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

Protein crystallography data

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

Resolution Low / High (Å) 48.14 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 40.861, 234.507, 48.143, 90.00, 90.13, 90.00
R / Rfree (%) 20.5 / 25.8

Other elements in 5wpl:

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

Magnesium (Mg) 5 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 8 in 5wpl

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Calcium binding site 1 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca203

b:21.8
occ:1.00
 O B:ALA32 2.2 21.5 1.0
OE2 A:GLU63 2.3 20.2 1.0
O A:HOH343 2.5 16.4 1.0
OE1 A:GLU63 2.6 19.9 1.0
CD A:GLU63 2.7 20.6 1.0
C B:ALA32 2.8 19.4 1.0
CA A:CA204 4.1 18.9 1.0
CG A:GLU63 4.2 20.9 1.0
CA B:ALA32 4.3 21.1 1.0
CB B:ALA32 4.9 21.3 1.0
CB A:GLU63 4.9 22.1 1.0

Calcium binding site 2 out of 8 in 5wpl

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Calcium binding site 2 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca204

b:18.9
occ:1.00
 O A:TYR64 2.3 19.9 1.0
OE1 A:GLU63 2.4 19.9 1.0
C A:TYR64 3.5 22.1 1.0
CD A:GLU63 3.6 20.6 1.0
CA A:CA203 4.1 21.8 1.0
CB A:SER65 4.2 20.1 1.0
CG A:GLU63 4.2 20.9 1.0
O A:HOH343 4.2 16.4 1.0
CA A:SER65 4.3 20.2 1.0
N A:SER65 4.3 20.5 1.0
O B:ALA32 4.3 21.5 1.0
OE2 A:GLU63 4.5 20.2 1.0
CA A:TYR64 4.6 23.9 1.0
N A:TYR64 4.7 23.9 1.0
CB A:GLU63 4.7 22.1 1.0
O A:HOH346 4.7 21.9 1.0
OG A:SER65 4.9 20.2 1.0
CD2 A:TYR64 5.0 27.7 1.0

Calcium binding site 3 out of 8 in 5wpl

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Calcium binding site 3 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca205

b:35.8
occ:1.00
 O A:HOH340 2.2 30.5 1.0
O A:HOH351 2.2 29.7 1.0
O A:GLN25 2.6 26.2 1.0
O A:HOH327 2.7 21.9 1.0
C A:GLN25 3.7 25.9 1.0
CA A:GLN25 4.3 28.1 1.0
CD2 A:HIS27 4.3 29.2 1.0
OE2 A:GLU31 4.5 34.2 1.0
CB A:GLN25 4.5 30.4 1.0
OE1 A:GLU31 4.7 32.1 1.0
N A:ASN26 4.8 26.6 1.0
O A:ASN26 4.8 26.3 1.0
OD1 A:ASN26 4.9 33.1 1.0
C A:ASN26 5.0 28.6 1.0
CB A:ASN26 5.0 28.7 1.0

Calcium binding site 4 out of 8 in 5wpl

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Calcium binding site 4 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:25.5
occ:1.00
 O E:HOH101 2.0 20.5 1.0
OE1 D:GLU63 2.3 19.7 1.0
OE2 D:GLU63 2.5 22.5 1.0
O E:ALA32 2.5 29.6 1.0
CD D:GLU63 2.7 24.1 1.0
C E:ALA32 3.0 26.5 1.0
CG D:GLU63 4.2 26.0 1.0
CA E:ALA32 4.5 23.1 1.0
CB D:GLU63 4.9 27.6 1.0

Calcium binding site 5 out of 8 in 5wpl

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Calcium binding site 5 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca204

b:21.3
occ:1.00
 O G:TYR64 2.2 22.4 1.0
OE1 G:GLU63 2.6 27.1 1.0
C G:TYR64 3.4 25.2 1.0
CD G:GLU63 3.7 32.2 1.0
MG G:MG203 3.9 9.4 1.0
CB G:SER65 4.1 20.6 1.0
CA G:SER65 4.1 21.3 1.0
N G:SER65 4.2 22.8 1.0
O H:ALA32 4.2 21.6 1.0
CG G:GLU63 4.3 34.7 1.0
CA G:TYR64 4.5 28.7 1.0
CB G:GLU63 4.5 36.4 1.0
N G:TYR64 4.6 29.8 1.0
OE2 G:GLU63 4.7 32.6 1.0
CB G:TYR64 4.9 33.7 1.0
O G:HOH325 5.0 23.8 1.0

Calcium binding site 6 out of 8 in 5wpl

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Calcium binding site 6 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca203

b:23.8
occ:1.00
 O K:HOH106 2.0 29.3 1.0
OE1 J:GLU63 2.3 23.1 1.0
OE2 J:GLU63 2.5 24.7 1.0
O K:ALA32 2.6 22.8 1.0
CD J:GLU63 2.7 24.0 1.0
C K:ALA32 3.0 23.8 1.0
CA J:CA204 3.9 23.8 1.0
CG J:GLU63 4.2 24.8 1.0
CA K:ALA32 4.5 24.4 1.0
O K:HOH104 4.5 23.1 1.0
CB J:GLU63 4.9 25.0 1.0

Calcium binding site 7 out of 8 in 5wpl

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Calcium binding site 7 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca204

b:23.8
occ:1.00
 O J:TYR64 2.3 24.0 1.0
OE1 J:GLU63 2.5 23.1 1.0
C J:TYR64 3.6 23.0 1.0
CD J:GLU63 3.6 24.0 1.0
CA J:CA203 3.9 23.8 1.0
CG J:GLU63 4.1 24.8 1.0
CB J:SER65 4.2 22.7 1.0
CA J:SER65 4.3 22.0 1.0
N J:SER65 4.3 21.9 1.0
OE2 J:GLU63 4.6 24.7 1.0
CA J:TYR64 4.6 24.5 1.0
N J:TYR64 4.7 23.9 1.0
CB J:GLU63 4.8 25.0 1.0
C K:ALA32 4.9 23.8 1.0
CD1 J:TYR64 4.9 35.9 1.0

Calcium binding site 8 out of 8 in 5wpl

Go back to Calcium Binding Sites List in 5wpl
Calcium binding site 8 out of 8 in the Kras G12V, 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, Bound to Gppnhp and Miniprotein 225-11 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca101

b:19.3
occ:1.00
 OD1 L:ASP16 2.2 14.6 1.0
O L:HOH202 2.4 19.9 1.0
OE2 L:GLU19 2.5 22.7 1.0
O L:HOH206 2.6 24.0 1.0
OE1 L:GLU19 2.6 22.6 1.0
CD L:GLU19 2.9 23.1 1.0
CG L:ASP16 3.5 15.7 1.0
CA L:ASP16 4.2 18.2 1.0
O L:HOH207 4.3 19.3 1.0
OD2 L:ASP16 4.4 16.5 1.0
CB L:ASP16 4.4 17.2 1.0
CG L:GLU19 4.4 22.5 1.0
N L:ASP16 4.5 17.9 1.0
OE1 L:GLU15 4.7 18.9 1.0
O L:GLU15 4.8 19.8 1.0
C L:GLU15 4.8 18.9 1.0
O L:HOH201 4.9 21.8 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: Wed Jul 9 11:19:51 2025

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