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Calcium in PDB 6s9m: Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw

Protein crystallography data

The structure of Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw, PDB code: 6s9m was solved by P.Ernst, F.Zosel, C.Reichen, B.Schuler, A.Pluckthun, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.20 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.853, 85.474, 193.970, 90.00, 96.32, 90.00
R / Rfree (%) 17.7 / 21.3

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw (pdb code 6s9m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw, PDB code: 6s9m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 6s9m

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Calcium binding site 1 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:25.1
occ:1.00
 O E:HOH541 2.0 39.8 1.0
O A:HOH514 2.0 39.3 1.0
O A:PRO107 2.2 18.8 1.0
O E:PRO149 2.3 24.1 1.0
OE1 A:GLU109 2.4 21.9 1.0
OE1 E:GLU151 2.5 22.4 1.0
O E:HOH654 2.5 41.8 1.0
CD A:GLU109 3.4 22.7 1.0
CD E:GLU151 3.4 22.1 1.0
C A:PRO107 3.5 21.0 1.0
C E:PRO149 3.6 23.8 1.0
OE2 A:GLU109 3.6 24.6 1.0
OE2 E:GLU151 3.6 25.5 1.0
CA A:ASN108 4.2 19.2 1.0
CA E:ASN150 4.3 20.1 1.0
N A:ASN108 4.3 18.8 1.0
N E:GLU151 4.3 19.7 1.0
N E:ASN150 4.3 22.1 1.0
N A:GLU109 4.4 19.6 1.0
CA A:PRO107 4.5 20.4 1.0
CA E:PRO149 4.6 24.6 1.0
O A:HOH700 4.6 49.1 1.0
CB A:PRO107 4.6 21.8 1.0
CB E:PRO149 4.7 25.6 1.0
CG A:GLU109 4.8 21.8 1.0
CG E:GLU151 4.8 21.1 1.0
C E:ASN150 4.8 20.5 1.0
C A:ASN108 4.8 18.8 1.0

Calcium binding site 2 out of 18 in 6s9m

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Calcium binding site 2 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:25.2
occ:1.00
 O E:HOH514 2.1 40.9 1.0
O A:HOH530 2.1 36.8 1.0
O E:PRO107 2.3 25.1 1.0
O A:PRO149 2.4 27.2 1.0
OE1 E:GLU109 2.5 25.0 1.0
O A:HOH669 2.5 27.7 1.0
OE2 A:GLU151 2.5 24.4 1.0
CD E:GLU109 3.4 31.1 1.0
CD A:GLU151 3.4 26.1 1.0
C E:PRO107 3.5 25.9 1.0
C A:PRO149 3.6 23.8 1.0
OE1 A:GLU151 3.6 31.1 1.0
OE2 E:GLU109 3.6 33.6 1.0
CA A:ASN150 4.3 19.4 1.0
CA E:ASN108 4.3 22.5 1.0
N A:ASN150 4.3 21.3 1.0
N A:GLU151 4.3 20.3 1.0
N E:ASN108 4.3 23.6 1.0
N E:GLU109 4.4 25.5 1.0
CA E:PRO107 4.5 26.1 1.0
CA A:PRO149 4.6 25.1 1.0
CB E:PRO107 4.7 26.6 1.0
CB A:PRO149 4.7 26.0 1.0
O E:HOH626 4.8 41.1 1.0
CG E:GLU109 4.8 27.0 1.0
CG A:GLU151 4.8 24.5 1.0
C A:ASN150 4.8 18.9 1.0
C E:ASN108 4.9 24.0 1.0

Calcium binding site 3 out of 18 in 6s9m

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Calcium binding site 3 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:28.3
occ:1.00
 O A:HOH536 2.0 36.5 1.0
O E:HOH542 2.1 36.5 1.0
O A:PRO191 2.3 27.2 1.0
O E:PRO65 2.3 27.7 1.0
OE2 E:GLU67 2.4 27.5 1.0
O E:HOH653 2.5 25.3 1.0
OE1 A:GLU193 2.5 29.0 1.0
CD E:GLU67 3.4 28.1 1.0
CD A:GLU193 3.4 29.1 1.0
C A:PRO191 3.5 25.9 1.0
C E:PRO65 3.5 27.9 1.0
OE2 A:GLU193 3.6 33.3 1.0
OE1 E:GLU67 3.7 30.9 1.0
CA E:ASN66 4.2 25.8 1.0
CA A:ASN192 4.2 22.7 1.0
N A:ASN192 4.3 24.1 1.0
N E:GLU67 4.3 23.1 1.0
N E:ASN66 4.3 25.5 1.0
N A:GLU193 4.4 23.6 1.0
CA A:PRO191 4.5 25.8 1.0
CA E:PRO65 4.6 29.8 1.0
CB A:PRO191 4.6 26.7 1.0
CB E:PRO65 4.7 29.9 1.0
C E:ASN66 4.8 25.1 1.0
CG E:GLU67 4.8 25.9 1.0
C A:ASN192 4.8 22.6 1.0
CG A:GLU193 4.9 26.9 1.0

Calcium binding site 4 out of 18 in 6s9m

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Calcium binding site 4 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:35.1
occ:1.00
 O E:HOH539 2.2 33.4 1.0
O E:HOH644 2.4 35.5 1.0
O E:PRO23 2.4 35.5 1.0
OE1 E:GLN25 2.4 46.5 1.0
O A:PRO233 2.4 26.6 1.0
OE1 A:GLU235 2.6 36.2 1.0
OE2 A:GLU235 2.8 43.7 1.0
CD A:GLU235 3.1 38.4 1.0
CD E:GLN25 3.5 44.9 1.0
C E:PRO23 3.6 38.7 1.0
C A:PRO233 3.6 27.6 1.0
NE2 E:GLN25 4.0 44.8 1.0
N E:GLN25 4.2 39.3 1.0
CA E:ASP24 4.3 41.9 1.0
O B:HOH592 4.3 56.5 1.0
N E:ASP24 4.3 39.6 1.0
CA A:ASN234 4.3 25.2 1.0
O E:HOH635 4.4 36.9 1.0
O A:HOH628 4.4 33.3 1.0
N A:ASN234 4.4 24.6 1.0
N A:GLU235 4.4 28.0 1.0
CA A:PRO233 4.5 28.5 1.0
CB A:PRO233 4.5 29.2 1.0
OE1 B:GLU269 4.6 44.4 1.0
CA E:PRO23 4.6 37.6 1.0
O B:HOH529 4.6 33.9 1.0
CG A:GLU235 4.6 36.8 1.0
C E:ASP24 4.7 41.6 1.0
CG E:GLN25 4.7 44.4 1.0
C A:ASN234 4.9 26.3 1.0
CB E:PRO23 4.9 38.9 1.0
CB E:GLN25 5.0 40.9 1.0

Calcium binding site 5 out of 18 in 6s9m

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Calcium binding site 5 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:23.4
occ:1.00
 O E:PRO191 2.2 17.7 1.0
O E:HOH517 2.3 20.3 1.0
O A:PRO65 2.4 25.8 1.0
OE1 A:GLU67 2.4 20.9 1.0
OE1 E:GLU193 2.4 21.7 1.0
O E:HOH648 2.5 19.9 1.0
O A:HOH504 2.5 28.1 1.0
C E:PRO191 3.4 19.1 1.0
CD E:GLU193 3.4 24.1 1.0
CD A:GLU67 3.4 23.0 1.0
C A:PRO65 3.5 23.9 1.0
OE2 E:GLU193 3.6 25.6 1.0
OE2 A:GLU67 3.7 24.6 1.0
O E:HOH649 4.0 40.8 1.0
CA E:ASN192 4.1 18.9 1.0
N E:ASN192 4.1 17.9 1.0
CA A:ASN66 4.2 20.8 1.0
N A:GLU67 4.3 19.3 1.0
N E:GLU193 4.3 20.0 1.0
N A:ASN66 4.3 21.9 1.0
CA E:PRO191 4.4 19.0 1.0
CB E:PRO191 4.5 19.3 1.0
CA A:PRO65 4.6 25.4 1.0
CB A:PRO65 4.6 26.9 1.0
C E:ASN192 4.7 18.8 1.0
C A:ASN66 4.7 20.1 1.0
CG A:GLU67 4.8 20.6 1.0
CG E:GLU193 4.8 22.5 1.0

Calcium binding site 6 out of 18 in 6s9m

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Calcium binding site 6 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:28.5
occ:1.00
 O A:HOH576 2.2 30.1 1.0
O A:PRO23 2.4 30.7 1.0
O A:HOH587 2.4 41.4 1.0
O E:PRO233 2.4 23.4 1.0
OE2 E:GLU235 2.4 27.8 1.0
O E:HOH646 2.6 52.5 1.0
OE1 E:GLU235 2.6 23.9 1.0
CD E:GLU235 2.9 25.7 1.0
C A:PRO23 3.5 28.6 1.0
C E:PRO233 3.6 26.2 1.0
O E:HOH629 4.2 54.8 1.0
O2 A:EDO405 4.2 78.1 1.0
CA E:PRO233 4.4 29.0 1.0
N A:ASP24 4.4 28.4 1.0
O A:HOH560 4.4 37.4 1.0
N A:GLN25 4.4 30.7 1.0
CG E:GLU235 4.5 24.1 1.0
CA A:ASP24 4.5 29.6 1.0
CA A:PRO23 4.5 29.1 1.0
N E:GLU235 4.6 22.5 1.0
CB E:PRO233 4.6 29.3 1.0
N E:ASN234 4.6 22.9 1.0
O E:HOH665 4.7 33.1 1.0
CA E:ASN234 4.7 23.0 1.0
CB A:PRO23 4.8 28.6 1.0
C A:ASP24 5.0 30.7 1.0

Calcium binding site 7 out of 18 in 6s9m

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Calcium binding site 7 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:25.3
occ:1.00
 O C:PRO107 2.3 22.6 1.0
O B:HOH571 2.3 30.6 1.0
O B:PRO149 2.4 22.0 1.0
OE2 C:GLU109 2.5 27.8 1.0
OE2 B:GLU151 2.5 24.9 1.0
O C:HOH569 2.6 35.9 1.0
O C:HOH604 2.6 32.1 1.0
CD C:GLU109 3.4 29.1 1.0
CD B:GLU151 3.4 25.5 1.0
C C:PRO107 3.5 24.0 1.0
C B:PRO149 3.5 22.4 1.0
OE1 B:GLU151 3.5 28.5 1.0
OE1 C:GLU109 3.6 33.4 1.0
O B:HOH656 4.1 32.7 1.0
CA B:ASN150 4.1 21.6 1.0
N B:ASN150 4.3 20.8 1.0
CA C:ASN108 4.3 24.6 1.0
N B:GLU151 4.3 22.5 1.0
N C:ASN108 4.3 22.6 1.0
N C:GLU109 4.4 22.8 1.0
CA C:PRO107 4.5 26.1 1.0
CA B:PRO149 4.6 22.6 1.0
CB B:PRO149 4.6 23.3 1.0
CB C:PRO107 4.7 26.3 1.0
CG C:GLU109 4.8 28.6 1.0
C B:ASN150 4.8 21.5 1.0
C C:ASN108 4.9 22.2 1.0
CG B:GLU151 4.9 25.1 1.0

Calcium binding site 8 out of 18 in 6s9m

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Calcium binding site 8 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:25.7
occ:1.00
 O B:HOH552 2.2 36.1 1.0
O C:HOH519 2.3 36.5 1.0
O B:PRO107 2.3 30.9 1.0
O C:PRO149 2.4 24.1 1.0
OE1 B:GLU109 2.4 25.3 1.0
O C:HOH605 2.5 35.9 1.0
OE1 C:GLU151 2.5 25.2 1.0
CD C:GLU151 3.4 26.6 1.0
CD B:GLU109 3.4 28.4 1.0
OE2 C:GLU151 3.5 29.1 1.0
C B:PRO107 3.5 27.3 1.0
C C:PRO149 3.6 23.7 1.0
OE2 B:GLU109 3.6 32.0 1.0
CA B:ASN108 4.3 23.1 1.0
CA C:ASN150 4.3 21.8 1.0
N B:ASN108 4.3 25.9 1.0
N C:GLU151 4.4 22.2 1.0
N C:ASN150 4.4 22.0 1.0
N B:GLU109 4.4 21.4 1.0
CA B:PRO107 4.6 27.6 1.0
CA C:PRO149 4.6 25.0 1.0
O B:HOH644 4.7 40.1 1.0
CB B:PRO107 4.7 27.7 1.0
CB C:PRO149 4.7 26.9 1.0
CG C:GLU151 4.8 25.7 1.0
CG B:GLU109 4.8 25.4 1.0
C C:ASN150 4.9 21.7 1.0
C B:ASN108 4.9 23.3 1.0

Calcium binding site 9 out of 18 in 6s9m

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Calcium binding site 9 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:30.1
occ:1.00
 O B:HOH523 2.0 36.2 1.0
O C:HOH526 2.3 39.1 1.0
O B:HOH658 2.3 32.0 1.0
O C:PRO191 2.4 31.6 1.0
O B:PRO65 2.4 32.6 1.0
OE2 C:GLU193 2.5 28.1 1.0
OE1 B:GLU67 2.5 28.2 1.0
CD C:GLU193 3.3 30.9 1.0
OE1 C:GLU193 3.4 34.2 1.0
CD B:GLU67 3.4 30.8 1.0
C B:PRO65 3.5 28.5 1.0
C C:PRO191 3.5 29.5 1.0
OE2 B:GLU67 3.7 33.4 1.0
CA B:ASN66 4.2 25.6 1.0
CA C:ASN192 4.2 26.1 1.0
N B:ASN66 4.2 26.9 1.0
N B:GLU67 4.3 27.6 1.0
N C:ASN192 4.3 26.4 1.0
N C:GLU193 4.4 26.7 1.0
CA B:PRO65 4.5 29.8 1.0
CA C:PRO191 4.5 30.5 1.0
CB B:PRO65 4.6 29.9 1.0
CB C:PRO191 4.6 30.8 1.0
C B:ASN66 4.7 26.3 1.0
CG C:GLU193 4.8 29.8 1.0
C C:ASN192 4.8 25.6 1.0
CG B:GLU67 4.8 28.6 1.0

Calcium binding site 10 out of 18 in 6s9m

Go back to Calcium Binding Sites List in 6s9m
Calcium binding site 10 out of 18 in the Designed Armadillo Repeat Protein LOCK2 Fused to Target Peptide Krkrkakitw


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 LOCK2 Fused to Target Peptide Krkrkakitw within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:36.1
occ:1.00
 O B:HOH507 2.3 46.1 1.0
O B:PRO191 2.3 26.0 1.0
O C:HOH566 2.3 39.0 1.0
O C:PRO65 2.4 29.9 1.0
OE1 C:GLU67 2.4 36.2 1.0
OE1 B:GLU193 2.5 29.9 1.0
O B:HOH666 2.5 39.1 1.0
CD B:GLU193 3.4 31.9 1.0
OE2 B:GLU193 3.4 34.7 1.0
CD C:GLU67 3.4 38.1 1.0
C B:PRO191 3.5 27.4 1.0
C C:PRO65 3.6 32.6 1.0
OE2 C:GLU67 3.6 39.4 1.0
CA C:ASN66 4.2 30.5 1.0
CA B:ASN192 4.3 26.8 1.0
N C:GLU67 4.3 29.0 1.0
N B:ASN192 4.3 25.9 1.0
N C:ASN66 4.3 31.0 1.0
N B:GLU193 4.4 26.2 1.0
CA B:PRO191 4.5 29.0 1.0
CB B:PRO191 4.6 29.5 1.0
CA C:PRO65 4.6 32.7 1.0
CB C:PRO65 4.7 32.9 1.0
CG C:GLU67 4.7 35.1 1.0
CG B:GLU193 4.8 29.9 1.0
C C:ASN66 4.8 27.9 1.0
C B:ASN192 4.9 26.0 1.0

Reference:

P.Ernst, F.Zosel, C.Reichen, D.Nettels, B.Schuler, A.Pluckthun. Structure-Guided Design of A Peptide Lock For Modular Peptide Binders. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 31985201
DOI: 10.1021/ACSCHEMBIO.9B00928
Page generated: Tue Jul 16 14:36:57 2024

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