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Calcium in PDB 4v3o: Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.

Protein crystallography data

The structure of Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap., PDB code: 4v3o was solved by C.Reichen, C.Madhurantakam, A.Pluckthun, P.Mittl, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 111.11 / 2.00
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 102.586, 102.586, 111.107, 90.00, 90.00, 90.00
R / Rfree (%) 16.786 / 22.426

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. (pdb code 4v3o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap., PDB code: 4v3o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 4v3o

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Calcium binding site 1 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1293

b:21.9
occ:1.00
 O A:HOH2174 2.2 18.5 1.0
O D:PRO65 2.3 25.1 1.0
O A:PRO149 2.4 25.5 1.0
O A:HOH2176 2.4 23.2 1.0
OE1 D:GLU67 2.4 21.6 1.0
O A:HOH2175 2.4 24.0 1.0
OE1 A:GLU151 2.4 22.2 1.0
CD A:GLU151 3.4 24.9 1.0
CD D:GLU67 3.4 22.7 1.0
C D:PRO65 3.5 22.2 1.0
OE2 A:GLU151 3.5 29.7 1.0
C A:PRO149 3.5 23.6 1.0
OE2 D:GLU67 3.7 24.9 1.0
CA D:ASN66 4.0 22.4 1.0
N D:GLU67 4.2 21.7 1.0
N D:ASN66 4.2 21.4 1.0
CA A:ASN150 4.2 20.3 1.0
N A:ASN150 4.3 21.7 1.0
N A:GLU151 4.4 19.6 1.0
O D:HOH2049 4.4 35.6 1.0
CA A:PRO149 4.6 26.8 1.0
CA D:PRO65 4.6 25.8 1.0
C D:ASN66 4.6 20.7 1.0
CB D:PRO65 4.7 25.9 1.0
CB A:PRO149 4.7 26.0 1.0
CG D:GLU67 4.7 22.3 1.0
CG A:GLU151 4.8 23.9 1.0
C A:ASN150 4.9 19.4 1.0

Calcium binding site 2 out of 12 in 4v3o

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Calcium binding site 2 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1294

b:30.5
occ:1.00
 O A:HOH2088 2.2 43.2 1.0
O A:HOH2089 2.3 36.0 1.0
O A:PRO65 2.4 32.9 1.0
O D:PRO149 2.4 31.7 1.0
OE1 D:GLU151 2.4 31.0 1.0
OE1 A:GLU67 2.4 26.7 1.0
CD A:GLU67 3.3 27.8 1.0
CD D:GLU151 3.3 31.2 1.0
C D:PRO149 3.5 29.4 1.0
C A:PRO65 3.5 28.6 1.0
OE2 A:GLU67 3.5 33.0 1.0
OE2 D:GLU151 3.6 37.7 1.0
CA A:ASN66 4.1 25.4 1.0
CA D:ASN150 4.1 26.4 1.0
O D:HOH2091 4.2 52.9 1.0
N A:ASN66 4.2 27.9 1.0
N D:ASN150 4.3 27.0 1.0
N D:GLU151 4.3 26.8 1.0
N A:GLU67 4.3 25.5 1.0
CA D:PRO149 4.5 30.8 1.0
CA A:PRO65 4.6 31.4 1.0
CB D:PRO149 4.6 31.7 1.0
CG A:GLU67 4.7 26.0 1.0
CG D:GLU151 4.7 28.4 1.0
CB A:PRO65 4.7 29.1 1.0
C A:ASN66 4.7 26.2 1.0
C D:ASN150 4.8 25.8 1.0
O D:HOH2089 4.9 46.0 1.0

Calcium binding site 3 out of 12 in 4v3o

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Calcium binding site 3 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1295

b:25.9
occ:1.00
 O A:HOH2136 2.0 40.8 1.0
O A:HOH2138 2.2 42.2 1.0
O A:PRO107 2.3 27.0 1.0
O D:PRO107 2.4 24.8 1.0
OE1 A:GLU109 2.4 22.4 1.0
OE1 D:GLU109 2.4 27.6 1.0
O A:HOH2137 2.4 43.4 1.0
CD A:GLU109 3.1 23.4 1.0
OE2 A:GLU109 3.1 31.9 1.0
CD D:GLU109 3.2 26.9 1.0
OE2 D:GLU109 3.3 34.6 1.0
C A:PRO107 3.5 24.3 1.0
C D:PRO107 3.6 25.9 1.0
CA A:ASN108 4.1 23.0 1.0
CA D:ASN108 4.2 25.9 1.0
N A:ASN108 4.2 24.2 1.0
N D:GLU109 4.3 24.5 1.0
N A:GLU109 4.3 19.2 1.0
N D:ASN108 4.3 26.4 1.0
CG A:GLU109 4.5 22.5 1.0
CA A:PRO107 4.6 25.4 1.0
CA D:PRO107 4.6 26.9 1.0
CG D:GLU109 4.7 25.0 1.0
CB A:PRO107 4.7 26.0 1.0
CB D:PRO107 4.7 26.9 1.0
C A:ASN108 4.8 21.5 1.0
C D:ASN108 4.8 26.7 1.0
O A:HOH2134 4.9 32.3 1.0

Calcium binding site 4 out of 12 in 4v3o

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Calcium binding site 4 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1296

b:29.0
occ:1.00
 O A:HOH2212 2.2 32.6 1.0
O A:HOH2213 2.3 37.0 1.0
O A:PRO191 2.3 29.9 1.0
O D:PRO23 2.4 27.1 1.0
OE1 D:GLN25 2.5 30.9 1.0
OE1 A:GLU193 2.5 29.5 1.0
O A:HOH2215 2.6 39.6 1.0
OE2 A:GLU193 2.7 36.9 1.0
CD A:GLU193 3.0 30.7 1.0
CD D:GLN25 3.5 34.1 1.0
C A:PRO191 3.6 26.2 1.0
C D:PRO23 3.6 28.9 1.0
NE2 D:GLN25 3.9 43.6 1.0
CA D:ASP24 4.1 27.5 1.0
N D:GLN25 4.2 24.8 1.0
N D:ASP24 4.3 26.9 1.0
N A:GLU193 4.4 21.4 1.0
CA A:ASN192 4.4 23.6 1.0
N A:ASN192 4.4 23.1 1.0
CG A:GLU193 4.5 29.1 1.0
CA A:PRO191 4.5 26.0 1.0
CA D:PRO23 4.7 25.9 1.0
C D:ASP24 4.7 24.4 1.0
O A:HOH2210 4.8 35.1 1.0
CB A:PRO191 4.8 25.4 1.0
CG D:GLN25 4.9 26.2 1.0
C A:ASN192 4.9 24.6 1.0
CB D:PRO23 4.9 25.9 1.0

Calcium binding site 5 out of 12 in 4v3o

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Calcium binding site 5 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1293

b:28.7
occ:1.00
 O B:HOH2191 2.2 32.8 1.0
O B:PRO191 2.3 29.6 1.0
O B:HOH2190 2.3 37.7 1.0
O C:PRO23 2.4 28.4 1.0
OE1 C:GLN25 2.5 28.5 1.0
OE1 B:GLU193 2.5 27.0 1.0
O B:HOH2193 2.6 41.5 1.0
OE2 B:GLU193 2.8 34.3 1.0
CD B:GLU193 3.0 28.3 1.0
CD C:GLN25 3.5 32.9 1.0
C B:PRO191 3.6 26.5 1.0
C C:PRO23 3.6 28.1 1.0
NE2 C:GLN25 3.9 42.0 1.0
CA C:ASP24 4.2 27.7 1.0
N C:GLN25 4.2 27.6 1.0
N B:GLU193 4.4 22.6 1.0
N C:ASP24 4.4 26.6 1.0
CA B:ASN192 4.4 24.3 1.0
N B:ASN192 4.4 22.9 1.0
CA B:PRO191 4.5 27.8 1.0
CG B:GLU193 4.5 27.0 1.0
O B:HOH2188 4.6 34.9 1.0
CA C:PRO23 4.7 25.6 1.0
CB B:PRO191 4.7 26.0 1.0
C C:ASP24 4.8 24.8 1.0
CG C:GLN25 4.9 26.6 1.0
CB C:PRO23 4.9 25.7 1.0
C B:ASN192 4.9 24.3 1.0

Calcium binding site 6 out of 12 in 4v3o

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Calcium binding site 6 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1294

b:32.6
occ:1.00
 OE1 B:GLU44 2.2 33.0 1.0
O A:SER124 2.4 22.5 1.0
O A:HOH2108 2.4 23.1 1.0
O B:HOH2041 2.4 31.8 1.0
O A:HOH2150 2.5 26.2 1.0
O A:HOH2149 2.5 21.7 1.0
O B:HOH2036 2.6 27.0 1.0
CD B:GLU44 3.4 35.8 1.0
C A:SER124 3.5 22.9 1.0
CA A:GLY125 4.2 25.0 1.0
CB B:GLU44 4.2 30.5 1.0
OE2 B:GLU44 4.2 43.3 1.0
N A:GLY125 4.3 23.2 1.0
O A:HOH2106 4.3 19.4 1.0
CG B:GLU44 4.4 31.3 1.0
CA B:GLU44 4.4 27.8 1.0
CB A:SER124 4.5 23.1 1.0
OG A:SER124 4.5 24.9 1.0
OD1 A:ASN85 4.5 25.9 1.0
O A:HOH2109 4.5 35.7 1.0
CA A:SER124 4.5 21.7 1.0
O A:GLY125 4.6 26.0 1.0
C A:GLY125 4.6 26.0 1.0
O B:HOH2050 4.6 29.2 1.0
O B:HOH2040 4.7 34.5 1.0
O B:HOH2039 4.9 49.4 1.0
N B:GLU44 5.0 24.8 1.0

Calcium binding site 7 out of 12 in 4v3o

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Calcium binding site 7 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1295

b:31.1
occ:1.00
 OE1 A:GLU44 2.2 31.8 1.0
O B:SER124 2.3 20.6 1.0
O B:HOH2091 2.4 22.2 1.0
O A:HOH2051 2.4 33.0 1.0
O A:HOH2052 2.5 28.2 1.0
O A:HOH2053 2.5 28.9 1.0
O A:HOH2055 2.5 22.0 1.0
C B:SER124 3.5 22.3 1.0
CD A:GLU44 3.5 37.0 1.0
CA B:GLY125 4.1 24.6 1.0
N B:GLY125 4.2 23.6 1.0
O B:HOH2089 4.3 24.7 1.0
OE2 A:GLU44 4.3 45.6 1.0
CB A:GLU44 4.3 31.6 1.0
OG B:SER124 4.4 24.7 1.0
OD1 B:ASN85 4.4 25.2 1.0
CG A:GLU44 4.5 32.8 1.0
CA A:GLU44 4.5 26.4 1.0
CB B:SER124 4.5 21.4 1.0
CA B:SER124 4.5 21.8 1.0
O B:GLY125 4.6 25.0 1.0
C B:GLY125 4.6 25.6 1.0
O B:HOH2092 4.6 32.4 1.0
O A:HOH2054 4.6 34.3 1.0
O A:HOH2066 4.7 28.9 1.0

Calcium binding site 8 out of 12 in 4v3o

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Calcium binding site 8 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1296

b:30.1
occ:1.00
 O B:HOH2075 1.9 41.4 1.0
O B:HOH2074 2.3 37.9 1.0
O B:HOH2076 2.3 43.2 1.0
OE1 C:GLU151 2.3 31.5 1.0
O C:PRO149 2.4 29.4 1.0
O B:PRO65 2.4 33.2 1.0
OE1 B:GLU67 2.4 29.1 1.0
CD C:GLU151 3.3 33.0 1.0
CD B:GLU67 3.3 29.9 1.0
OE2 B:GLU67 3.5 31.9 1.0
C C:PRO149 3.5 29.5 1.0
C B:PRO65 3.5 30.2 1.0
OE2 C:GLU151 3.5 37.8 1.0
CA B:ASN66 4.1 25.6 1.0
CA C:ASN150 4.2 29.1 1.0
N C:GLU151 4.2 25.7 1.0
N B:ASN66 4.2 27.5 1.0
N C:ASN150 4.3 29.0 1.0
N B:GLU67 4.3 24.5 1.0
CA C:PRO149 4.6 31.4 1.0
CA B:PRO65 4.6 32.5 1.0
CG C:GLU151 4.7 29.7 1.0
CB C:PRO149 4.7 33.3 1.0
CG B:GLU67 4.7 27.1 1.0
C B:ASN66 4.7 25.6 1.0
C C:ASN150 4.7 26.0 1.0
CB B:PRO65 4.8 30.4 1.0

Calcium binding site 9 out of 12 in 4v3o

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Calcium binding site 9 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1297

b:25.7
occ:1.00
 O B:HOH2116 2.2 35.9 1.0
O B:HOH2118 2.2 42.7 1.0
O B:HOH2117 2.3 41.3 1.0
O C:PRO107 2.3 23.6 1.0
O B:PRO107 2.3 23.1 1.0
OE1 B:GLU109 2.4 24.6 1.0
OE1 C:GLU109 2.5 25.6 1.0
CD B:GLU109 3.1 23.0 1.0
OE2 B:GLU109 3.2 29.4 1.0
CD C:GLU109 3.3 26.1 1.0
OE2 C:GLU109 3.4 32.2 1.0
C C:PRO107 3.5 25.0 1.0
C B:PRO107 3.5 22.6 1.0
CA B:ASN108 4.2 23.1 1.0
CA C:ASN108 4.2 23.9 1.0
N B:ASN108 4.3 23.3 1.0
N C:ASN108 4.3 24.2 1.0
N B:GLU109 4.4 18.6 1.0
N C:GLU109 4.4 22.4 1.0
CA C:PRO107 4.6 25.8 1.0
CG B:GLU109 4.6 21.9 1.0
CA B:PRO107 4.6 23.5 1.0
CG C:GLU109 4.7 24.6 1.0
CB C:PRO107 4.7 26.5 1.0
CB B:PRO107 4.8 25.7 1.0
C C:ASN108 4.8 24.1 1.0
C B:ASN108 4.8 20.2 1.0
O B:HOH2114 4.8 34.5 1.0

Calcium binding site 10 out of 12 in 4v3o

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Calcium binding site 10 out of 12 in the Designed Armadillo Repeat Protein with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap.


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 with 5 Internal Repeats, 2ND Generation C-Cap and 3RD Generation N-Cap. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1292

b:22.1
occ:1.00
 O B:HOH2158 2.2 20.2 1.0
O C:PRO65 2.4 21.8 1.0
O B:PRO149 2.4 23.9 1.0
O B:HOH2161 2.4 24.1 1.0
O B:HOH2157 2.4 20.8 1.0
OE1 C:GLU67 2.4 20.3 1.0
OE1 B:GLU151 2.5 22.6 1.0
CD B:GLU151 3.4 22.7 1.0
CD C:GLU67 3.4 20.7 1.0
C C:PRO65 3.5 22.3 1.0
C B:PRO149 3.5 23.7 1.0
OE2 B:GLU151 3.6 27.5 1.0
O C:HOH2112 3.6 38.1 1.0
OE2 C:GLU67 3.7 23.4 1.0
CA C:ASN66 4.0 21.6 1.0
N C:ASN66 4.2 20.6 1.0
N C:GLU67 4.2 21.1 1.0
CA B:ASN150 4.2 20.2 1.0
N B:ASN150 4.3 21.5 1.0
O C:HOH2052 4.3 31.6 1.0
N B:GLU151 4.4 18.6 1.0
CA B:PRO149 4.6 26.9 1.0
CA C:PRO65 4.6 24.7 1.0
C C:ASN66 4.6 20.9 1.0
CB C:PRO65 4.7 26.1 1.0
CB B:PRO149 4.7 26.3 1.0
CG C:GLU67 4.8 21.6 1.0
CG B:GLU151 4.8 22.7 1.0
C B:ASN150 4.9 18.6 1.0

Reference:

C.Reichen, C.Madhurantakam, S.Hansen, M.G.Grutter, A.Pluckthun, P.R.E.Mittl. Structures of Designed Armadillo-Repeat Proteins Show Propagation of Inter-Repeat Interface Effects Acta Crystallogr.,Sect.D V. 72 168 2016.
ISSN: ISSN 0907-4449
PubMed: 26894544
DOI: 10.1107/S2059798315023116
Page generated: Sun Jul 14 13:57:34 2024

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