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Calcium in PDB 5aei: Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (Kr)5

Protein crystallography data

The structure of Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (Kr)5, PDB code: 5aei was solved by S.Hansen, D.Tremmel, C.Madhurantakam, C.Reichen, P.Mittl, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 107.64 / 1.83
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.830, 215.280, 105.990, 90.00, 90.00, 90.00
R / Rfree (%) 14.864 / 17.914

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (Kr)5 (pdb code 5aei). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (Kr)5, PDB code: 5aei:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 5aei

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Calcium binding site 1 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1295

b:12.3
occ:1.00
 O A:PRO107 2.4 12.8 1.0
O A:HOH2138 2.4 20.0 1.0
O A:HOH2137 2.4 16.8 1.0
OE1 A:GLU109 2.5 16.6 1.0
CD A:GLU109 3.4 18.0 1.0
C A:PRO107 3.5 13.8 1.0
OE2 A:GLU109 3.6 23.1 1.0
CA A:ASN108 4.1 12.3 1.0
N A:ASN108 4.2 12.0 1.0
N A:GLU109 4.4 12.8 1.0
O A:HOH2053 4.5 28.7 1.0
CA A:PRO107 4.5 13.6 1.0
CB A:PRO107 4.7 15.0 1.0
C A:ASN108 4.8 12.0 1.0
CG A:GLU109 4.8 15.2 1.0

Calcium binding site 2 out of 13 in 5aei

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Calcium binding site 2 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1296

b:14.5
occ:1.00
 O A:PRO191 2.4 14.8 1.0
O A:HOH2299 2.5 13.8 1.0
OE1 A:GLU193 2.5 15.1 1.0
O A:HOH2220 2.6 29.4 1.0
CD A:GLU193 3.4 17.5 1.0
O A:HOH2224 3.4 33.4 1.0
C A:PRO191 3.6 14.4 1.0
O A:HOH2300 3.6 41.7 1.0
OE2 A:GLU193 3.8 20.4 1.0
CA A:ASN192 4.3 13.9 1.0
N A:ASN192 4.4 13.9 1.0
N A:GLU193 4.4 12.2 1.0
O A:HOH2223 4.5 24.1 1.0
CA A:PRO191 4.6 14.8 1.0
CB A:PRO191 4.6 14.6 1.0
CG A:GLU193 4.7 15.7 1.0
C A:ASN192 4.9 12.8 1.0

Calcium binding site 3 out of 13 in 5aei

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Calcium binding site 3 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1297

b:19.7
occ:1.00
 O A:PRO23 2.3 17.5 1.0
O A:HOH2012 2.4 27.9 1.0
OE1 A:GLN25 2.5 16.1 1.0
CD A:GLN25 3.4 22.6 1.0
C A:PRO23 3.5 18.9 1.0
NE2 A:GLN25 3.7 31.6 1.0
CA A:ASP24 4.2 17.9 1.0
N A:GLN25 4.3 15.8 1.0
N A:ASP24 4.3 17.3 1.0
CA A:PRO23 4.6 19.1 1.0
CB A:PRO23 4.7 20.7 1.0
C A:ASP24 4.8 16.5 1.0
CG A:GLN25 4.8 18.2 1.0

Calcium binding site 4 out of 13 in 5aei

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Calcium binding site 4 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1294

b:12.2
occ:1.00
 OD1 B:ASN21 2.2 14.2 1.0
OE1 B:GLN60 2.3 14.5 1.0
O B:HOH2073 2.4 13.0 1.0
O B:HOH2010 2.4 9.5 1.0
O B:HOH2011 2.4 13.4 1.0
CD B:GLN60 3.4 15.8 1.0
CG B:ASN21 3.4 14.8 1.0
NE2 B:GLN60 4.1 15.1 1.0
O B:LEU20 4.2 13.8 1.0
CA B:ASN21 4.3 13.0 1.0
CB B:ASN21 4.3 13.5 1.0
ND2 B:ASN21 4.4 16.0 1.0
CG B:GLN60 4.5 16.9 1.0
CB B:GLN60 4.5 14.7 1.0
CB B:ALA57 4.9 13.0 1.0
O B:ALA57 4.9 13.5 1.0
N B:ASN21 5.0 13.0 1.0
C B:LEU20 5.0 12.8 1.0

Calcium binding site 5 out of 13 in 5aei

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Calcium binding site 5 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1295

b:14.3
occ:1.00
 O B:HOH2226 2.3 23.5 1.0
O B:PRO191 2.3 14.0 1.0
O C:PRO65 2.4 14.3 1.0
O B:HOH2224 2.4 16.9 1.0
O B:HOH2223 2.4 20.0 1.0
OE1 C:GLU67 2.5 12.6 1.0
OE1 B:GLU193 2.5 13.8 1.0
O B:HOH2303 3.1 40.7 1.0
CD C:GLU67 3.4 17.4 1.0
CD B:GLU193 3.5 14.5 1.0
C B:PRO191 3.5 13.5 1.0
C C:PRO65 3.5 13.4 1.0
OE2 C:GLU67 3.7 23.0 1.0
OE2 B:GLU193 3.8 16.7 1.0
CA B:ASN192 4.1 12.7 1.0
CA C:ASN66 4.2 11.5 1.0
O B:HOH2225 4.2 22.1 1.0
N B:ASN192 4.2 12.7 1.0
N C:ASN66 4.2 11.9 1.0
N B:GLU193 4.3 12.6 1.0
N C:GLU67 4.4 11.8 1.0
CA B:PRO191 4.5 14.8 1.0
CA C:PRO65 4.5 14.4 1.0
CB C:PRO65 4.6 14.9 1.0
CB B:PRO191 4.6 16.2 1.0
O C:HOH2091 4.6 36.1 1.0
O B:HOH2102 4.7 18.0 1.0
CG B:GLU193 4.8 14.4 1.0
C B:ASN192 4.8 13.0 1.0
CG C:GLU67 4.8 14.5 1.0
O B:HOH2103 4.8 32.0 1.0
O B:HOH2105 4.8 34.2 1.0
C C:ASN66 4.9 11.7 1.0

Calcium binding site 6 out of 13 in 5aei

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Calcium binding site 6 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1296

b:13.8
occ:1.00
 O C:PRO107 2.3 17.2 1.0
O B:PRO149 2.3 17.5 1.0
O B:HOH2187 2.4 24.9 1.0
O B:HOH2189 2.4 28.1 1.0
OE1 B:GLU151 2.4 15.0 1.0
OE1 C:GLU109 2.4 15.1 1.0
O B:HOH2186 2.5 22.5 1.0
CD B:GLU151 3.4 16.9 1.0
CD C:GLU109 3.4 19.0 1.0
C B:PRO149 3.5 18.1 1.0
C C:PRO107 3.5 15.6 1.0
OE2 B:GLU151 3.6 20.7 1.0
OE2 C:GLU109 3.7 20.7 1.0
CA C:ASN108 4.2 13.5 1.0
CA B:ASN150 4.3 14.4 1.0
N C:ASN108 4.3 13.9 1.0
N C:GLU109 4.3 13.7 1.0
N B:ASN150 4.3 15.9 1.0
N B:GLU151 4.4 12.6 1.0
CA B:PRO149 4.6 18.9 1.0
CA C:PRO107 4.6 17.6 1.0
CB B:PRO149 4.7 19.9 1.0
CB C:PRO107 4.7 19.5 1.0
CG B:GLU151 4.8 15.3 1.0
C C:ASN108 4.8 13.6 1.0
CG C:GLU109 4.8 16.8 1.0
O B:HOH2184 4.8 27.3 1.0
C B:ASN150 4.9 13.4 1.0
O C:HOH2130 5.0 29.1 1.0

Calcium binding site 7 out of 13 in 5aei

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Calcium binding site 7 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1297

b:14.2
occ:1.00
 O B:HOH2150 2.2 32.7 1.0
O C:PRO149 2.3 18.7 1.0
O B:PRO107 2.4 17.4 1.0
O B:HOH2149 2.4 27.6 1.0
OE1 C:GLU151 2.4 16.5 1.0
O B:HOH2148 2.4 25.5 1.0
OE1 B:GLU109 2.4 19.0 1.0
CD C:GLU151 3.3 18.5 1.0
CD B:GLU109 3.4 20.9 1.0
C C:PRO149 3.5 16.7 1.0
C B:PRO107 3.6 16.6 1.0
OE2 C:GLU151 3.6 22.8 1.0
OE2 B:GLU109 3.7 26.3 1.0
CA B:ASN108 4.2 13.5 1.0
CA C:ASN150 4.3 14.1 1.0
N B:GLU109 4.3 12.8 1.0
N C:ASN150 4.3 14.4 1.0
N B:ASN108 4.3 13.8 1.0
N C:GLU151 4.4 12.2 1.0
CA C:PRO149 4.5 18.3 1.0
CA B:PRO107 4.6 19.9 1.0
CG C:GLU151 4.7 15.5 1.0
CB C:PRO149 4.7 18.9 1.0
C B:ASN108 4.8 12.9 1.0
CB B:PRO107 4.8 20.7 1.0
CG B:GLU109 4.8 17.9 1.0
O C:HOH2161 4.8 28.8 1.0
C C:ASN150 4.9 12.9 1.0

Calcium binding site 8 out of 13 in 5aei

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Calcium binding site 8 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1298

b:13.5
occ:1.00
 O B:PRO23 2.3 13.1 1.0
O C:PRO233 2.3 12.9 1.0
OE1 C:GLU235 2.4 15.6 1.0
O B:HOH2017 2.5 21.7 1.0
OE1 B:GLN25 2.5 14.3 1.0
O B:HOH2304 2.9 21.6 1.0
CD C:GLU235 3.2 15.7 1.0
OE2 C:GLU235 3.4 19.6 1.0
CD B:GLN25 3.5 14.7 1.0
C B:PRO23 3.5 12.8 1.0
C C:PRO233 3.5 12.6 1.0
NE2 B:GLN25 3.8 15.5 1.0
CA B:ASP24 4.2 13.2 1.0
N B:ASP24 4.3 13.2 1.0
N B:GLN25 4.3 13.2 1.0
CA C:ASN234 4.4 12.5 1.0
N C:ASN234 4.4 12.5 1.0
N C:GLU235 4.5 13.7 1.0
CA C:PRO233 4.5 12.7 1.0
CA B:PRO23 4.6 11.5 1.0
CB B:PRO23 4.6 11.7 1.0
O C:HOH2219 4.6 18.1 1.0
CG C:GLU235 4.7 15.2 1.0
CB C:PRO233 4.7 12.8 1.0
C B:ASP24 4.8 12.8 1.0
CG B:GLN25 4.9 14.1 1.0
C C:ASN234 5.0 13.5 1.0

Calcium binding site 9 out of 13 in 5aei

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Calcium binding site 9 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1299

b:13.1
occ:1.00
 O B:HOH2082 2.2 20.6 1.0
O B:PRO65 2.3 14.8 1.0
O C:PRO191 2.3 14.2 1.0
O B:HOH2083 2.4 19.8 1.0
OE1 C:GLU193 2.4 13.4 1.0
O B:HOH2080 2.4 17.9 1.0
OE1 B:GLU67 2.5 13.4 1.0
CD B:GLU67 3.4 17.1 1.0
CD C:GLU193 3.4 13.8 1.0
C B:PRO65 3.5 14.4 1.0
C C:PRO191 3.5 15.0 1.0
OE2 B:GLU67 3.6 21.8 1.0
OE2 C:GLU193 3.8 15.3 1.0
CA B:ASN66 4.1 12.6 1.0
CA C:ASN192 4.2 13.8 1.0
O C:HOH2191 4.2 25.3 1.0
N B:ASN66 4.3 12.8 1.0
N C:ASN192 4.3 14.1 1.0
N C:GLU193 4.3 12.8 1.0
O B:HOH2081 4.3 36.7 1.0
N B:GLU67 4.3 11.6 1.0
CA B:PRO65 4.6 15.2 1.0
CB B:PRO65 4.6 16.3 1.0
CA C:PRO191 4.6 15.2 1.0
CB C:PRO191 4.7 17.0 1.0
CG C:GLU193 4.7 14.2 1.0
C C:ASN192 4.8 13.6 1.0
CG B:GLU67 4.8 15.0 1.0
C B:ASN66 4.8 12.4 1.0

Calcium binding site 10 out of 13 in 5aei

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Calcium binding site 10 out of 13 in the Designed Armadillo Repeat Protein YIIIM5AII in Complex with Peptide (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 YIIIM5AII in Complex with Peptide (Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1295

b:12.0
occ:0.47
 OE1 C:GLN60 2.2 12.4 1.0
O C:HOH2077 2.4 25.9 0.7
O C:HOH2011 2.4 15.0 0.6
O C:HOH2010 2.4 11.9 1.0
CD C:GLN60 3.4 13.1 1.0
NE2 C:GLN60 4.2 13.1 1.0
O C:LEU20 4.3 13.3 1.0
CG C:GLN60 4.5 14.6 1.0
CB C:GLN60 4.7 14.2 1.0
CA C:ASN21 4.7 13.1 1.0
O C:HOH2076 4.8 23.3 1.0
OD1 C:ASN21 4.9 13.4 1.0
CD2 C:LEU61 4.9 14.9 1.0

Reference:

S.Hansen, D.Tremmel, C.Madhurantakam, C.Reichen, P.R.E.Mittl, A.Pluckthun. Structure and Energetic Contributions of A Designed Modular Peptide-Binding Protein with Picomolar Affinity. J.Am.Chem.Soc. V. 138 3526 2016.
ISSN: ISSN 0002-7863
PubMed: 26878586
DOI: 10.1021/JACS.6B00099
Page generated: Sun Jul 14 16:31:12 2024

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