Calcium in PDB 5whb: Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)

Protein crystallography data

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R), PDB code: 5whb 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) 116.00 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 41.002, 232.043, 47.924, 90.00, 90.10, 90.00
R / Rfree (%) 20.5 / 25.2

Other elements in 5whb:

The structure of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) (pdb code 5whb). 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, Bound to Gdp and Miniprotein 225-11(A30R), PDB code: 5whb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5whb

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Calcium binding site 1 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:44.8
occ:1.00
 OXT B:ALA32 2.6 57.9 1.0
OE1 A:GLU63 2.6 36.9 1.0
O B:ALA32 2.7 66.3 1.0
OE2 A:GLU63 3.0 44.1 1.0
C B:ALA32 3.1 57.6 1.0
CD A:GLU63 3.2 40.2 1.0
O B:HOH101 4.0 34.5 1.0
O B:HOH108 4.1 38.6 1.0
CA A:CA204 4.5 44.1 1.0
CA B:ALA32 4.6 44.1 1.0
CG A:GLU63 4.7 37.4 1.0

Calcium binding site 2 out of 10 in 5whb

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Calcium binding site 2 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:44.1
occ:1.00
 O A:TYR64 2.4 81.8 1.0
OE1 A:GLU63 2.9 36.9 1.0
O B:HOH101 2.9 34.5 1.0
C A:TYR64 3.6 79.0 1.0
CD A:GLU63 3.9 40.2 1.0
CG A:GLU63 4.2 37.4 1.0
CB A:SER65 4.3 33.2 1.0
CA A:SER65 4.3 51.4 1.0
OXT B:ALA32 4.4 57.9 1.0
N A:SER65 4.4 61.0 1.0
CA A:CA203 4.5 44.8 1.0
CA A:TYR64 4.6 84.1 1.0
N A:TYR64 4.6 77.1 1.0
CB A:GLU63 4.7 49.8 1.0
OG A:SER65 4.7 36.9 1.0
CD2 A:TYR64 4.9 0.9 1.0

Calcium binding site 3 out of 10 in 5whb

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Calcium binding site 3 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:60.0
occ:1.00
 O C:HOH205 2.6 36.7 1.0
OD2 C:ASP16 2.6 54.0 1.0
OD1 C:ASP16 3.2 35.9 1.0
CG C:ASP16 3.3 44.5 1.0
OG C:SER13 4.2 36.2 1.0
CA C:CA102 4.2 42.5 1.0
N C:SER13 4.6 49.9 1.0
CB C:ASP16 4.7 35.0 1.0
CB C:SER13 4.9 47.4 1.0
CA C:ALA12 5.0 54.2 1.0

Calcium binding site 4 out of 10 in 5whb

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Calcium binding site 4 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:42.5
occ:1.00
 OD1 C:ASP16 2.4 35.9 1.0
OE1 C:GLU19 2.8 43.8 1.0
OE2 C:GLU19 3.0 35.5 1.0
CD C:GLU19 3.2 35.5 1.0
O C:HOH205 3.5 36.7 1.0
CG C:ASP16 3.6 44.5 1.0
CA C:CA101 4.2 60.0 1.0
OD2 C:ASP16 4.4 54.0 1.0
CA C:ASP16 4.4 34.7 1.0
CB C:ASP16 4.6 35.0 1.0
CG C:GLU19 4.6 34.9 1.0
N C:ASP16 4.7 45.6 1.0
OE1 C:GLU15 4.9 66.5 1.0
CD C:GLU15 5.0 72.3 1.0

Calcium binding site 5 out of 10 in 5whb

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Calcium binding site 5 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:55.0
occ:1.00
 OXT E:ALA32 2.5 55.5 1.0
OE1 D:GLU63 2.6 54.4 1.0
OE2 D:GLU63 2.7 54.5 1.0
O E:ALA32 2.8 52.1 1.0
CD D:GLU63 3.0 50.4 1.0
C E:ALA32 3.0 45.6 1.0
O D:HOH318 4.1 35.2 1.0
CA D:CA204 4.3 39.1 1.0
CG D:GLU63 4.5 46.0 1.0
O E:HOH109 4.5 42.8 1.0
CA E:ALA32 4.5 35.8 1.0
O E:HOH110 4.7 48.7 1.0

Calcium binding site 6 out of 10 in 5whb

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Calcium binding site 6 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:39.1
occ:1.00
 O D:TYR64 2.4 41.6 1.0
O D:HOH318 2.4 35.2 1.0
O E:HOH109 2.5 42.8 1.0
OE1 D:GLU63 2.6 54.4 1.0
C D:TYR64 3.6 40.0 1.0
CD D:GLU63 3.7 50.4 1.0
OXT E:ALA32 4.2 55.5 1.0
CG D:GLU63 4.2 46.0 1.0
CA D:CA203 4.3 55.0 1.0
CB D:SER65 4.3 35.3 1.0
CA D:SER65 4.3 33.1 1.0
N D:SER65 4.4 30.9 1.0
N D:TYR64 4.5 44.3 1.0
CB D:GLU63 4.5 50.1 1.0
CA D:TYR64 4.6 40.6 1.0
OE2 D:GLU63 4.8 54.5 1.0
OG D:SER65 4.9 37.2 1.0

Calcium binding site 7 out of 10 in 5whb

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Calcium binding site 7 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:47.0
occ:1.00
 OD1 F:ASP16 2.5 50.8 1.0
OE2 F:GLU19 2.7 67.5 1.0
O F:HOH203 2.9 31.6 1.0
OE1 F:GLU19 2.9 58.9 1.0
CD F:GLU19 3.1 59.8 1.0
CG F:ASP16 3.7 42.4 1.0
CA F:ASP16 4.5 30.0 1.0
OD2 F:ASP16 4.5 44.7 1.0
CB F:ASP16 4.6 36.2 1.0
CG F:GLU19 4.6 49.5 1.0
CA F:CA102 4.7 59.6 1.0
N F:ASP16 4.9 30.0 1.0

Calcium binding site 8 out of 10 in 5whb

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Calcium binding site 8 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca102

b:59.6
occ:1.00
 OD2 F:ASP16 2.5 44.7 1.0
CG F:ASP16 3.3 42.4 1.0
OD1 F:ASP16 3.5 50.8 1.0
CA F:ALA12 4.7 64.8 1.0
O F:HOH203 4.7 31.6 1.0
CB F:ASP16 4.7 36.2 1.0
CA F:CA101 4.7 47.0 1.0
N F:SER13 4.8 39.9 1.0
OG F:SER13 4.8 54.7 1.0

Calcium binding site 9 out of 10 in 5whb

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Calcium binding site 9 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca203

b:62.4
occ:1.00
 NZ J:LYS5 3.3 43.3 1.0
CE J:LYS5 3.4 35.2 1.0
CD1 L:TRP25 3.5 35.8 1.0
NE1 L:TRP25 4.0 31.0 1.0
CB L:LEU28 4.1 37.9 1.0
CG L:TRP25 4.2 38.2 1.0
O L:TRP25 4.3 37.5 1.0
CA L:TRP25 4.4 30.2 1.0
CE1 K:HIS18 4.4 29.0 1.0
CD1 L:LEU28 4.5 29.0 1.0
CE2 K:TRP21 4.5 30.5 1.0
CZ2 K:TRP21 4.6 30.8 1.0
ND1 K:HIS18 4.6 31.8 1.0
CD2 K:TRP21 4.6 42.8 1.0
CH2 K:TRP21 4.7 30.8 1.0
CB L:TRP25 4.7 45.7 1.0
CA J:CA204 4.7 75.3 1.0
CE3 K:TRP21 4.7 36.2 1.0
CZ3 K:TRP21 4.8 35.0 1.0
C L:TRP25 4.8 37.5 1.0
CE2 L:TRP25 4.8 46.3 1.0
C L:LEU28 4.9 43.5 1.0
CG L:LEU28 5.0 28.9 1.0
CD J:LYS5 5.0 32.6 1.0
CD2 L:TRP25 5.0 43.2 1.0
N L:TYR29 5.0 45.9 1.0
CG J:GLU3 5.0 51.9 1.0
NE1 K:TRP21 5.0 38.0 1.0

Calcium binding site 10 out of 10 in 5whb

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Calcium binding site 10 out of 10 in the Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Kras G12V, Bound to Gdp and Miniprotein 225-11(A30R) within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca204

b:75.3
occ:1.00
 OD2 J:ASP54 2.7 53.5 1.0
O K:HIS18 2.8 32.7 1.0
ND1 K:HIS18 3.1 31.8 1.0
CA K:HIS18 3.2 28.9 1.0
CG J:ASP54 3.3 43.3 1.0
OD1 J:ASP54 3.3 42.9 1.0
C K:HIS18 3.3 36.3 1.0
CB K:HIS18 3.3 32.8 1.0
CE3 K:TRP21 3.5 36.2 1.0
CG K:HIS18 3.6 32.4 1.0
OE1 J:GLU3 3.6 62.4 1.0
NH1 J:ARG41 3.8 39.4 1.0
CB K:TRP21 4.1 40.2 1.0
CD2 K:TRP21 4.2 42.8 1.0
CE1 K:HIS18 4.2 29.0 1.0
CZ3 K:TRP21 4.3 35.0 1.0
N K:ALA22 4.3 30.0 1.0
CD J:ARG41 4.4 30.9 1.0
CG K:TRP21 4.5 38.9 1.0
CB K:ALA22 4.5 30.1 1.0
N K:GLU19 4.5 35.8 1.0
CB J:ASP54 4.6 30.4 1.0
N K:HIS18 4.6 28.7 1.0
CD1 L:LEU28 4.7 29.0 1.0
CZ J:ARG41 4.7 45.7 1.0
CA J:CA203 4.7 62.4 1.0
CD J:GLU3 4.8 60.2 1.0
CA K:ALA22 4.8 34.6 1.0
CD2 K:HIS18 4.9 39.2 1.0
C K:TRP21 4.9 30.1 1.0
CE J:LYS5 4.9 35.2 1.0
NE J:ARG41 5.0 37.2 1.0
CA K:TRP21 5.0 38.8 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: Sat Dec 12 05:49:03 2020

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