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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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