Calcium in PDB 5mfd: Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5

The structure of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5, PDB code: 5mfd was solved by S.Hansen, J.Kiefer, C.Madhurantakam, P.Mittl, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.12 / 2.30
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	194.660, 194.660, 241.740, 90.00, 90.00, 120.00
R / Rfree (%)	19 / 21.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 49;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 (pdb code 5mfd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 49 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5, PDB code: 5mfd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:71.4 occ:1.00 O A:PRO275 2.3 65.9 1.0 O C:PRO65 2.3 69.8 1.0 OE2 A:GLU277 2.3 91.6 1.0 OE2 C:GLU67 2.6 83.5 1.0 OE1 A:GLU277 3.0 94.5 1.0 CD A:GLU277 3.0 94.9 1.0 C C:PRO65 3.4 69.9 1.0 C A:PRO275 3.5 64.6 1.0 CD C:GLU67 3.8 94.9 1.0 CA C:ASN66 4.2 65.0 1.0 N C:ASN66 4.2 65.5 1.0 OE1 C:GLU67 4.3 89.5 1.0 N A:ASN276 4.4 60.5 1.0 N C:GLU67 4.4 66.5 1.0 CA A:ASN276 4.4 59.7 1.0 CG A:GLU277 4.4 71.7 1.0 N A:GLU277 4.4 61.2 1.0 CA A:PRO275 4.4 57.7 1.0 CA C:PRO65 4.4 66.3 1.0 CB A:PRO275 4.5 58.9 1.0 CB C:PRO65 4.6 68.5 1.0 C C:ASN66 4.8 69.5 1.0 C A:ASN276 5.0 64.3 1.0 CG C:GLU67 5.0 78.6 1.0

Calcium binding site 2 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:77.5 occ:1.00 O C:PRO149 2.4 69.7 1.0 O A:PRO191 2.5 76.5 1.0 OE2 C:GLU151 2.6 87.7 1.0 OE2 A:GLU193 2.7 81.3 1.0 CD A:GLU193 3.4 94.1 1.0 OE1 A:GLU193 3.4 84.8 1.0 CD C:GLU151 3.4 92.5 1.0 C A:PRO191 3.6 77.2 1.0 OE1 C:GLU151 3.6 90.6 1.0 C C:PRO149 3.6 69.6 1.0 N A:ASN192 4.4 71.4 1.0 CA A:ASN192 4.5 69.2 1.0 CA A:PRO191 4.5 76.9 1.0 CB A:PRO191 4.5 79.5 1.0 CA C:PRO149 4.5 68.2 1.0 N C:ASN150 4.5 63.9 1.0 CB C:PRO149 4.6 71.2 1.0 CA C:ASN150 4.7 62.8 1.0 N A:GLU193 4.7 68.5 1.0 N C:GLU151 4.7 62.9 1.0 CG A:GLU193 4.8 76.6 1.0 CG C:GLU151 4.8 71.9 1.0

Calcium binding site 3 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:72.4 occ:1.00 O C:PRO233 2.2 63.2 1.0 O A:PRO107 2.4 63.3 1.0 OE2 C:GLU235 2.5 75.4 1.0 OE2 A:GLU109 2.6 75.9 1.0 CD A:GLU109 3.3 86.6 1.0 OE1 A:GLU109 3.4 83.5 1.0 C C:PRO233 3.4 62.9 1.0 CD C:GLU235 3.5 83.1 1.0 C A:PRO107 3.5 63.7 1.0 OE1 C:GLU235 3.7 85.1 1.0 N C:ASN234 4.2 56.7 1.0 CA C:ASN234 4.2 55.5 1.0 N C:GLU235 4.4 55.0 1.0 N A:ASN108 4.4 58.3 1.0 CA C:PRO233 4.4 60.9 1.0 CA A:PRO107 4.5 62.9 1.0 CA A:ASN108 4.5 57.1 1.0 CB A:PRO107 4.6 65.3 1.0 CB C:PRO233 4.6 63.9 1.0 N A:GLU109 4.6 60.8 1.0 CG A:GLU109 4.7 72.5 1.0 CG C:GLU235 4.8 64.6 1.0 C C:ASN234 4.8 58.4 1.0

Calcium binding site 4 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:65.0 occ:1.00 O A:PRO65 2.1 64.5 1.0 O C:HOH515 2.3 62.9 1.0 O C:PRO275 2.3 60.3 1.0 OE2 C:GLU277 2.4 73.1 1.0 OE2 A:GLU67 2.4 79.6 1.0 CD C:GLU277 3.1 84.6 1.0 OE1 C:GLU277 3.2 83.7 1.0 C A:PRO65 3.3 64.7 1.0 CD A:GLU67 3.5 90.2 1.0 C C:PRO275 3.6 59.0 1.0 OE1 A:GLU67 3.8 81.0 1.0 N A:ASN66 4.1 59.7 1.0 CA A:ASN66 4.1 58.8 1.0 N A:GLU67 4.3 61.9 1.0 CA C:ASN276 4.3 52.4 1.0 CA A:PRO65 4.4 63.2 1.0 N C:ASN276 4.4 53.6 1.0 O C:HOH532 4.4 45.0 1.0 N C:GLU277 4.5 54.8 1.0 CG C:GLU277 4.6 66.8 1.0 CA C:PRO275 4.6 53.7 1.0 CB A:PRO65 4.6 65.1 1.0 CB C:PRO275 4.7 56.5 1.0 C A:ASN66 4.7 64.1 1.0 CG A:GLU67 4.8 75.3 1.0 C C:ASN276 5.0 56.7 1.0

Calcium binding site 5 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:0.8 occ:1.00 OG A:SER250 2.7 0.4 1.0 O A:SER208 3.6 92.1 1.0 O A:GLY209 3.6 96.1 1.0 CB A:SER250 3.9 92.9 1.0 C A:SER208 4.0 91.3 1.0 O A:ASN247 4.2 86.6 1.0 O A:ALA207 4.3 90.7 1.0 CA A:SER208 4.3 85.4 1.0 OD1 A:ASN247 4.5 80.0 1.0 C A:GLY209 4.8 97.2 1.0 O A:SER250 4.8 98.3 1.0 CD1 A:ILE214 4.8 0.3 1.0 N A:GLY209 4.8 88.3 1.0 C A:SER250 5.0 96.9 1.0

Calcium binding site 6 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:0.3 occ:1.00 CG B:PRO114 3.8 0.5 1.0 OE2 A:GLU240 3.8 93.8 1.0 CG A:TRP243 3.9 80.9 1.0 NH1 B:ARG116 4.0 75.2 1.0 CD2 A:TRP243 4.0 81.9 1.0 OE1 A:GLU282 4.0 0.1 1.0 CB A:TRP243 4.1 78.3 1.0 CE3 A:TRP243 4.3 83.9 1.0 CD1 A:TRP243 4.4 84.1 1.0 CD A:GLU282 4.5 0.6 1.0 CE2 A:TRP243 4.6 86.5 1.0 OE2 A:GLU282 4.6 96.2 1.0 CD A:GLU240 4.7 97.1 1.0 NE1 A:TRP243 4.8 84.5 1.0 CB B:PRO114 4.9 1.0 1.0 OE1 A:GLU240 4.9 79.2 1.0 CD B:PRO114 4.9 0.8 1.0 O A:GLN239 5.0 74.3 1.0 NE2 A:GLN278 5.0 88.9 1.0

Calcium binding site 7 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:72.7 occ:1.00 O A:PRO233 2.3 64.2 1.0 O C:PRO107 2.4 66.3 1.0 OE2 C:GLU109 2.6 84.5 1.0 OE2 A:GLU235 2.6 77.8 1.0 OE1 C:GLU109 3.3 73.0 1.0 CD C:GLU109 3.3 87.6 1.0 C A:PRO233 3.5 65.8 1.0 C C:PRO107 3.5 65.9 1.0 CD A:GLU235 3.6 88.7 1.0 OE1 A:GLU235 3.9 92.7 1.0 N A:ASN234 4.3 62.4 1.0 CA C:PRO107 4.4 63.0 1.0 N C:ASN108 4.4 60.5 1.0 CA A:PRO233 4.4 64.2 1.0 CA A:ASN234 4.4 61.6 1.0 CB C:PRO107 4.5 65.4 1.0 CB A:PRO233 4.5 66.3 1.0 CA C:ASN108 4.5 59.7 1.0 N A:GLU235 4.6 62.1 1.0 N C:GLU109 4.6 60.1 1.0 CG C:GLU109 4.7 71.6 1.0 CG A:GLU235 5.0 71.7 1.0

Calcium binding site 8 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca408 b:77.1 occ:1.00 O C:PRO191 2.5 70.9 1.0 OE2 A:GLU151 2.5 81.5 1.0 O A:PRO149 2.5 70.8 1.0 OE2 C:GLU193 2.6 73.9 1.0 OE1 C:GLU193 3.2 78.6 1.0 CD C:GLU193 3.3 84.8 1.0 CD A:GLU151 3.5 89.0 1.0 C A:PRO149 3.6 71.7 1.0 C C:PRO191 3.6 70.6 1.0 OE1 A:GLU151 3.8 85.4 1.0 N A:ASN150 4.4 67.0 1.0 CA A:ASN150 4.5 64.8 1.0 N C:ASN192 4.5 64.5 1.0 CB A:PRO149 4.5 72.3 1.0 CA C:ASN192 4.5 63.0 1.0 CA A:PRO149 4.5 69.6 1.0 N A:GLU151 4.5 65.4 1.0 CA C:PRO191 4.6 69.5 1.0 N C:GLU193 4.6 61.4 1.0 CG C:GLU193 4.7 70.7 1.0 CB C:PRO191 4.8 72.9 1.0 CG A:GLU151 4.8 73.9 1.0

Calcium binding site 9 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:0.8 occ:1.00 O C:HOH514 2.3 55.9 1.0 OG C:SER250 2.7 70.1 1.0 CB C:SER250 3.8 58.6 1.0 O C:GLY209 3.9 56.4 1.0 O C:SER208 4.2 57.1 1.0 O C:ASN247 4.6 59.8 1.0 O C:SER250 4.6 60.6 1.0 OD1 C:ASN247 4.7 69.1 1.0 C C:SER208 4.7 56.6 1.0 CD1 C:ILE214 4.8 52.8 1.0 O C:ALA207 4.9 57.1 1.0 C C:SER250 4.9 60.2 1.0 C C:GLY209 4.9 57.0 1.0 CA C:SER250 5.0 55.9 1.0

Calcium binding site 10 out of 49 in the Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Designed Armadillo Repeat Protein Yiiim''6AII in Complex with PD_(Kr)5 within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:67.0 occ:1.00 O E:HOH548 2.1 61.2 1.0 O E:PRO65 2.3 64.7 1.0 O E:HOH509 2.3 53.3 1.0 O I:PRO275 2.4 60.6 1.0 OE2 I:GLU277 2.5 78.0 1.0 OE2 E:GLU67 2.7 74.1 1.0 C E:PRO65 3.3 64.0 1.0 CD I:GLU277 3.3 85.5 1.0 OE1 I:GLU277 3.5 73.4 1.0 C I:PRO275 3.5 59.1 1.0 CD E:GLU67 3.6 84.2 1.0 OE1 E:GLU67 3.9 77.5 1.0 N E:ASN66 4.1 58.2 1.0 CA E:ASN66 4.1 57.9 1.0 CA I:ASN276 4.2 53.5 1.0 N I:ASN276 4.3 54.2 1.0 CA E:PRO65 4.3 61.6 1.0 CB E:PRO65 4.4 64.0 1.0 N I:GLU277 4.4 55.8 1.0 N E:GLU67 4.5 59.8 1.0 O I:HOH542 4.5 53.6 1.0 CA I:PRO275 4.6 54.1 1.0 CB I:PRO275 4.6 56.5 1.0 CG I:GLU277 4.8 68.7 1.0 C E:ASN66 4.8 63.0 1.0 C I:ASN276 4.8 57.9 1.0 CG E:GLU67 5.0 71.8 1.0

S.Hansen, J.D.Kiefer, C.Madhurantakam, P.R.E.Mittl, A.Pluckthun. Structures of Designed Armadillo Repeat Proteins Binding to Peptides Fused to Globular Domains. Protein Sci. V. 26 1942 2017.
ISSN: ESSN 1469-896X
PubMed: 28691351
DOI: 10.1002/PRO.3229