Calcium in PDB 7sgx: Crystal Structure of Turtle Cadherin-23 EC1-2

Protein crystallography data

The structure of Crystal Structure of Turtle Cadherin-23 EC1-2, PDB code: 7sgx was solved by C.R.Nisler, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.06 / 3.13
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.984, 94.984, 358.356, 90, 90, 90
R / Rfree (%) 25.3 / 31

Other elements in 7sgx:

The structure of Crystal Structure of Turtle Cadherin-23 EC1-2 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 31;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Turtle Cadherin-23 EC1-2 (pdb code 7sgx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 31 binding sites of Calcium where determined in the Crystal Structure of Turtle Cadherin-23 EC1-2, PDB code: 7sgx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 31 in 7sgx

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Calcium binding site 1 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:77.7
occ:1.00
 O A:GLY139 2.2 84.8 1.0
OD1 A:ASN101 2.2 103.3 1.0
OD2 A:ASP184 2.2 84.7 1.0
O A:ASN103 2.3 90.2 1.0
OD2 A:ASP135 2.4 91.7 1.0
OD1 A:ASP133 2.6 103.0 1.0
OD2 A:ASP133 3.0 107.3 1.0
CG A:ASP133 3.1 102.2 1.0
C A:GLY139 3.2 90.5 1.0
CG A:ASN101 3.4 102.0 1.0
CG A:ASP184 3.4 91.2 1.0
CG A:ASP135 3.4 91.5 1.0
C A:ASN103 3.5 92.8 1.0
CA A:GLY139 3.7 92.1 1.0
CB A:ASP135 3.7 91.1 1.0
CB A:ASP184 3.9 93.1 1.0
ND2 A:ASN101 4.0 109.8 1.0
N A:GLY140 4.3 98.2 1.0
CA A:ASN103 4.4 94.2 1.0
CD1 A:LEU191 4.4 91.7 1.0
OD1 A:ASP184 4.4 95.2 1.0
N A:ASN103 4.4 96.5 1.0
CB A:ASP133 4.5 101.8 1.0
CB A:ASN103 4.5 96.0 1.0
N A:ALA104 4.5 89.5 1.0
OD1 A:ASP135 4.5 96.0 1.0
CB A:ASN101 4.6 100.1 1.0
CA A:ALA104 4.8 89.2 1.0
CA A:ASN101 4.8 96.8 1.0
CA A:GLY140 4.8 106.1 1.0
C A:ALA104 5.0 92.0 1.0
CB A:LEU191 5.0 93.6 1.0

Calcium binding site 2 out of 31 in 7sgx

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Calcium binding site 2 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:82.6
occ:1.00
 OD1 A:ASP99 2.4 111.0 1.0
OD1 A:ASP135 2.4 96.0 1.0
OD1 A:ASP102 2.4 78.9 1.0
O A:VAL100 2.4 91.1 1.0
OE1 A:GLU19 2.6 104.2 1.0
OE1 A:GLU71 2.6 86.8 1.0
OE2 A:GLU71 2.8 94.3 1.0
CD A:GLU71 3.0 98.8 1.0
CG A:ASP99 3.4 108.5 1.0
CD A:GLU19 3.5 104.9 1.0
CG A:ASP102 3.6 87.3 1.0
CG A:ASP135 3.6 91.5 1.0
C A:VAL100 3.7 92.9 1.0
OE2 A:GLU19 3.7 100.4 1.0
OD2 A:ASP99 3.8 108.4 1.0
NH1 A:ARG70 3.9 123.7 1.0
CA A:CA303 3.9 86.7 1.0
N A:VAL100 4.0 93.6 1.0
OD2 A:ASP102 4.0 79.5 1.0
ND2 A:ASN103 4.1 103.7 1.0
CA A:ASP135 4.3 96.2 1.0
N A:ASP102 4.3 88.3 1.0
CB A:ASP135 4.3 91.1 1.0
CA A:VAL100 4.5 97.7 1.0
CG A:GLU71 4.5 109.2 1.0
NE A:ARG70 4.5 119.3 1.0
OD2 A:ASP135 4.6 91.7 1.0
CB A:ASP99 4.6 106.1 1.0
N A:ASN101 4.6 94.4 1.0
CZ A:ARG70 4.7 119.8 1.0
CA A:ASP99 4.7 99.0 1.0
CB A:ASP102 4.8 94.5 1.0
CG A:GLU19 4.8 104.3 1.0
CA A:ASN101 4.8 96.8 1.0
C A:ASP99 4.9 94.8 1.0
CG2 A:VAL100 4.9 107.6 1.0

Calcium binding site 3 out of 31 in 7sgx

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Calcium binding site 3 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:86.7
occ:1.00
 OD2 A:ASP102 2.1 79.5 1.0
OD1 A:ASP69 2.2 121.7 1.0
OE2 A:GLU71 2.4 94.3 1.0
OE1 A:GLU19 3.0 104.2 1.0
CG A:ASP102 3.1 87.3 1.0
CG A:ASP69 3.2 124.2 1.0
OD1 A:ASP102 3.4 78.9 1.0
CD A:GLU19 3.5 104.9 1.0
CD A:GLU71 3.5 98.8 1.0
OE2 A:GLU19 3.6 100.4 1.0
OD2 A:ASP69 3.8 124.2 1.0
CA A:CA302 3.9 82.6 1.0
ND2 A:ASN103 4.1 103.7 1.0
CG A:GLU71 4.2 109.2 1.0
CB A:ASP69 4.3 127.3 1.0
CB A:ASP102 4.4 94.5 1.0
CB A:GLU71 4.4 114.2 1.0
OE1 A:GLU71 4.5 86.8 1.0
CG A:GLU19 4.5 104.3 1.0
CA A:ASP69 4.7 126.4 1.0
N A:ARG70 4.8 122.5 1.0
N A:GLU71 4.9 126.8 1.0

Calcium binding site 4 out of 31 in 7sgx

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Calcium binding site 4 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:106.2
occ:1.00
 O A:ARG2 2.2 133.4 1.0
OD2 A:ASP34 2.7 120.2 1.0
OD2 A:ASP84 2.9 122.6 1.0
OD1 A:ASP84 3.0 131.5 1.0
OD1 A:ASP38 3.0 118.3 1.0
OD1 A:ASN1 3.1 139.5 1.0
OD1 A:ASP34 3.1 116.4 1.0
ND2 A:ASN1 3.2 134.3 1.0
CG A:ASP34 3.3 119.5 1.0
CG A:ASP84 3.3 128.9 1.0
C A:ARG2 3.4 136.2 1.0
CG A:ASN1 3.4 137.1 1.0
CB A:ASP36 3.5 127.5 1.0
N A:ARG2 3.6 135.9 1.0
CG A:ASP36 3.7 130.1 1.0
CG A:ASP38 3.8 121.2 1.0
OD2 A:ASP36 4.0 133.2 1.0
CA A:ARG2 4.0 136.0 1.0
OD1 A:ASP36 4.3 124.5 1.0
C A:ASN1 4.3 133.4 1.0
OD2 A:ASP38 4.3 121.0 1.0
N A:LEU3 4.4 135.1 1.0
CB A:ASN1 4.6 138.4 1.0
CB A:ARG2 4.6 140.8 1.0
N A:ASP36 4.6 125.3 1.0
CA A:ASP36 4.6 125.9 1.0
CA A:ASN1 4.6 136.3 1.0
CA A:LEU3 4.7 133.7 1.0
CB A:ASP34 4.8 119.4 1.0
CB A:ASP38 4.8 122.9 1.0
CB A:ASP84 4.8 131.2 1.0
C A:LEU3 5.0 130.2 1.0

Calcium binding site 5 out of 31 in 7sgx

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Calcium binding site 5 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca305

b:82.5
occ:1.00
 OE1 A:GLU171 2.3 108.4 1.0
O A:VAL204 2.3 102.9 1.0
OE2 A:GLU118 2.3 86.8 1.0
OD2 A:ASP206 2.4 111.3 1.0
OD1 A:ASP203 2.5 72.8 1.0
CD A:GLU171 3.2 103.3 1.0
OE2 A:GLU171 3.4 97.7 1.0
CD A:GLU118 3.4 88.4 1.0
C A:VAL204 3.5 88.3 1.0
CG A:ASP203 3.6 75.5 1.0
CG A:ASP206 3.6 120.0 1.0
N A:VAL204 3.7 75.1 1.0
OE1 A:GLU118 3.8 97.1 1.0
CA A:CA306 4.1 95.0 1.0
OD2 A:ASP203 4.2 71.7 1.0
CA A:VAL204 4.3 78.3 1.0
N A:GLN205 4.4 93.0 1.0
OD1 A:ASP206 4.4 121.8 1.0
CB A:ASP206 4.5 118.4 1.0
N A:ASP206 4.5 112.8 1.0
CA A:GLN205 4.6 98.5 1.0
CG A:GLU171 4.6 100.5 1.0
C A:ASP203 4.7 72.9 1.0
C A:GLN205 4.7 101.9 1.0
CA A:ASP203 4.7 75.5 1.0
CB A:ASP203 4.7 75.0 1.0
CG A:GLU118 4.8 82.4 1.0
CG2 A:VAL204 4.9 72.5 1.0
CB A:TYR170 5.0 67.2 1.0

Calcium binding site 6 out of 31 in 7sgx

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Calcium binding site 6 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca306

b:95.0
occ:1.00
 OD1 A:ASP169 2.3 97.9 1.0
OE1 A:GLU118 2.4 97.1 1.0
OE2 A:GLU171 2.4 97.7 1.0
OD2 A:ASP206 2.7 111.3 1.0
CG A:ASP206 3.2 120.0 1.0
CD A:GLU118 3.4 88.4 1.0
CG A:ASP169 3.4 91.3 1.0
CD A:GLU171 3.6 103.3 1.0
OD1 A:ASP206 3.8 121.8 1.0
OE2 A:GLU118 3.8 86.8 1.0
CB A:ASP206 4.0 118.4 1.0
CA A:CA305 4.1 82.5 1.0
OD2 A:ASP169 4.1 96.8 1.0
OE1 A:GLU171 4.2 108.4 1.0
CB A:ASP169 4.4 86.3 1.0
CA A:ASP169 4.5 79.9 1.0
N A:TYR170 4.6 69.1 1.0
CG A:GLU118 4.7 82.4 1.0
CG A:GLU171 4.8 100.5 1.0
CB A:GLU171 5.0 94.0 1.0
N A:GLU171 5.0 78.3 1.0

Calcium binding site 7 out of 31 in 7sgx

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Calcium binding site 7 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca307

b:75.4
occ:1.00
 O A:ASP133 2.3 100.2 1.0
O A:GLY140 2.4 110.1 1.0
C A:GLY140 3.5 106.6 1.0
C A:ASP133 3.5 100.9 1.0
O A:HOH408 3.7 60.4 1.0
CA A:GLY140 4.0 106.1 1.0
N A:ASP133 4.1 94.4 1.0
CA A:ASP133 4.3 98.7 1.0
N A:PRO134 4.5 106.3 1.0
CB A:ASP133 4.6 101.8 1.0
N A:SER141 4.7 103.8 1.0
CA A:PRO134 4.7 108.0 1.0
O A:ASP135 4.7 94.2 1.0

Calcium binding site 8 out of 31 in 7sgx

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Calcium binding site 8 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:106.0
occ:1.00
 OD2 B:ASP135 2.2 96.7 1.0
O B:ASN103 2.3 80.1 1.0
O B:GLY139 2.3 102.8 1.0
OD1 B:ASN101 2.4 114.0 1.0
OD2 B:ASP133 2.4 113.5 1.0
OD2 B:ASP184 2.5 140.6 1.0
OD1 B:ASP133 2.5 112.8 1.0
CG B:ASP133 2.8 111.8 1.0
CG B:ASP135 3.4 105.0 1.0
CG B:ASN101 3.4 113.3 1.0
C B:GLY139 3.5 114.3 1.0
C B:ASN103 3.5 88.3 1.0
CG B:ASP184 3.5 128.7 1.0
CB B:ASP184 3.8 121.4 1.0
CB B:ASP135 3.9 108.9 1.0
ND2 B:ASN101 3.9 116.1 1.0
CA B:GLY139 4.1 117.5 1.0
CB B:ASP133 4.3 107.1 1.0
N B:ALA104 4.4 90.7 1.0
OD1 B:ASP135 4.4 105.7 1.0
CA B:ASN103 4.5 94.3 1.0
CA B:ALA104 4.5 98.4 1.0
N B:GLY140 4.5 113.6 1.0
N B:ASN103 4.6 97.6 1.0
OD1 B:ASP184 4.7 136.5 1.0
CB B:ASN101 4.7 112.2 1.0
CB B:ASN103 4.7 96.3 1.0
CD1 B:LEU191 4.7 101.6 1.0
C B:ALA104 4.7 104.4 1.0
CB B:LEU191 4.8 107.2 1.0
CA B:ASN101 4.9 110.1 1.0
CA B:GLY140 4.9 110.8 1.0

Calcium binding site 9 out of 31 in 7sgx

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Calcium binding site 9 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:85.5
occ:1.00
 O B:VAL100 2.3 98.9 1.0
OD1 B:ASP102 2.3 113.5 1.0
OD1 B:ASP135 2.7 105.7 1.0
OE2 B:GLU19 2.8 107.6 1.0
OD1 B:ASP99 3.0 102.0 1.0
OD2 B:ASP99 3.0 103.3 1.0
OE1 B:GLU71 3.0 114.0 1.0
OE2 B:GLU71 3.1 120.5 1.0
CG B:ASP99 3.2 107.3 1.0
CG B:ASP102 3.3 112.3 1.0
CD B:GLU19 3.4 116.5 1.0
OE1 B:GLU19 3.4 120.4 1.0
CD B:GLU71 3.4 122.1 1.0
C B:VAL100 3.5 100.2 1.0
CG B:ASP135 3.8 105.0 1.0
N B:VAL100 3.8 97.7 1.0
N B:ASP102 4.0 105.3 1.0
OD2 B:ASP102 4.1 119.3 1.0
CA B:CA303 4.2 96.4 1.0
CB B:ASP102 4.2 111.5 1.0
CA B:VAL100 4.3 97.0 1.0
CB B:ASP135 4.3 108.9 1.0
CA B:ASP135 4.4 111.2 1.0
N B:ASN101 4.5 107.2 1.0
CB B:ASP99 4.6 108.7 1.0
ND2 B:ASN103 4.6 101.5 1.0
CA B:ASP102 4.6 107.9 1.0
CG B:GLU19 4.7 117.8 1.0
CA B:ASN101 4.7 110.1 1.0
OD2 B:ASP135 4.8 96.7 1.0
C B:ASP99 4.8 99.2 1.0
CB B:VAL100 4.8 94.4 1.0
CA B:ASP99 4.8 104.6 1.0
C B:ASN101 4.9 108.7 1.0
N B:ASN103 4.9 97.6 1.0
CG B:GLU71 4.9 126.8 1.0

Calcium binding site 10 out of 31 in 7sgx

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Calcium binding site 10 out of 31 in the Crystal Structure of Turtle Cadherin-23 EC1-2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Turtle Cadherin-23 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:96.4
occ:1.00
 OD2 B:ASP102 2.2 119.3 1.0
OD1 B:ASP69 2.2 110.9 1.0
OE2 B:GLU71 2.5 120.5 1.0
OE2 B:GLU19 2.8 107.6 1.0
CG B:ASP69 3.0 110.8 1.0
CG B:ASP102 3.1 112.3 1.0
OD1 B:ASP102 3.4 113.5 1.0
OD2 B:ASP69 3.4 112.9 1.0
CD B:GLU19 3.5 116.5 1.0
CD B:GLU71 3.7 122.1 1.0
OE1 B:GLU19 3.8 120.4 1.0
CB B:ASP69 4.2 106.9 1.0
ND2 B:ASN103 4.2 101.5 1.0
CA B:CA302 4.2 85.5 1.0
CB B:ASP102 4.4 111.5 1.0
CG B:GLU71 4.5 126.8 1.0
CA B:ASP69 4.5 109.4 1.0
OE1 B:GLU71 4.6 114.0 1.0
CB B:GLU71 4.7 127.2 1.0
CG B:GLU19 4.7 117.8 1.0

Reference:

C.R.Nisler, M.Sotomayor. Crystal Structure of Turtle Cadherin-23 EC1-2 To Be Published.
Page generated: Fri Jul 19 04:01:25 2024

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