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Calcium in PDB 5mfm: Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5

Protein crystallography data

The structure of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5, PDB code: 5mfm was solved by S.Hansen, P.Ernst, C.Reichen, C.Ewald, P.Mittl, A.Plueckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.69 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.760, 89.390, 123.850, 90.00, 97.07, 90.00
R / Rfree (%) 21.7 / 25.1

Other elements in 5mfm:

The structure of Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 23;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5 (pdb code 5mfm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 23 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(Kr)5, PDB code: 5mfm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 23 in 5mfm

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Calcium binding site 1 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:55.9
occ:1.00
 O A:PRO233 2.3 52.9 1.0
OE1 A:GLU235 2.4 72.7 1.0
C A:PRO233 3.3 52.5 1.0
CD A:GLU235 3.4 76.0 1.0
OE2 A:GLU235 3.8 69.7 1.0
N A:ASN234 4.0 46.5 1.0
CA A:ASN234 4.0 44.7 1.0
N A:GLU235 4.3 44.6 1.0
CA A:PRO233 4.4 50.2 1.0
CB A:PRO233 4.5 53.4 1.0
C A:ASN234 4.6 48.2 1.0
CG A:GLU235 4.7 57.0 1.0

Calcium binding site 2 out of 23 in 5mfm

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Calcium binding site 2 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:56.6
occ:1.00
 O A:HOH560 2.4 50.9 1.0
O A:PRO149 2.4 61.5 1.0
OE1 A:GLU151 2.5 61.7 1.0
C A:PRO149 3.5 61.6 1.0
CD A:GLU151 3.5 77.4 1.0
OE2 A:GLU151 3.8 75.2 1.0
N A:ASN150 4.3 55.8 1.0
CA A:ASN150 4.3 53.9 1.0
N A:GLU151 4.5 51.2 1.0
CA A:PRO149 4.5 59.7 1.0
CB A:PRO149 4.6 63.2 1.0
CG A:GLU151 4.9 60.5 1.0
C A:ASN150 4.9 55.7 1.0

Calcium binding site 3 out of 23 in 5mfm

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Calcium binding site 3 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:74.2
occ:1.00
 O A:PRO107 2.4 63.1 1.0
OE1 A:GLU109 2.7 73.2 1.0
C A:PRO107 3.6 63.3 1.0
CD A:GLU109 3.6 85.4 1.0
OE2 A:GLU109 3.8 83.1 1.0
N A:ASN108 4.4 58.0 1.0
CA A:PRO107 4.5 61.5 1.0
CA A:ASN108 4.5 56.3 1.0
CB A:PRO107 4.6 65.2 1.0
N A:GLU109 4.6 54.3 1.0
CG A:GLU109 5.0 65.5 1.0

Calcium binding site 4 out of 23 in 5mfm

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Calcium binding site 4 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:62.4
occ:1.00
 O A:PRO191 2.2 49.9 1.0
OE1 A:GLU193 2.4 59.6 1.0
CD A:GLU193 3.4 71.5 1.0
C A:PRO191 3.4 50.1 1.0
OE2 A:GLU193 3.7 70.6 1.0
N A:ASN192 4.2 44.9 1.0
CA A:ASN192 4.2 43.4 1.0
N A:GLU193 4.4 41.2 1.0
CA A:PRO191 4.4 48.8 1.0
CB A:PRO191 4.6 52.2 1.0
CG A:GLU193 4.7 53.1 1.0
C A:ASN192 4.8 45.3 1.0

Calcium binding site 5 out of 23 in 5mfm

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Calcium binding site 5 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:0.2
occ:1.00
 OE1 A:GLN25 2.2 0.6 1.0
O A:PRO23 2.4 1.0 1.0
CD A:GLN25 3.2 0.5 1.0
NE2 A:GLN25 3.5 0.9 1.0
C A:PRO23 3.5 0.1 1.0
NE2 B:GLN18 3.9 0.1 1.0
N A:GLN25 4.3 96.4 1.0
CA A:ASP24 4.4 99.9 1.0
N A:ASP24 4.4 0.2 1.0
CA A:PRO23 4.5 0.5 1.0
CG A:GLN25 4.6 0.3 1.0
C A:ASP24 4.8 0.2 1.0
CB A:PRO23 4.9 0.4 1.0
CB A:GLN25 4.9 95.2 1.0
CD B:GLN18 5.0 0.3 1.0

Calcium binding site 6 out of 23 in 5mfm

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Calcium binding site 6 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:61.3
occ:1.00
 O B:PRO65 2.2 61.5 1.0
O B:HOH526 2.3 63.8 1.0
OE1 B:GLU67 2.5 82.7 1.0
C B:PRO65 3.4 62.3 1.0
CD B:GLU67 3.5 85.6 1.0
OE2 B:GLU67 3.8 77.3 1.0
CA B:ASN66 4.2 56.4 1.0
N B:ASN66 4.2 57.9 1.0
N B:GLU67 4.4 56.2 1.0
CA B:PRO65 4.4 60.6 1.0
CB B:PRO65 4.6 64.2 1.0
C B:ASN66 4.8 59.9 1.0
CG B:GLU67 4.9 66.7 1.0

Calcium binding site 7 out of 23 in 5mfm

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Calcium binding site 7 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:81.0
occ:1.00
 OE1 B:GLU277 2.5 87.2 1.0
O B:PRO275 2.6 81.3 1.0
CD B:GLU277 3.2 0.5 1.0
OE2 B:GLU277 3.3 98.0 1.0
C B:PRO275 3.5 81.2 1.0
N B:ASN276 4.3 75.4 1.0
CA B:ASN276 4.3 72.8 1.0
CB B:PRO275 4.5 82.7 1.0
CA B:PRO275 4.5 79.5 1.0
N B:GLU277 4.5 72.1 1.0
CG B:GLU277 4.7 84.6 1.0
C B:ASN276 4.9 75.7 1.0

Calcium binding site 8 out of 23 in 5mfm

Go back to Calcium Binding Sites List in 5mfm
Calcium binding site 8 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:0.5
occ:1.00
 O B:PRO149 3.4 54.4 1.0
OE1 B:GLU151 3.6 57.4 1.0
OE2 B:GLU151 4.2 69.2 1.0
CD B:GLU151 4.3 73.2 1.0
C B:PRO149 4.5 54.6 1.0
CA B:PRO149 4.9 53.2 1.0
CB B:PRO149 4.9 56.6 1.0

Calcium binding site 9 out of 23 in 5mfm

Go back to Calcium Binding Sites List in 5mfm
Calcium binding site 9 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:0.3
occ:1.00
 O B:PRO107 3.5 54.3 1.0
CB B:PRO107 3.7 56.2 1.0
C B:PRO107 3.8 54.6 1.0
CG B:PRO107 4.0 61.1 1.0
N B:ASN108 4.3 49.6 1.0
CA B:PRO107 4.4 52.8 1.0
CA B:ASN108 4.6 47.8 1.0
OE1 B:GLU109 5.0 61.5 1.0

Calcium binding site 10 out of 23 in 5mfm

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Calcium binding site 10 out of 23 in the Designed Armadillo Repeat Protein Peptide Fusion YIIIM6AII_GS11_(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 Peptide Fusion YIIIM6AII_GS11_(Kr)5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca401

b:67.7
occ:1.00
 O C:PRO149 2.4 62.2 1.0
OE1 C:GLU151 2.5 71.5 1.0
O E:PRO191 2.6 69.0 1.0
OE1 E:GLU193 2.8 85.7 1.0
O E:HOH553 3.1 45.8 1.0
C E:PRO191 3.5 69.2 1.0
CD C:GLU151 3.5 84.3 1.0
CD E:GLU193 3.5 91.2 1.0
OE2 E:GLU193 3.6 86.0 1.0
C C:PRO149 3.6 62.4 1.0
OE2 C:GLU151 3.8 81.5 1.0
CB E:PRO191 4.2 72.6 1.0
N E:ASN192 4.2 62.7 1.0
CA E:ASN192 4.3 59.3 1.0
CA E:PRO191 4.4 68.8 1.0
CA C:PRO149 4.4 60.5 1.0
CB C:PRO149 4.5 64.7 1.0
N C:ASN150 4.6 57.3 1.0
N C:GLU151 4.6 53.4 1.0
N E:GLU193 4.7 57.9 1.0
CA C:ASN150 4.7 55.7 1.0
CG C:GLU151 4.8 64.1 1.0
CG E:GLU193 4.9 71.4 1.0
C E:ASN192 5.0 61.9 1.0

Reference:

S.Hansen, P.Ernst, S.L.B.Konig, C.Reichen, C.Ewald, D.Nettels, P.R.E.Mittl, B.Schuler, A.Pluckthun. Curvature of Designed Armadillo Repeat Proteins Allows Modular Peptide Binding. J. Struct. Biol. V. 201 108 2018.
ISSN: ESSN 1095-8657
PubMed: 28864298
DOI: 10.1016/J.JSB.2017.08.009
Page generated: Mon Jul 15 08:07:41 2024

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