Atomistry » Calcium » PDB 5w78-5wn2 » 5whe
Atomistry »
  Calcium »
    PDB 5w78-5wn2 »
      5whe »

Calcium in PDB 5whe: Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11

Protein crystallography data

The structure of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11, PDB code: 5whe was solved by S.Y.Shim, J.H.Mcgee, S.-J.Lee, G.L.Verdine, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.54 / 1.91
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.549, 232.525, 48.213, 90.00, 90.16, 90.00
R / Rfree (%) 18.4 / 22.7

Other elements in 5whe:

The structure of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 (pdb code 5whe). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11, PDB code: 5whe:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 1 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:25.3
occ:1.00
 O A:HOH984 2.4 22.8 1.0
O A:HOH939 2.4 24.8 1.0
O A:GLN25 2.5 19.0 1.0
O A:HOH991 2.5 22.2 1.0
O A:HOH906 2.6 20.7 1.0
C A:GLN25 3.6 20.8 1.0
CA A:GLN25 4.1 20.2 1.0
CB A:GLN25 4.3 23.1 1.0
CD2 A:HIS27 4.3 23.7 1.0
OE2 A:GLU31 4.6 26.6 1.0
N A:ASN26 4.7 24.2 1.0
OE1 A:GLU31 4.7 26.5 1.0
CB A:ASN26 4.8 32.9 1.0
O A:ASN26 5.0 30.0 1.0
C A:ASN26 5.0 27.1 1.0

Calcium binding site 2 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 2 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:20.6
occ:1.00
 O A:HOH968 2.4 18.0 1.0
OE2 A:GLU63 2.5 29.3 1.0
OXT B:ALA32 2.6 21.2 1.0
OE1 A:GLU63 2.6 26.0 1.0
O B:ALA32 2.7 25.3 1.0
CD A:GLU63 2.8 20.6 1.0
C B:ALA32 3.0 30.1 1.0
O B:HOH104 4.1 22.1 1.0
CA A:CA804 4.1 18.3 1.0
O A:HOH970 4.3 23.9 1.0
CG A:GLU63 4.3 24.4 1.0
CA B:ALA32 4.5 28.1 1.0
O A:HOH927 4.8 26.6 1.0
CB A:GLU63 5.0 22.3 1.0

Calcium binding site 3 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 3 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca804

b:18.3
occ:1.00
 O A:TYR64 2.4 21.5 1.0
O A:HOH970 2.5 23.9 1.0
O B:HOH104 2.5 22.1 1.0
OE1 A:GLU63 2.5 26.0 1.0
C A:TYR64 3.6 17.6 1.0
CD A:GLU63 3.7 20.6 1.0
CA A:CA803 4.1 20.6 1.0
O A:HOH968 4.1 18.0 1.0
CB A:SER65 4.1 16.9 1.0
OXT B:ALA32 4.2 21.2 1.0
CA A:SER65 4.2 23.3 1.0
N A:SER65 4.4 22.0 1.0
CG A:GLU63 4.4 24.4 1.0
CA A:TYR64 4.6 17.7 1.0
N A:TYR64 4.7 18.3 1.0
OE2 A:GLU63 4.7 29.3 1.0
CB A:GLU63 4.7 22.3 1.0
O A:HOH992 4.8 33.1 1.0
CD2 A:TYR64 4.9 28.2 1.0
O A:HOH948 4.9 28.2 1.0
O A:HOH947 4.9 19.0 1.0
OG A:SER65 5.0 18.8 1.0

Calcium binding site 4 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 4 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca805

b:70.8
occ:1.00
 OE1 A:GLU91 4.4 35.4 1.0
OE2 A:GLU91 4.4 36.6 1.0
CD A:GLU91 4.9 38.9 1.0

Calcium binding site 5 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 5 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca802

b:24.0
occ:1.00
 O D:TYR64 2.4 31.6 1.0
O E:HOH107 2.4 20.4 1.0
OE1 D:GLU63 2.5 21.1 1.0
O D:HOH948 2.5 24.0 1.0
C D:TYR64 3.6 27.1 1.0
CD D:GLU63 3.6 26.8 1.0
CA D:CA803 4.0 24.3 1.0
CG D:GLU63 4.1 26.6 1.0
CB D:SER65 4.1 19.8 1.0
CA D:SER65 4.3 24.3 1.0
OXT E:ALA32 4.3 23.6 1.0
N D:SER65 4.4 24.0 1.0
CA D:TYR64 4.7 33.2 1.0
OE2 D:GLU63 4.7 24.4 1.0
N D:TYR64 4.7 26.9 1.0
CB D:GLU63 4.8 27.9 1.0
O D:HOH936 4.9 24.9 1.0
OG D:SER65 4.9 26.0 1.0

Calcium binding site 6 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 6 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca803

b:24.3
occ:1.00
 OE1 D:GLU63 2.4 21.1 1.0
OXT E:ALA32 2.4 23.6 1.0
OE2 D:GLU63 2.6 24.4 1.0
O E:ALA32 2.7 25.2 1.0
CD D:GLU63 2.8 26.8 1.0
C E:ALA32 2.9 29.4 1.0
O E:HOH107 3.9 20.4 1.0
CA D:CA802 4.0 24.0 1.0
CG D:GLU63 4.3 26.6 1.0
O E:HOH103 4.4 23.4 1.0
CA E:ALA32 4.4 18.6 1.0
O D:HOH948 4.6 24.0 1.0

Calcium binding site 7 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 7 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca802

b:22.5
occ:1.00
 O H:HOH108 2.4 21.7 1.0
O G:HOH941 2.4 23.3 1.0
O G:TYR64 2.4 26.3 1.0
OE2 G:GLU63 2.5 21.4 1.0
CD G:GLU63 3.6 30.6 1.0
C G:TYR64 3.7 21.7 1.0
CA G:CA803 4.0 28.1 1.0
CG G:GLU63 4.1 20.7 1.0
O H:ALA32 4.2 25.7 1.0
CB G:SER65 4.2 26.4 1.0
CA G:SER65 4.4 25.3 1.0
O G:HOH942 4.4 22.7 1.0
N G:SER65 4.5 21.3 1.0
OE1 G:GLU63 4.6 24.9 1.0
CA G:TYR64 4.7 21.9 1.0
O G:HOH948 4.7 32.6 1.0
N G:TYR64 4.7 21.7 1.0
CB G:GLU63 4.8 29.6 1.0
O G:HOH933 4.9 29.2 1.0
OG G:SER65 4.9 21.4 1.0

Calcium binding site 8 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 8 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca803

b:28.1
occ:1.00
 O G:HOH942 2.4 22.7 1.0
OE2 G:GLU63 2.5 21.4 1.0
O H:ALA32 2.6 25.7 1.0
OE1 G:GLU63 2.7 24.9 1.0
OXT H:ALA32 2.7 30.3 1.0
CD G:GLU63 2.9 30.6 1.0
C H:ALA32 3.1 31.0 1.0
O H:HOH108 4.0 21.7 1.0
CA G:CA802 4.0 22.5 1.0
O G:HOH941 4.2 23.3 1.0
CG G:GLU63 4.4 20.7 1.0
CA H:ALA32 4.6 25.5 1.0

Calcium binding site 9 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 9 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:19.1
occ:1.00
 O F:HOH203 2.3 17.8 1.0
OD1 F:ASP16 2.4 16.2 1.0
OE1 F:GLU19 2.5 22.0 1.0
OE2 F:GLU19 2.5 19.0 1.0
O F:HOH214 2.6 21.8 1.0
CD F:GLU19 2.9 18.4 1.0
CG F:ASP16 3.6 16.1 1.0
CA F:CA102 4.0 25.4 1.0
O F:HOH209 4.1 25.5 1.0
CA F:ASP16 4.2 19.7 1.0
CG F:GLU19 4.4 22.7 1.0
CB F:ASP16 4.4 16.1 1.0
N F:ASP16 4.5 16.0 1.0
OD2 F:ASP16 4.6 21.0 1.0
OE1 F:GLU15 4.6 22.8 1.0
C F:GLU15 4.9 18.9 1.0
O F:GLU15 5.0 15.7 1.0

Calcium binding site 10 out of 10 in 5whe

Go back to Calcium Binding Sites List in 5whe
Calcium binding site 10 out of 10 in the Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Kras G12V/D38P, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:25.4
occ:1.00
 O F:HOH209 2.4 25.5 1.0
OD2 F:ASP16 2.5 21.0 1.0
OD1 F:ASP16 2.7 16.2 1.0
CG F:ASP16 2.9 16.1 1.0
O F:HOH203 3.9 17.8 1.0
CA F:CA101 4.0 19.1 1.0
OG F:SER13 4.1 20.1 1.0
O F:HOH214 4.4 21.8 1.0
CB F:ASP16 4.5 16.1 1.0
CB F:SER13 4.8 21.4 1.0
N F:SER13 4.9 22.5 1.0

Reference:

J.H.Mcgee, S.Y.Shim, S.J.Lee, P.K.Swanson, S.Y.Jiang, M.A.Durney, G.L.Verdine. Exceptionally High-Affinity Ras Binders That Remodel Its Effector Domain. J. Biol. Chem. V. 293 3265 2018.
ISSN: ESSN 1083-351X
PubMed: 29282294
DOI: 10.1074/JBC.M117.816348
Page generated: Mon Jul 15 13:10:55 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy