Calcium in PDB 6pgp: Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor

Protein crystallography data

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

Resolution Low / High (Å) 35.00 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 33.420, 39.606, 62.451, 76.91, 81.38, 77.30
R / Rfree (%) 19 / 21.6

Other elements in 6pgp:

The structure of Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor (pdb code 6pgp). 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 Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor, PDB code: 6pgp:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6pgp

Go back to Calcium Binding Sites List in 6pgp
Calcium binding site 1 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:10.7
occ:1.00
O A:HOH642 2.3 15.7 1.0
O2B A:GDP501 2.3 10.0 1.0
OG A:SER17 2.3 10.4 1.0
O A:HOH608 2.3 13.2 1.0
O A:HOH641 2.4 12.7 1.0
O A:HOH615 2.4 10.9 1.0
CB A:SER17 3.4 9.8 1.0
PB A:GDP501 3.5 10.0 1.0
O1B A:GDP501 3.6 10.8 1.0
N A:SER17 4.1 9.5 1.0
OD2 A:ASP57 4.3 17.8 1.0
O1A A:GDP501 4.3 12.0 1.0
CA A:SER17 4.3 9.6 1.0
OD1 A:ASP57 4.4 17.1 1.0
CA A:PRO34 4.5 20.1 1.0
O A:ASP33 4.5 19.7 1.0
O3B A:GDP501 4.5 10.2 1.0
O3A A:GDP501 4.5 10.8 1.0
O A:THR58 4.6 15.2 1.0
O A:ILE36 4.6 19.2 1.0
CD2 A:TYR32 4.6 19.1 1.0
PA A:GDP501 4.7 11.2 1.0
CG A:ASP57 4.7 16.9 1.0
O A:PRO34 4.8 21.4 1.0
O3 A:OHY504 4.9 18.0 1.0
O2A A:GDP501 4.9 11.1 1.0
C A:PRO34 4.9 20.3 1.0
CB A:LYS16 4.9 9.6 1.0
CB A:ALA59 5.0 17.8 1.0

Calcium binding site 2 out of 4 in 6pgp

Go back to Calcium Binding Sites List in 6pgp
Calcium binding site 2 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:15.3
occ:1.00
OE2 A:GLU63 2.3 16.4 1.0
OE1 A:GLU63 2.3 16.1 1.0
CD A:GLU63 2.7 16.0 1.0
CG A:GLU63 4.2 16.7 1.0
OE1 A:GLN61 4.6 16.9 1.0
O A:HOH678 4.9 24.9 1.0

Calcium binding site 3 out of 4 in 6pgp

Go back to Calcium Binding Sites List in 6pgp
Calcium binding site 3 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:12.2
occ:1.00
O B:HOH620 2.2 17.1 1.0
O B:HOH648 2.3 14.8 1.0
O1B B:GDP501 2.3 11.9 1.0
OG B:SER17 2.3 11.8 1.0
O B:HOH617 2.3 12.8 1.0
O B:HOH610 2.4 12.9 1.0
CB B:SER17 3.4 11.0 1.0
PB B:GDP501 3.4 11.6 1.0
O3B B:GDP501 3.6 12.2 1.0
N B:SER17 4.1 10.7 1.0
OD2 B:ASP57 4.2 18.0 1.0
O2A B:GDP501 4.3 13.8 1.0
CA B:SER17 4.3 10.9 1.0
CA B:PRO34 4.4 22.5 1.0
O B:ASP33 4.5 20.4 1.0
OD1 B:ASP57 4.5 17.5 1.0
O3A B:GDP501 4.5 12.4 1.0
O2B B:GDP501 4.5 11.4 1.0
O B:THR58 4.6 16.0 1.0
O B:PRO34 4.7 24.4 1.0
O B:ILE36 4.7 22.9 1.0
CD2 B:TYR32 4.7 22.9 1.0
O3 B:OHY504 4.7 18.8 1.0
PA B:GDP501 4.7 13.2 1.0
CG B:ASP57 4.8 17.1 1.0
C B:PRO34 4.8 22.9 1.0
CE B:LYS16 4.9 10.6 1.0
O1A B:GDP501 4.9 13.3 1.0
O B:HOH622 5.0 19.4 1.0
CB B:LYS16 5.0 10.5 1.0

Calcium binding site 4 out of 4 in 6pgp

Go back to Calcium Binding Sites List in 6pgp
Calcium binding site 4 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:17.4
occ:1.00
OE2 B:GLU63 2.3 19.1 1.0
OE1 B:GLU63 2.3 19.1 1.0
CD B:GLU63 2.7 18.6 1.0
O B:HOH634 4.1 42.3 1.0
CG B:GLU63 4.2 18.5 1.0
OE1 B:GLN61 4.6 17.0 1.0
O B:HOH665 4.9 20.0 1.0

Reference:

B.A.Lanman, J.R.Allen, J.G.Allen, A.K.Amegadzie, K.S.Ashton, S.K.Booker, J.J.Chen, N.Chen, M.J.Frohn, G.Goodman, D.J.Kopecky, L.Liu, P.Lopez, J.D.Low, V.Ma, A.E.Minatti, T.T.Nguyen, N.Nishimura, A.J.Pickrell, A.B.Reed, Y.Shin, A.Siegmund, N.A.Tamayo, C.M.Tegley, M.C.Walton, H.L.Wang, R.P.Wurz, M.Xue, K.C.Yang, P.Achanta, M.D.Bartberger, J.Canon, L.S.Hollis, J.D.Mccarter, C.Mohr, K.Rex, A.Y.Saiki, T.San Miguel, L.Volak, K.H.Wang, D.A.Whittington, S.G.Zech, J.R.Lipford, V.J.Cee. Discovery of A Covalent Inhibitor of KRASG12C (Amg 510) For the Treatment of Solid Tumors. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31820981
DOI: 10.1021/ACS.JMEDCHEM.9B01180
Page generated: Sat Dec 12 07:25:19 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