG F:ASP57 4.7 27.0 1.0
O F:THR58 4.7 29.6 1.0
O2A F:GDP201 4.8 29.2 1.0
C F:ASP33 4.9 29.8 1.0
N F:PRO34 5.0 29.7 1.0
CE F:LYS16 5.0 24.5 1.0

Reference:

J.Lu, R.A.Harrison, L.Li, M.Zeng, S.Gondi, D.Scott, N.S.Gray, J.R.Engen, K.D.Westover. Kras G12C Drug Development: Discrimination Between Switch II Pocket Configurations Using Hydrogen/Deuterium-Exchange Mass Spectrometry. Structure V. 25 1442 2017.
ISSN: ISSN 1878-4186
PubMed: 28781083
DOI: 10.1016/J.STR.2017.07.003
Page generated: Mon Dec 14 21:17:47 2020

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