Calcium in PDB 6b0v: Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C

Protein crystallography data

The structure of Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C, PDB code: 6b0v was solved by R.Hansen, U.Peters, A.Babbar, Y.Chen, J.Feng, M.R.Janes, L.-S.Li, P.Ren, Y.Liu, P.P.Zarrinkar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.17 / 1.29
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.140, 39.880, 62.430, 77.00, 81.24, 77.58
R / Rfree (%) 18.2 / 21.8

Other elements in 6b0v:

The structure of Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C (pdb code 6b0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Small Molecule Ars-107 Covalently Bound to K-Ras G12C, PDB code: 6b0v:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6b0v

Go back to Calcium Binding Sites List in 6b0v
Calcium binding site 1 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:10.8
occ:1.00
O1B A:GDP204 2.3 10.0 1.0
O A:HOH349 2.4 12.0 1.0
O A:HOH354 2.4 11.7 1.0
O A:HOH313 2.4 13.8 1.0
O A:HOH324 2.4 16.1 1.0
OG A:SER17 2.5 10.5 1.0
O A:HOH375 2.5 17.3 1.0
PB A:GDP204 3.5 10.1 1.0
CB A:SER17 3.5 10.0 1.0
O2B A:GDP204 3.8 13.0 1.0
N A:SER17 4.1 8.0 1.0
OD2 A:ASP57 4.3 14.9 1.0
CA A:PRO34 4.3 13.9 1.0
O1 A:C8G203 4.4 13.0 1.0
O A:THR58 4.4 13.6 1.0
CA A:SER17 4.4 8.7 1.0
O2A A:GDP204 4.4 13.3 1.0
OD1 A:ASP57 4.4 13.5 1.0
O A:PRO34 4.5 15.2 1.0
O3B A:GDP204 4.6 10.1 1.0
O A:ILE36 4.6 12.7 1.0
O A:ASP33 4.6 14.2 1.0
O3A A:GDP204 4.7 11.6 1.0
C A:PRO34 4.7 15.0 1.0
CG A:ASP57 4.8 13.2 1.0
CD2 A:TYR32 4.8 15.2 1.0
PA A:GDP204 4.9 12.3 1.0
CE A:LYS16 5.0 11.0 1.0

Calcium binding site 2 out of 4 in 6b0v

Go back to Calcium Binding Sites List in 6b0v
Calcium binding site 2 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:12.4
occ:1.00
O A:HOH305 2.2 24.2 1.0
O A:GLY138 2.3 10.8 1.0
O A:HOH457 2.4 14.1 1.0
O A:HOH337 2.5 13.2 1.0
O A:HOH373 2.5 15.1 1.0
C A:GLY138 3.4 9.2 1.0
CA A:GLY138 4.1 9.6 1.0
OD1 A:ASP108 4.3 35.0 1.0
O A:HOH308 4.4 26.4 1.0
O A:HOH480 4.5 18.8 0.5
O A:HOH316 4.5 10.4 1.0
N A:ILE139 4.6 7.9 1.0
OE1 A:GLU162 4.6 11.8 1.0
O A:HOH355 4.6 14.5 1.0
CG2 A:ILE139 4.7 8.6 1.0
O A:TYR137 4.7 12.4 1.0
CA A:ILE139 4.8 8.2 1.0
O A:HOH391 4.9 15.8 1.0

Calcium binding site 3 out of 4 in 6b0v

Go back to Calcium Binding Sites List in 6b0v
Calcium binding site 3 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:10.2
occ:1.00
O3B B:GDP204 2.3 10.3 1.0
OG B:SER17 2.4 10.8 1.0
O B:HOH347 2.4 12.9 1.0
O B:HOH374 2.4 10.5 1.0
O B:HOH342 2.4 12.8 1.0
O B:HOH354 2.4 10.3 1.0
O B:HOH382 2.6 17.5 1.0
CB B:SER17 3.5 9.3 1.0
PB B:GDP204 3.5 9.8 1.0
O1B B:GDP204 3.8 11.2 1.0
N B:SER17 4.2 8.1 1.0
OD2 B:ASP57 4.3 14.2 1.0
O1A B:GDP204 4.3 12.8 1.0
CA B:PRO34 4.4 14.3 1.0
CA B:SER17 4.4 8.3 1.0
O1 B:C8G203 4.4 12.9 1.0
O B:THR58 4.4 13.2 1.0
OD1 B:ASP57 4.5 15.3 1.0
O B:PRO34 4.5 13.7 1.0
O3A B:GDP204 4.6 11.3 1.0
O B:ASP33 4.6 12.1 1.0
O B:ILE36 4.6 12.2 1.0
O2B B:GDP204 4.6 9.4 1.0
CD2 B:TYR32 4.8 15.5 1.0
CG B:ASP57 4.8 13.7 1.0
C B:PRO34 4.8 13.1 1.0
PA B:GDP204 4.8 11.0 1.0
NZ B:LYS16 5.0 9.9 1.0

Calcium binding site 4 out of 4 in 6b0v

Go back to Calcium Binding Sites List in 6b0v
Calcium binding site 4 out of 4 in the Crystal Structure of Small Molecule Ars-107 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-107 Covalently Bound to K-Ras G12C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:12.3
occ:1.00
O B:GLY138 2.2 11.4 1.0
O B:HOH356 2.3 17.6 1.0
O B:HOH468 2.4 15.1 1.0
O B:HOH337 2.4 15.0 1.0
O B:HOH415 2.4 25.9 1.0
C B:GLY138 3.4 9.4 1.0
CA B:GLY138 4.0 10.2 1.0
OD1 B:ASP108 4.4 22.8 1.0
OD2 B:ASP108 4.5 24.1 1.0
O B:HOH333 4.5 12.4 1.0
N B:ILE139 4.5 9.1 1.0
OE1 B:GLU162 4.6 12.6 1.0
O B:HOH319 4.6 20.3 1.0
O B:HOH490 4.7 27.6 1.0
O B:HOH400 4.8 17.4 1.0
O B:TYR137 4.8 11.7 1.0
CA B:ILE139 4.8 8.6 1.0
CG2 B:ILE139 4.9 9.9 1.0
CG B:ASP108 4.9 20.1 1.0
O B:HOH379 5.0 16.7 1.0

Reference:

R.Hansen, U.Peters, A.Babbar, Y.Chen, J.Feng, M.R.Janes, L.S.Li, P.Ren, Y.Liu, P.P.Zarrinkar. The Reactivity-Driven Biochemical Mechanism of Covalent KRASG12CINHIBITORS. Nat. Struct. Mol. Biol. V. 25 454 2018.
ISSN: ESSN 1545-9985
PubMed: 29760531
DOI: 10.1038/S41594-018-0061-5
Page generated: Sat Dec 12 05:57:49 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy