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Calcium in PDB 6p8x: Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.

Protein crystallography data

The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor., PDB code: 6p8x was solved by C.Mohr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.11
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.327, 66.150, 78.629, 66.48, 78.75, 89.47
R / Rfree (%) 26.5 / 31.3

Other elements in 6p8x:

The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. also contains other interesting chemical elements:

Bromine (Br) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. (pdb code 6p8x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor., PDB code: 6p8x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 6p8x

Go back to Calcium Binding Sites List in 6p8x
Calcium binding site 1 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:22.1
occ:1.00
 O A:HOH421 2.3 25.2 1.0
O A:HOH442 2.3 21.8 1.0
O A:HOH425 2.3 22.0 1.0
O A:HOH413 2.3 20.5 1.0
OG A:SER17 2.3 19.8 1.0
O1B A:GDP304 2.4 24.8 1.0
CB A:SER17 3.4 21.3 1.0
PB A:GDP304 3.5 26.5 1.0
O3B A:GDP304 3.5 26.4 1.0
OD2 A:ASP57 4.2 40.8 1.0
N A:SER17 4.2 21.8 1.0
CD2 A:TYR32 4.2 40.8 1.0
O2A A:GDP304 4.2 29.2 1.0
CA A:SER17 4.4 21.6 1.0
O A:ASP33 4.4 30.2 1.0
O3A A:GDP304 4.5 27.6 1.0
O2B A:GDP304 4.5 24.5 1.0
CA A:PRO34 4.5 31.5 1.0
CE2 A:TYR32 4.6 43.4 1.0
O A:PRO34 4.6 26.8 1.0
O A:ILE36 4.6 29.3 1.0
O A:THR58 4.7 29.3 1.0
OD1 A:ASP57 4.7 36.9 1.0
PA A:GDP304 4.7 28.4 1.0
CG A:ASP57 4.8 37.7 1.0
CE A:LYS16 4.8 21.7 1.0
O1A A:GDP304 4.8 29.1 1.0
C A:PRO34 4.8 30.8 1.0
CB A:ALA59 4.8 30.4 1.0
O04 A:O5V305 4.9 22.2 1.0
CB A:LYS16 4.9 21.2 1.0

Calcium binding site 2 out of 10 in 6p8x

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Calcium binding site 2 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:30.6
occ:1.00
 OE1 A:GLU63 2.7 30.5 1.0
OE2 A:GLU63 2.7 33.1 1.0
CD A:GLU63 3.0 33.4 1.0
CG A:GLU63 4.5 35.7 1.0
O A:HOH433 4.9 27.9 1.0
OE1 A:GLN61 4.9 32.3 1.0

Calcium binding site 3 out of 10 in 6p8x

Go back to Calcium Binding Sites List in 6p8x
Calcium binding site 3 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:40.1
occ:1.00
 O A:HOH445 2.3 37.1 1.0
OD1 A:ASP105 2.3 30.4 1.0
OD2 A:ASP105 2.3 31.4 1.0
O A:HOH428 2.3 35.8 1.0
CG A:ASP105 2.7 29.5 1.0
CB A:ASP105 4.2 28.4 1.0
O A:ASP105 4.3 23.4 1.0
C A:ASP105 4.8 25.8 1.0
CA A:ASP105 4.9 27.2 1.0

Calcium binding site 4 out of 10 in 6p8x

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Calcium binding site 4 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:23.2
occ:1.00
 OG B:SER17 2.3 22.4 1.0
O B:HOH413 2.3 20.1 1.0
O B:HOH429 2.3 23.6 1.0
O B:HOH412 2.3 22.4 1.0
O B:HOH410 2.3 27.2 1.0
O1B B:GDP304 2.4 24.9 1.0
CB B:SER17 3.3 23.6 1.0
PB B:GDP304 3.5 25.9 1.0
O3B B:GDP304 3.6 24.6 1.0
O2A B:GDP304 4.1 22.1 1.0
N B:SER17 4.1 22.7 1.0
OD2 B:ASP57 4.3 37.2 1.0
CA B:SER17 4.3 22.8 1.0
OD1 B:ASP57 4.3 33.2 1.0
CD2 B:TYR32 4.5 40.5 1.0
O3A B:GDP304 4.5 25.4 1.0
O B:ILE36 4.5 39.1 1.0
O B:ASP33 4.6 29.8 1.0
O2B B:GDP304 4.6 24.2 1.0
PA B:GDP304 4.6 25.6 1.0
CA B:PRO34 4.6 30.7 1.0
O B:PRO34 4.7 25.2 1.0
O1A B:GDP304 4.7 24.6 1.0
CG B:ASP57 4.7 33.9 1.0
O B:THR58 4.7 31.0 1.0
O04 B:O5V305 4.8 37.3 1.0
CB B:ALA59 4.9 33.9 1.0
CE B:LYS16 4.9 20.1 1.0
CB B:LYS16 4.9 21.0 1.0
C B:PRO34 4.9 28.8 1.0

Calcium binding site 5 out of 10 in 6p8x

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Calcium binding site 5 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:26.4
occ:1.00
 OE1 B:GLU63 2.3 27.6 1.0
OE2 B:GLU63 2.4 32.1 1.0
CD B:GLU63 2.7 33.6 1.0
CG B:GLU63 4.3 36.1 1.0
O B:HOH427 4.9 21.5 1.0

Calcium binding site 6 out of 10 in 6p8x

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Calcium binding site 6 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:37.7
occ:1.00
 OD1 B:ASP105 2.3 26.2 1.0
O B:HOH411 2.3 32.9 1.0
OD2 B:ASP105 2.5 27.9 1.0
CG B:ASP105 2.7 26.4 1.0
CB B:ASP105 4.2 25.8 1.0
O B:ASP105 4.3 22.0 1.0
CA B:ASP105 4.8 26.8 1.0
C B:ASP105 4.9 25.6 1.0

Calcium binding site 7 out of 10 in 6p8x

Go back to Calcium Binding Sites List in 6p8x
Calcium binding site 7 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:26.4
occ:1.00
 O1B C:GDP303 2.3 21.7 1.0
O C:HOH413 2.3 23.0 1.0
OG C:SER17 2.3 18.9 1.0
O C:HOH417 2.3 25.2 1.0
O C:HOH408 2.3 21.2 1.0
O C:HOH437 2.3 26.0 1.0
CB C:SER17 3.3 19.6 1.0
PB C:GDP303 3.5 22.2 1.0
O3B C:GDP303 3.7 21.7 1.0
N C:SER17 4.1 19.0 1.0
O2A C:GDP303 4.2 23.2 1.0
CA C:SER17 4.3 19.2 1.0
OD2 C:ASP57 4.4 42.9 1.0
O3A C:GDP303 4.5 22.9 1.0
CA C:PRO34 4.5 36.8 1.0
O2B C:GDP303 4.5 20.3 1.0
O C:ASP33 4.5 30.6 1.0
O C:PRO34 4.6 38.0 1.0
OD1 C:ASP57 4.6 42.1 1.0
CD2 C:TYR32 4.6 36.0 1.0
O C:ILE36 4.6 34.5 1.0
PA C:GDP303 4.7 25.0 1.0
O1A C:GDP303 4.8 23.1 1.0
O C:THR58 4.8 31.7 1.0
C C:PRO34 4.8 37.0 1.0
CB C:ALA59 4.9 32.9 1.0
CG C:ASP57 4.9 38.8 1.0
CE C:LYS16 4.9 23.3 1.0
CB C:LYS16 5.0 21.4 1.0
O C:TYR32 5.0 36.6 1.0

Calcium binding site 8 out of 10 in 6p8x

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Calcium binding site 8 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:21.5
occ:1.00
 O C:HOH427 2.3 23.6 1.0
OE2 C:GLU63 2.3 22.5 1.0
O C:HOH432 2.3 19.2 1.0
OE1 C:GLU63 2.3 20.1 1.0
O C:HOH407 2.3 23.7 1.0
CD C:GLU63 2.7 24.7 1.0
CG C:GLU63 4.2 26.7 1.0
OE1 C:GLN61 4.3 32.3 1.0
CB C:GLN61 4.7 30.9 1.0
CG C:GLN61 4.7 31.6 1.0
CD C:GLN61 4.9 31.6 1.0
CB C:GLU63 4.9 28.5 1.0

Calcium binding site 9 out of 10 in 6p8x

Go back to Calcium Binding Sites List in 6p8x
Calcium binding site 9 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:21.9
occ:1.00
 O1B D:GDP303 2.3 23.4 1.0
OG D:SER17 2.3 21.2 1.0
O D:HOH407 2.3 21.8 1.0
O D:HOH429 2.3 21.6 1.0
O D:HOH423 2.3 17.7 1.0
O D:HOH439 2.3 18.8 1.0
CB D:SER17 3.4 20.7 1.0
PB D:GDP303 3.5 24.7 1.0
O3B D:GDP303 3.8 24.9 1.0
N D:SER17 4.1 21.4 1.0
OD2 D:ASP57 4.2 37.2 1.0
CA D:SER17 4.3 20.7 1.0
OD1 D:ASP57 4.4 39.6 1.0
O2B D:GDP303 4.4 22.3 1.0
O D:ILE36 4.5 38.5 1.0
O2A D:GDP303 4.5 21.3 1.0
O D:PRO34 4.6 42.0 1.0
O D:THR58 4.6 31.2 1.0
CA D:PRO34 4.6 41.6 1.0
O3A D:GDP303 4.7 24.9 1.0
CG D:ASP57 4.7 37.8 1.0
O D:ASP33 4.7 38.1 1.0
CD2 D:TYR32 4.7 42.1 1.0
CE D:LYS16 4.8 19.5 1.0
CB D:ALA59 4.8 34.4 1.0
O04 D:O5V304 4.8 21.8 1.0
O1A D:GDP303 4.9 22.2 1.0
CB D:LYS16 4.9 20.9 1.0
C D:PRO34 4.9 40.0 1.0
PA D:GDP303 4.9 24.4 1.0

Calcium binding site 10 out of 10 in 6p8x

Go back to Calcium Binding Sites List in 6p8x
Calcium binding site 10 out of 10 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:20.5
occ:1.00
 O D:HOH447 2.3 23.5 1.0
O D:HOH421 2.3 26.0 1.0
OE1 D:GLU63 2.3 21.6 1.0
OE2 D:GLU63 2.4 25.4 1.0
CD D:GLU63 2.7 25.9 1.0
O D:HOH451 4.1 26.6 1.0
CG D:GLU63 4.2 28.1 1.0
O D:HOH418 4.4 29.6 1.0
OE1 D:GLN61 4.8 36.0 1.0

Reference:

Y.Shin, J.W.Jeong, R.P.Wurz, P.Achanta, T.Arvedson, M.D.Bartberger, I.D.G.Campuzano, R.Fucini, S.K.Hansen, J.Ingersoll, J.S.Iwig, J.R.Lipford, V.Ma, D.J.Kopecky, J.Mccarter, T.San Miguel, C.Mohr, S.Sabet, A.Y.Saiki, A.Sawayama, S.Sethofer, C.M.Tegley, L.P.Volak, K.Yang, B.A.Lanman, D.A.Erlanson, V.J.Cee. Discovery Ofn-(1-Acryloylazetidin-3-Yl)-2-(1H-Indol-1-Yl) Acetamides As Covalent Inhibitors of KRASG12C. Acs Med.Chem.Lett. V. 10 1302 2019.
ISSN: ISSN 1948-5875
PubMed: 31531201
DOI: 10.1021/ACSMEDCHEMLETT.9B00258
Page generated: Tue Jul 16 12:49:01 2024

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