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Calcium in PDB 5mfo: Designed Armadillo Repeat Protein YIIIM3AIII

Protein crystallography data

The structure of Designed Armadillo Repeat Protein YIIIM3AIII, PDB code: 5mfo 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) 48.29 / 1.30
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 83.920, 83.920, 166.150, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.8

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein YIIIM3AIII (pdb code 5mfo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 19 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein YIIIM3AIII, PDB code: 5mfo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 19 in 5mfo

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Calcium binding site 1 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:19.1
occ:0.91
O A:GLN18 2.3 21.4 1.0
O A:HOH523 2.4 24.5 1.0
OD1 A:ASN21 2.4 21.1 1.0
HD21 A:ASN21 3.3 27.9 1.0
C A:GLN18 3.4 21.5 1.0
CG A:ASN21 3.4 24.3 1.0
HA A:GLN18 3.5 25.4 1.0
ND2 A:ASN21 3.7 23.3 1.0
HB3 A:GLN18 3.8 26.6 1.0
CA A:GLN18 3.9 21.2 1.0
H A:ASN21 4.1 24.7 1.0
O A:HOH540 4.3 50.9 1.0
CB A:GLN18 4.4 22.2 1.0
HA A:GLN19 4.4 28.4 1.0
O A:HOH484 4.5 27.1 1.0
N A:GLN19 4.5 22.6 1.0
HD22 A:ASN21 4.6 27.9 1.0
HG2 A:GLN18 4.7 26.5 1.0
CB A:ASN21 4.7 21.4 1.0
C A:ASN21 4.8 22.2 1.0
N A:ASN21 4.8 20.6 1.0
HA A:SER22 4.9 29.0 1.0
CA A:GLN19 4.9 23.6 1.0
O A:ASN21 5.0 23.8 1.0

Calcium binding site 2 out of 19 in 5mfo

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Calcium binding site 2 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:29.8
occ:0.53
O A:HOH526 2.2 40.7 1.0
O A:SER166 2.3 32.3 1.0
O B:HOH427 2.3 41.2 1.0
O A:HOH434 2.7 38.5 1.0
OD1 B:ASN21 2.9 65.3 1.0
O A:HOH429 3.4 41.5 1.0
C A:SER166 3.5 26.9 1.0
HB3 A:SER166 3.6 40.1 1.0
HB3 B:ASN21 3.8 32.0 1.0
HA2 A:GLY167 3.9 34.2 1.0
CG B:ASN21 4.0 51.3 1.0
O A:HOH507 4.3 31.2 1.0
HA A:SER166 4.3 36.0 1.0
CA A:SER166 4.4 30.0 1.0
CB B:ASN21 4.4 26.6 1.0
CB A:SER166 4.4 33.4 1.0
N A:GLY167 4.4 27.3 1.0
O A:GLY167 4.4 32.3 1.0
O B:ASN21 4.4 26.3 1.0
HA B:ASN21 4.5 27.9 1.0
CA A:GLY167 4.5 28.5 1.0
O B:HOH477 4.5 32.8 1.0
C A:GLY167 4.7 31.2 1.0
O A:HOH515 4.8 45.5 1.0
O A:HOH462 4.9 32.6 1.0
CA B:ASN21 4.9 23.3 1.0
HB2 A:SER166 5.0 40.1 1.0

Calcium binding site 3 out of 19 in 5mfo

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Calcium binding site 3 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:21.2
occ:0.61
O A:HOH490 2.1 35.2 1.0
O B:HOH492 2.3 25.3 1.0
O A:HOH444 2.3 25.1 1.0
O A:HOH522 2.3 33.5 1.0
O A:HOH511 2.5 59.9 1.0
O B:HOH544 2.6 48.6 1.0
OG A:SER124 2.6 22.8 1.0
O A:HOH494 3.1 47.0 1.0
O B:HOH403 3.2 59.0 1.0
HB2 A:SER124 3.5 25.3 1.0
CB A:SER124 3.6 21.1 1.0
HA A:SER82 3.9 23.5 1.0
HE22 B:GLN19 4.0 50.0 1.0
HB3 A:SER124 4.1 25.3 1.0
HD11 A:ILE88 4.2 21.9 1.0
O A:HOH478 4.2 28.3 1.0
O A:SER82 4.3 20.5 1.0
OE1 B:GLU27 4.3 28.1 1.0
O A:SER124 4.4 21.2 1.0
O B:HOH582 4.5 28.5 1.0
O A:HOH499 4.5 50.6 1.0
O A:GLY83 4.5 20.7 1.0
O A:ASN121 4.6 16.6 1.0
OE2 B:GLU27 4.7 34.9 1.0
C A:SER82 4.7 19.3 1.0
O A:HOH537 4.7 28.3 1.0
C A:SER124 4.7 19.6 1.0
O A:ALA81 4.7 19.3 1.0
CA A:SER82 4.7 19.6 1.0
CA A:SER124 4.8 19.2 1.0
HA A:ASN121 4.8 18.3 1.0
O A:HOH450 4.8 45.1 1.0
NE2 B:GLN19 4.8 41.7 1.0
CD B:GLU27 4.9 34.4 1.0

Calcium binding site 4 out of 19 in 5mfo

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Calcium binding site 4 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:20.6
occ:0.60
O D:HOH408 2.1 27.3 1.0
O B:HOH406 2.1 27.6 1.0
O B:HOH568 2.3 52.0 1.0
OE1 B:GLU67 2.5 20.6 1.0
OE1 D:GLU109 2.6 18.9 1.0
O D:PRO107 2.6 22.1 1.0
O B:PRO65 2.7 29.1 1.0
O B:HOH473 2.9 36.2 1.0
O D:HOH435 3.0 35.4 1.0
HA D:ASN108 3.1 20.0 1.0
HA B:ASN66 3.3 23.7 1.0
CD D:GLU109 3.5 19.7 1.0
CD B:GLU67 3.5 23.9 1.0
H B:GLU67 3.6 21.1 1.0
H D:GLU109 3.6 18.0 1.0
C D:PRO107 3.7 18.9 1.0
OE2 D:GLU109 3.7 24.9 1.0
OE2 B:GLU67 3.7 29.4 1.0
C B:PRO65 3.8 26.7 1.0
CA D:ASN108 4.0 16.7 1.0
HB2 D:PRO107 4.1 24.7 1.0
CA B:ASN66 4.1 19.7 1.0
HB2 B:PRO65 4.3 31.4 1.0
O D:HOH570 4.3 32.9 1.0
N D:ASN108 4.3 16.9 1.0
N B:GLU67 4.3 17.6 1.0
N D:GLU109 4.3 15.0 1.0
N B:ASN66 4.4 20.1 1.0
O B:HOH512 4.5 40.0 1.0
C D:ASN108 4.7 15.4 1.0
C B:ASN66 4.8 18.0 1.0
CA D:PRO107 4.8 19.6 1.0
CG B:GLU67 4.8 19.1 1.0
HB2 B:GLU67 4.8 22.4 1.0
CG D:GLU109 4.9 18.6 1.0
CB D:PRO107 4.9 20.6 1.0
O B:HOH613 4.9 50.9 1.0
HB2 D:ASN108 5.0 19.0 1.0
CA B:PRO65 5.0 23.8 1.0

Calcium binding site 5 out of 19 in 5mfo

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Calcium binding site 5 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:18.6
occ:0.70
O B:HOH559 2.4 31.7 1.0
O B:HOH501 2.4 27.0 1.0
OD1 B:ASN121 2.5 18.8 1.0
CG B:ASN121 3.7 17.8 1.0
O B:HOH421 3.8 39.3 1.0
HD21 B:ASN121 4.0 34.0 1.0
ND2 B:ASN121 4.3 28.3 1.0
HA B:ASN121 4.3 16.9 1.0
O B:HOH538 4.7 20.7 1.0
HZ2 B:TRP117 4.7 37.5 0.5
HE1 B:TRP117 4.7 28.8 0.5
O B:HOH454 4.7 16.6 1.0
O B:HOH511 4.8 78.0 1.0
OG B:SER82 4.8 24.3 1.0
CB B:ASN121 4.8 14.6 1.0
HB3 B:SER82 5.0 22.3 1.0

Calcium binding site 6 out of 19 in 5mfo

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Calcium binding site 6 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:37.9
occ:0.91
O B:HOH535 2.3 39.5 1.0
O E:HOH509 2.3 39.0 1.0
O B:HOH503 2.3 30.5 1.0
O E:PRO149 2.4 23.2 1.0
O E:HOH409 2.4 48.4 1.0
O B:PRO149 2.4 22.6 1.0
O B:HOH401 2.5 18.4 1.0
O F:HOH469 2.7 59.9 1.0
HB2 E:PRO149 3.1 29.5 1.0
HB2 B:PRO149 3.1 29.6 1.0
C E:PRO149 3.4 21.5 1.0
C B:PRO149 3.5 22.2 1.0
HA E:PRO149 3.8 27.0 1.0
CB E:PRO149 3.8 24.6 1.0
HA B:PRO149 3.8 27.2 1.0
CB B:PRO149 3.8 24.7 1.0
O E:HOH419 3.8 78.6 1.0
CA E:PRO149 3.9 22.5 1.0
CA B:PRO149 3.9 22.7 1.0
O B:HOH474 3.9 39.4 1.0
HB3 E:PRO149 4.0 29.5 1.0
HB3 B:PRO149 4.1 29.6 1.0
OE1 E:GLU151 4.2 25.3 1.0
OE2 B:GLU151 4.2 27.0 1.0
OE2 E:GLU151 4.3 20.1 1.0
OE1 B:GLU151 4.3 19.9 1.0
O B:HOH485 4.4 46.2 1.0
O E:HOH553 4.4 66.1 1.0
HA B:ASN150 4.4 20.1 1.0
HA E:ASN150 4.4 20.2 1.0
O E:HOH477 4.5 81.8 1.0
CD E:GLU151 4.6 18.3 1.0
CD B:GLU151 4.6 18.9 1.0
N E:ASN150 4.6 18.9 1.0
N B:ASN150 4.6 19.1 1.0
O D:HOH557 4.8 43.0 1.0
O D:PRO23 4.9 32.4 1.0
HG2 D:GLN25 4.9 23.7 1.0
O F:PRO23 4.9 31.4 1.0
HG2 F:GLN25 4.9 22.6 1.0

Calcium binding site 7 out of 19 in 5mfo

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Calcium binding site 7 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:17.8
occ:0.67
O D:HOH404 2.1 27.5 1.0
O B:HOH410 2.2 22.3 1.0
OE1 D:GLU67 2.5 17.5 1.0
O D:HOH612 2.5 51.5 1.0
O B:PRO107 2.6 23.2 1.0
OE1 B:GLU109 2.6 17.7 1.0
O D:PRO65 2.6 19.9 1.0
O B:HOH444 2.8 31.0 1.0
O D:HOH445 2.8 30.9 1.0
HA B:ASN108 3.2 19.3 1.0
HA D:ASN66 3.2 17.3 1.0
CD D:GLU67 3.4 19.9 1.0
CD B:GLU109 3.5 18.9 1.0
OE2 D:GLU67 3.6 27.2 1.0
H D:GLU67 3.6 17.0 1.0
H B:GLU109 3.7 18.2 1.0
C B:PRO107 3.7 21.6 1.0
C D:PRO65 3.7 17.0 1.0
OE2 B:GLU109 3.7 23.1 1.0
HB2 B:PRO107 4.0 31.8 1.0
CA B:ASN108 4.1 16.1 1.0
CA D:ASN66 4.1 14.4 1.0
HB2 D:PRO65 4.1 26.7 1.0
O B:HOH541 4.3 31.8 1.0
N B:ASN108 4.3 16.5 1.0
N D:ASN66 4.3 15.2 1.0
N D:GLU67 4.3 14.2 1.0
N B:GLU109 4.4 15.2 1.0
O D:HOH588 4.5 39.6 1.0
C D:ASN66 4.8 13.9 1.0
CA B:PRO107 4.8 20.5 1.0
CG D:GLU67 4.8 16.8 1.0
C B:ASN108 4.8 15.3 1.0
CB B:PRO107 4.8 26.5 1.0
CA D:PRO65 4.8 17.3 1.0
HB2 D:GLU67 4.9 18.5 1.0
CG B:GLU109 4.9 16.2 1.0
CB D:PRO65 4.9 22.2 1.0
O B:HOH595 4.9 45.3 1.0

Calcium binding site 8 out of 19 in 5mfo

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Calcium binding site 8 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:18.1
occ:0.84
O C:GLN18 2.3 21.6 1.0
OE1 F:GLN186 2.3 22.2 1.0
O C:HOH514 2.3 24.0 1.0
OD1 C:ASN21 2.4 21.4 1.0
O F:HOH512 2.4 18.8 1.0
O F:HOH563 2.5 27.1 1.0
CD F:GLN186 3.3 20.2 1.0
HD21 C:ASN21 3.3 29.0 1.0
C C:GLN18 3.4 21.8 1.0
CG C:ASN21 3.4 24.4 1.0
HA C:GLN18 3.4 25.7 1.0
HG2 F:GLN186 3.6 26.7 1.0
HG3 F:GLN186 3.7 26.7 1.0
ND2 C:ASN21 3.8 24.2 1.0
HB3 C:GLN18 3.8 27.2 1.0
CG F:GLN186 3.8 22.3 1.0
CA C:GLN18 3.9 21.4 1.0
H C:ASN21 4.1 26.3 1.0
O C:HOH531 4.3 66.2 1.0
CB C:GLN18 4.4 22.7 1.0
O C:HOH485 4.4 26.4 1.0
HA C:GLN19 4.5 28.7 1.0
NE2 F:GLN186 4.5 20.2 1.0
N C:GLN19 4.5 22.9 1.0
OE1 F:GLU185 4.5 28.2 1.0
HB2 F:PRO182 4.6 25.8 1.0
HD22 C:ASN21 4.6 29.0 1.0
O F:HOH629 4.6 28.9 1.0
O F:PRO182 4.6 20.4 1.0
HE22 F:GLN186 4.7 24.3 1.0
CB C:ASN21 4.7 21.5 1.0
HG2 C:GLN18 4.8 29.1 1.0
N C:ASN21 4.8 21.9 1.0
C C:ASN21 4.8 22.1 1.0
HA C:SER22 4.9 30.2 1.0
CA C:GLN19 5.0 23.9 1.0
O C:ASN21 5.0 23.5 1.0

Calcium binding site 9 out of 19 in 5mfo

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Calcium binding site 9 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:32.8
occ:0.65
O C:SER166 2.3 32.3 1.0
O C:HOH411 2.8 44.5 1.0
C C:SER166 3.5 26.7 1.0
HB3 C:SER166 3.6 38.6 1.0
HA2 C:GLY167 3.9 34.2 1.0
O C:HOH509 4.3 31.2 1.0
HA C:SER166 4.4 35.9 1.0
CA C:SER166 4.4 29.9 1.0
O C:GLY167 4.4 34.2 1.0
N C:GLY167 4.4 30.7 1.0
CB C:SER166 4.4 32.2 1.0
CA C:GLY167 4.5 28.5 1.0
C C:GLY167 4.7 30.2 1.0
O C:HOH505 4.8 43.8 1.0
O C:HOH478 4.9 35.5 1.0
HB2 C:SER166 5.0 38.6 1.0

Calcium binding site 10 out of 19 in 5mfo

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Calcium binding site 10 out of 19 in the Designed Armadillo Repeat Protein YIIIM3AIII


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 YIIIM3AIII within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:15.2
occ:1.00
O D:SER124 2.3 18.5 0.8
O D:HOH542 2.4 16.5 1.0
O D:HOH551 2.5 24.4 1.0
O D:GLY125 2.5 16.4 1.0
O D:SER124 2.6 16.6 0.2
C D:GLY125 3.4 14.6 1.0
C D:SER124 3.4 14.8 0.8
C D:SER124 3.4 15.7 0.2
HA2 D:GLY125 3.7 19.7 1.0
CA D:GLY125 3.9 16.4 1.0
HA2 D:GLY126 4.0 19.8 1.0
N D:GLY125 4.0 15.3 1.0
HA D:SER124 4.2 19.2 0.2
HA D:SER124 4.2 18.0 0.8
N D:GLY126 4.3 15.6 1.0
O D:HOH446 4.4 22.5 1.0
CA D:SER124 4.4 16.0 0.2
CA D:SER124 4.4 15.0 0.8
O D:HOH617 4.5 31.2 1.0
O D:HOH489 4.5 26.7 1.0
O D:HOH500 4.5 18.0 1.0
CA D:GLY126 4.6 16.5 1.0
HB3 D:SER124 4.7 22.4 0.2
HB2 D:SER124 4.8 22.1 0.8
H D:GLY125 4.8 18.4 0.2
H D:GLY125 4.8 18.4 0.8
HA3 D:GLY125 4.8 19.7 1.0
HD11 D:ILE130 4.9 19.7 1.0
OD1 D:ASN85 4.9 16.9 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: Sat Dec 12 05:37:40 2020

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