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Calcium in PDB 5v9u: Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C

Protein crystallography data

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u was solved by M.R.Janes, J.Zhang, L.-S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, J.Feng, J.H.Chen, S.Li, D.Brehmer, L.Darjania, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, Y.Wang, Y.Yao, X.Deng, P.Zarrinkar, D.Dashyant, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 60.03 / 1.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.440, 39.740, 61.780, 77.48, 81.97, 77.20
R / Rfree (%) 14.9 / 18.9

Other elements in 5v9u:

The structure of Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C (pdb code 5v9u). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C, PDB code: 5v9u:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5v9u

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Calcium binding site 1 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:4.2
occ:1.00
 O1B A:GDP206 2.3 4.0 1.0
O A:HOH336 2.3 9.0 1.0
OG A:SER17 2.3 8.8 1.0
O A:HOH370 2.4 9.5 1.0
O A:HOH347 2.4 10.2 1.0
O A:HOH378 2.4 10.0 1.0
CB A:SER17 3.4 8.6 1.0
PB A:GDP206 3.5 4.6 1.0
O2B A:GDP206 3.7 4.8 1.0
N A:SER17 4.0 7.7 1.0
O A:ASP33 4.2 13.2 1.0
OD2 A:ASP57 4.2 10.4 1.0
CA A:SER17 4.3 8.3 1.0
O2A A:GDP206 4.3 6.1 1.0
CB A:ALA59 4.3 11.6 1.0
O A:PRO34 4.4 12.3 1.0
OD1 A:ASP57 4.4 10.0 1.0
O3A A:GDP206 4.5 4.8 1.0
O3B A:GDP206 4.6 3.8 1.0
O A:THR58 4.6 9.3 1.0
O A:ILE36 4.7 11.5 1.0
CA A:PRO34 4.7 12.9 1.0
CD2 A:TYR32 4.7 14.3 1.0
C A:PRO34 4.7 12.9 1.0
PA A:GDP206 4.7 5.4 1.0
CG A:ASP57 4.7 9.8 1.0
CE A:LYS16 4.8 8.2 1.0
O1A A:GDP206 4.9 5.5 1.0
CB A:LYS16 4.9 7.3 1.0

Calcium binding site 2 out of 8 in 5v9u

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Calcium binding site 2 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:8.8
occ:1.00
 O A:GLY138 2.4 8.4 1.0
O A:HOH344 2.4 11.9 1.0
O A:HOH473 2.4 13.4 1.0
O A:HOH391 2.6 17.6 1.0
C A:GLY138 3.5 7.7 1.0
CA A:GLY138 4.1 8.1 1.0
OD1 A:ASP108 4.3 42.6 1.0
O A:HOH331 4.5 9.8 1.0
O A:HOH458 4.6 23.8 1.0
N A:ILE139 4.6 7.3 1.0
O A:HOH441 4.6 41.5 1.0
OE1 A:GLU162 4.6 11.5 1.0
O A:HOH363 4.7 17.6 1.0
CG2 A:ILE139 4.7 7.2 1.0
O A:TYR137 4.8 8.7 1.0
CA A:ILE139 4.8 7.3 1.0
O A:HOH377 5.0 24.5 1.0

Calcium binding site 3 out of 8 in 5v9u

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Calcium binding site 3 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:7.1
occ:0.50
 CA A:CA203 0.0 7.1 0.5
CA A:CA203 1.6 19.6 0.5
O A:HOH442 2.1 34.0 1.0
OD1 A:ASP105 2.5 16.6 1.0
O A:HOH390 2.6 22.0 1.0
OD2 A:ASP105 2.7 15.8 1.0
CG A:ASP105 2.9 14.9 1.0
O A:HOH351 4.2 32.9 1.0
CB A:ASP105 4.4 13.6 1.0
O A:ASP105 4.4 13.5 1.0

Calcium binding site 4 out of 8 in 5v9u

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Calcium binding site 4 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:19.6
occ:0.50
 CA A:CA203 0.0 19.6 0.5
CA A:CA203 1.6 7.1 0.5
OD2 A:ASP105 2.4 15.8 1.0
OD1 A:ASP105 2.8 16.6 1.0
CG A:ASP105 2.9 14.9 1.0
O A:HOH442 3.5 34.0 1.0
O A:HOH390 3.9 22.0 1.0
CB A:ASP105 4.3 13.6 1.0
O A:HOH388 4.4 24.1 1.0
O A:HOH351 4.6 32.9 1.0
O B:HOH317 4.9 30.1 1.0

Calcium binding site 5 out of 8 in 5v9u

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Calcium binding site 5 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:9.6
occ:0.50
 CA A:CA207 0.0 9.6 0.5
CA A:CA207 1.8 12.5 0.5
O B:HOH401 2.2 18.8 1.0
O B:HOH344 2.4 26.5 1.0
OE1 B:GLU63 2.5 15.3 1.0
O A:HOH364 2.7 24.7 1.0
OE2 A:GLU107 3.4 41.3 1.0
CD B:GLU63 3.5 15.2 1.0
OE1 A:GLU107 3.7 39.1 1.0
CD A:GLU107 4.0 36.1 1.0
NZ A:LYS101 4.2 24.6 1.0
O B:TYR64 4.2 18.8 1.0
CG B:GLU63 4.3 14.0 1.0
CB B:GLU63 4.3 14.7 1.0
OE2 B:GLU63 4.4 15.9 1.0
O A:HOH454 4.5 30.8 1.0
O A:HOH402 4.6 16.6 1.0
O A:HOH312 4.7 34.7 1.0
OE2 A:GLU98 4.7 10.7 1.0
CE A:LYS101 4.8 24.6 1.0

Calcium binding site 6 out of 8 in 5v9u

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Calcium binding site 6 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca207

b:12.5
occ:0.50
 CA A:CA207 0.0 12.5 0.5
CA A:CA207 1.8 9.6 0.5
O B:HOH401 2.1 18.8 1.0
O A:HOH364 2.1 24.7 1.0
OE1 A:GLU107 2.2 39.1 1.0
NZ A:LYS101 2.6 24.6 1.0
OE2 A:GLU107 2.8 41.3 1.0
CD A:GLU107 2.9 36.1 1.0
CE A:LYS101 3.3 24.6 1.0
O B:HOH344 3.6 26.5 1.0
OE1 B:GLU63 4.0 15.3 1.0
O A:HOH454 4.1 30.8 1.0
O A:HOH402 4.3 16.6 1.0
OE2 A:GLU98 4.3 10.7 1.0
CG A:GLU107 4.4 33.4 1.0
OE1 A:GLU98 4.5 13.1 1.0
CD A:LYS101 4.6 21.3 1.0
CD A:GLU98 4.8 10.6 1.0
O A:HOH312 4.9 34.7 1.0
O B:TYR64 4.9 18.8 1.0

Calcium binding site 7 out of 8 in 5v9u

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Calcium binding site 7 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:4.5
occ:1.00
 O B:HOH361 2.3 11.9 1.0
O3B B:GDP207 2.3 5.1 1.0
O B:HOH325 2.4 10.7 1.0
OG B:SER17 2.4 9.2 1.0
O B:HOH377 2.4 11.7 1.0
O B:HOH363 2.4 10.8 1.0
CB B:SER17 3.4 9.0 1.0
PB B:GDP207 3.5 4.6 1.0
O1B B:GDP207 3.7 4.7 1.0
N B:SER17 4.1 8.0 1.0
OD2 B:ASP57 4.3 12.6 1.0
CA B:SER17 4.3 8.3 1.0
O B:ASP33 4.3 16.4 1.0
O1A B:GDP207 4.4 6.2 1.0
OD1 B:ASP57 4.4 12.1 1.0
CB B:ALA59 4.4 15.1 1.0
O B:PRO34 4.5 17.3 1.0
O3A B:GDP207 4.5 5.5 1.0
O2B B:GDP207 4.6 4.3 1.0
O B:ILE36 4.6 16.8 1.0
CA B:PRO34 4.6 14.8 1.0
O B:THR58 4.6 12.4 1.0
C B:PRO34 4.7 15.5 1.0
CD2 B:TYR32 4.7 13.9 1.0
CG B:ASP57 4.7 11.6 1.0
PA B:GDP207 4.7 5.5 1.0
O2A B:GDP207 4.8 5.9 1.0
CE B:LYS16 4.9 9.6 1.0
CB B:LYS16 4.9 8.1 1.0
O1 B:91S204 5.0 8.8 1.0

Calcium binding site 8 out of 8 in 5v9u

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Calcium binding site 8 out of 8 in the Crystal Structure of Small Molecule Ars-1620 Covalently Bound to K-Ras G12C


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 Small Molecule Ars-1620 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca203

b:5.3
occ:1.00
 O B:GLY138 2.3 10.2 1.0
O B:HOH335 2.4 12.8 1.0
O B:HOH463 2.4 12.3 1.0
O B:HOH412 2.4 20.0 0.5
O B:HOH437 2.5 17.9 1.0
O B:HOH412 2.7 16.5 0.5
C B:GLY138 3.5 9.4 1.0
CA B:GLY138 4.1 9.5 1.0
OD2 B:ASP108 4.5 21.0 1.0
O B:HOH338 4.5 11.0 1.0
N B:ILE139 4.6 9.0 1.0
O B:HOH370 4.6 14.2 1.0
OE1 B:GLU162 4.6 13.3 1.0
O B:HOH309 4.6 32.3 1.0
OD1 B:ASP108 4.6 22.4 1.0
O B:HOH400 4.7 20.7 1.0
O B:TYR137 4.8 9.5 1.0
CA B:ILE139 4.8 8.9 1.0
CG2 B:ILE139 4.9 8.2 1.0
CG B:ASP108 5.0 19.6 1.0

Reference:

M.R.Janes, J.Zhang, L.S.Li, R.Hansen, U.Peters, X.Guo, Y.Chen, A.Babbar, S.J.Firdaus, L.Darjania, J.Feng, J.H.Chen, S.Li, S.Li, Y.O.Long, C.Thach, Y.Liu, A.Zarieh, T.Ely, J.M.Kucharski, L.V.Kessler, T.Wu, K.Yu, Y.Wang, Y.Yao, X.Deng, P.P.Zarrinkar, D.Brehmer, D.Dhanak, M.V.Lorenzi, D.Hu-Lowe, M.P.Patricelli, P.Ren, Y.Liu. Targeting Kras Mutant Cancers with A Covalent G12C-Specific Inhibitor. Cell V. 172 578 2018.
ISSN: ISSN 1097-4172
PubMed: 29373830
DOI: 10.1016/J.CELL.2018.01.006
Page generated: Wed Jul 9 10:43:49 2025

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