Calcium in PDB 5cwf: Crystal Structure of De Novo Designed Helical Repeat Protein DHR8

The structure of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8, PDB code: 5cwf was solved by G.Bhabha, D.C.Ekiert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.38 / 1.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	75.690, 76.360, 133.140, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22

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>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 (pdb code 5cwf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 32 binding sites of Calcium where determined in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8, PDB code: 5cwf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


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 De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:25.0 occ:1.00 OD1 A:ASP25 2.4 24.5 1.0 CG A:ASP25 3.3 28.2 1.0 HB3 A:ASP25 3.8 29.3 1.0 OD2 A:ASP25 3.9 33.1 1.0 CB A:ASP25 4.1 24.4 1.0 O A:HOH345 4.1 21.9 1.0 HE2 A:LYS20 4.5 37.6 1.0 HH21 A:ARG29 4.6 41.1 0.4 O A:HOH342 4.6 32.3 1.0 HH22 A:ARG29 4.6 41.1 0.4 HG2 A:LYS20 4.7 29.2 1.0 HB2 A:ASP25 4.7 29.3 1.0 HA A:ASP25 4.9 24.3 1.0 NH2 A:ARG29 4.9 34.3 0.4 HD3 A:LYS20 4.9 32.4 1.0

Calcium binding site 2 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


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 De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:25.2 occ:0.74 O A:HOH302 2.2 40.9 1.0 O A:HOH357 2.3 40.5 1.0 HA A:ASN22 3.6 32.3 1.0 OD1 A:ASN22 3.8 45.8 1.0 HD21 D:ASN23 4.2 48.5 1.0 O D:HOH346 4.4 41.6 1.0 CA A:ASN22 4.5 26.9 1.0 HD22 D:ASN23 4.5 48.5 1.0 ND2 D:ASN23 4.7 40.4 1.0 O A:LYS21 4.7 24.9 1.0 CG A:ASN22 4.7 41.8 1.0 HB3 A:ASN22 4.8 38.4 1.0 CB A:ASN22 5.0 32.0 1.0

Calcium binding site 3 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


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 De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:29.4 occ:0.84 O A:ARG88 2.3 31.5 1.0 O A:HOH340 2.3 36.5 1.0 O A:HOH337 2.4 30.0 1.0 O A:HOH360 2.4 36.6 1.0 C A:ARG88 3.4 32.8 1.0 HA A:ARG88 3.7 39.2 1.0 HD22 A:ASN91 4.0 38.8 1.0 HA A:GLU89 4.1 40.3 1.0 CA A:ARG88 4.1 32.7 1.0 O A:GLU89 4.2 31.1 1.0 C A:GLU89 4.3 34.2 1.0 N A:GLU89 4.4 28.1 1.0 HB3 A:ARG88 4.5 39.0 1.0 CA A:GLU89 4.5 33.6 1.0 HD21 A:ASN91 4.6 38.8 1.0 ND2 A:ASN91 4.6 32.4 1.0 OE1 A:GLU44 4.6 50.1 1.0 O A:LEU87 4.6 31.9 1.0 N A:ASN90 4.8 33.1 1.0 HA A:ASN90 4.8 40.5 1.0 CB A:ARG88 4.9 32.5 1.0

Calcium binding site 4 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


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 De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:21.5 occ:0.56 OD2 A:ASP70 2.2 38.3 1.0 O A:HOH377 2.3 54.3 1.0 O A:HOH386 2.5 41.2 1.0 OD1 A:ASP24 2.5 25.3 1.0 OD2 A:ASP24 2.5 27.7 1.0 CG A:ASP24 2.8 29.4 1.0 CG A:ASP70 3.0 35.4 1.0 OD1 A:ASP70 3.2 40.4 1.0 HB3 A:ASN22 4.3 38.4 1.0 O A:HOH371 4.3 32.9 1.0 O A:HOH349 4.4 40.4 1.0 CB A:ASP24 4.4 20.7 1.0 CB A:ASP70 4.5 28.9 1.0 HB3 A:ASP24 4.7 24.9 1.0 HB2 A:ASP70 4.7 34.7 1.0 O A:ASN22 4.7 29.6 1.0 HB3 A:ASP70 4.7 34.7 1.0 HB2 A:ASP24 4.8 24.9 1.0 HB2 A:ASN22 5.0 38.4 1.0

Calcium binding site 5 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:39.4 occ:0.75 OE2 B:GLU82 2.5 46.3 1.0 OE1 A:GLU175 2.5 86.6 1.0 OE1 A:GLU172 2.6 85.7 1.0 OE1 B:GLU85 2.6 43.9 1.0 OE1 B:GLU82 2.9 47.2 1.0 OE2 A:GLU172 2.9 88.4 1.0 CD B:GLU82 3.1 44.4 1.0 HH12 B:ARG133 3.1 56.7 1.0 CD A:GLU172 3.1 84.2 1.0 OE2 B:GLU85 3.2 48.3 1.0 OE2 A:GLU175 3.2 92.8 1.0 CD B:GLU85 3.2 44.6 1.0 CD A:GLU175 3.3 86.6 1.0 HH12 B:ARG33 3.8 52.3 1.0 NH1 B:ARG133 3.9 47.3 1.0 HH22 B:ARG133 4.1 53.9 1.0 HH11 B:ARG133 4.3 56.7 1.0 NH1 B:ARG33 4.4 43.6 1.0 HH22 B:ARG33 4.5 48.8 1.0 HH12 B:ARG78 4.6 48.1 0.4 CG B:GLU82 4.6 36.9 1.0 CG A:GLU172 4.6 75.2 1.0 HH11 B:ARG78 4.6 48.1 0.4 CG B:GLU85 4.7 36.3 1.0 CG A:GLU175 4.7 78.7 1.0 HA B:GLU82 4.7 34.9 1.0 NH2 B:ARG133 4.7 44.9 1.0 O B:HOH303 4.7 34.2 1.0 CZ B:ARG133 4.8 43.5 1.0 HH11 B:ARG33 4.8 52.3 1.0 HB2 A:GLU175 4.9 84.8 1.0 HB2 B:GLU85 4.9 37.1 1.0 HG2 B:GLU82 4.9 44.2 1.0 HG3 A:GLU172 4.9 90.3 1.0 HG3 B:GLU82 4.9 44.2 1.0 NH1 B:ARG78 4.9 40.1 0.4 HG2 A:GLU172 5.0 90.3 1.0 HG3 B:GLU85 5.0 43.5 1.0 HA A:GLU172 5.0 62.5 1.0

Calcium binding site 6 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:31.5 occ:0.81 OD1 C:ASN113 2.0 41.9 1.0 OD1 A:ASP160 2.4 39.0 1.0 O A:HOH391 2.4 38.6 1.0 O C:HOH321 2.4 44.8 1.0 OE1 A:GLU161 2.6 51.6 1.0 OE2 A:GLU161 2.6 43.5 1.0 CD A:GLU161 3.0 50.1 1.0 CG C:ASN113 3.1 37.3 1.0 CG A:ASP160 3.4 44.3 1.0 OD2 A:ASP160 3.7 46.7 1.0 HD21 C:ASN113 3.8 47.9 1.0 H A:ASP160 3.8 39.1 1.0 ND2 C:ASN113 3.9 40.0 1.0 HB3 C:ASN113 3.9 41.5 1.0 CB C:ASN113 4.0 34.6 1.0 HA C:ASN113 4.0 35.8 1.0 H A:GLU161 4.2 43.6 1.0 O C:HOH314 4.2 45.2 1.0 O A:HOH355 4.4 36.7 1.0 O C:HOH338 4.4 33.9 1.0 CG A:GLU161 4.5 48.7 1.0 CA B:CA209 4.5 52.9 0.9 CA C:ASN113 4.6 29.8 1.0 N A:ASP160 4.6 32.6 1.0 HA A:ASP159 4.7 46.2 1.0 HD22 C:ASN113 4.7 47.9 1.0 CB A:ASP160 4.8 41.2 1.0 HB2 C:ASN113 4.8 41.5 1.0 HG3 A:GLU161 4.9 58.5 1.0 N A:GLU161 4.9 36.3 1.0 HG2 A:GLU161 4.9 58.5 1.0 O A:ASN158 5.0 42.1 1.0

Calcium binding site 7 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:88.0 occ:0.86 OE2 A:GLU49 2.4 43.7 0.5 O A:HOH365 2.6 61.1 1.0 CD A:GLU49 3.1 43.3 0.5 O A:HOH368 3.5 62.5 1.0 HG3 A:GLU49 3.5 49.8 0.5 O A:HOH301 3.6 47.2 1.0 OE1 A:GLU49 3.7 44.8 0.5 OD2 A:ASP93 3.8 51.2 1.0 CG A:GLU49 3.9 41.5 0.5 HB2 A:GLU49 4.1 49.0 0.6 OD1 A:ASP93 4.3 39.9 1.0 CG A:ASP93 4.3 44.5 1.0 HG2 A:GLU49 4.3 49.8 0.5 HG2 A:GLU49 4.9 46.6 0.6 HB2 A:GLU49 4.9 48.3 0.5

Calcium binding site 8 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca208 b:31.2 occ:0.55 O A:ASN67 2.2 38.5 1.0 O A:HOH381 2.3 45.5 1.0 OD1 A:ASN113 2.4 46.3 1.0 C A:ASN67 3.4 34.7 1.0 HD22 C:ASN158 3.5 55.0 1.0 CG A:ASN113 3.6 53.4 1.0 HA A:ASN67 3.8 38.8 1.0 HA A:ASN68 3.8 34.0 1.0 HB3 A:ASN67 4.0 40.9 1.0 HD21 A:ASN113 4.1 71.0 1.0 CA A:ASN67 4.2 32.3 1.0 ND2 C:ASN158 4.2 45.8 1.0 ND2 A:ASN113 4.3 59.2 1.0 HA A:ASN113 4.4 54.3 1.0 N A:ASN68 4.4 31.4 1.0 O A:ASN113 4.5 47.7 1.0 HD21 C:ASN158 4.5 55.0 1.0 HB2 C:ASN158 4.5 44.4 1.0 CA A:ASN68 4.6 28.3 1.0 CB A:ASN67 4.6 34.1 1.0 CB A:ASN113 4.7 47.0 1.0 O C:HOH363 4.8 46.5 1.0 HB3 A:ASN113 4.8 56.5 1.0 O C:ASN157 4.9 33.4 1.0 CA A:ASN113 5.0 45.3 1.0

Calcium binding site 9 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:16.6 occ:0.60 O A:HOH318 2.4 33.5 1.0 OE2 B:GLU172 2.4 35.3 1.0 OE1 A:GLU85 2.4 38.5 1.0 OE1 A:GLU82 2.5 36.0 1.0 OE1 B:GLU175 2.5 39.4 1.0 OE2 A:GLU82 2.6 34.1 1.0 OE2 B:GLU175 2.6 45.2 1.0 OE1 B:GLU172 2.7 37.0 1.0 CD A:GLU82 2.9 33.6 1.0 CD B:GLU175 2.9 40.9 1.0 CD B:GLU172 2.9 36.2 1.0 HH12 A:ARG133 3.0 52.3 1.0 CD A:GLU85 3.4 40.5 1.0 OE2 A:GLU85 3.6 44.8 1.0 NH1 A:ARG133 3.7 43.6 1.0 HH12 A:ARG33 3.8 46.7 1.0 HH22 A:ARG133 3.9 50.0 1.0 HH11 A:ARG133 4.1 52.3 1.0 HH22 A:ARG78 4.2 43.7 1.0 HH12 A:ARG78 4.3 49.3 1.0 HH22 A:ARG33 4.3 45.7 1.0 CG A:GLU82 4.4 29.2 1.0 CG B:GLU175 4.4 35.0 1.0 O A:HOH401 4.4 44.4 1.0 CG B:GLU172 4.4 29.6 1.0 NH1 A:ARG33 4.5 39.0 1.0 NH2 A:ARG133 4.5 41.7 1.0 CZ A:ARG133 4.5 40.8 1.0 HA A:GLU82 4.6 29.1 1.0 CA B:CA206 4.7 54.2 0.8 O B:HOH310 4.7 35.8 1.0 HG3 A:GLU82 4.7 35.1 1.0 HA B:GLU172 4.7 35.0 1.0 CG A:GLU85 4.8 36.4 1.0 HG2 B:GLU172 4.8 35.5 1.0 HG2 A:GLU82 4.8 35.1 1.0 NH2 A:ARG78 4.8 36.4 1.0 HG2 B:GLU175 4.8 42.0 1.0 O A:HOH348 4.8 33.0 1.0 HG3 B:GLU172 4.8 35.5 1.0 HB2 A:GLU85 4.8 38.8 1.0 HB3 B:GLU175 4.9 39.1 1.0 HB2 B:GLU175 4.9 39.1 1.0 HG3 B:GLU175 4.9 42.0 1.0 HB3 A:GLU85 4.9 38.8 1.0 NH1 A:ARG78 4.9 41.1 1.0 HH11 A:ARG33 4.9 46.7 1.0 NH2 A:ARG33 4.9 38.1 1.0

Calcium binding site 10 out of 32 in the Crystal Structure of De Novo Designed Helical Repeat Protein DHR8


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of De Novo Designed Helical Repeat Protein DHR8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:23.3 occ:1.00 O A:HOH328 2.4 29.5 1.0 OE1 B:GLU161 2.5 24.5 1.0 OE2 B:GLU161 2.6 24.2 1.0 O A:HOH361 2.7 34.7 1.0 CD B:GLU161 2.9 23.5 1.0 OE1 A:GLU26 4.0 26.0 1.0 OE2 A:GLU71 4.3 34.9 1.0 O A:HOH371 4.3 32.9 1.0 CG B:GLU161 4.4 19.9 1.0 HH12 A:ARG74 4.4 29.5 1.0 O B:HOH332 4.5 39.2 1.0 O A:HOH394 4.6 30.0 1.0 HH11 A:ARG74 4.6 29.5 1.0 O B:HOH375 4.7 42.5 1.0 HG3 B:GLU161 4.8 23.9 1.0 HG2 B:GLU161 4.8 23.9 1.0 NH1 A:ARG74 4.8 24.6 1.0 O B:HOH357 4.9 26.9 1.0

T.J.Brunette, F.Parmeggiani, P.S.Huang, G.Bhabha, D.C.Ekiert, S.E.Tsutakawa, G.L.Hura, J.A.Tainer, D.Baker. Exploring the Repeat Protein Universe Through Computational Protein Design. Nature V. 528 580 2015.
ISSN: ESSN 1476-4687
PubMed: 26675729
DOI: 10.1038/NATURE16162