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Calcium in PDB 2a62: Crystal Structure of Mouse Cadherin-8 EC1-3

Protein crystallography data

The structure of Crystal Structure of Mouse Cadherin-8 EC1-3, PDB code: 2a62 was solved by S.D.Patel, C.Ciatto, C.P.Chen, F.Bahna, N.Arkus, I.Schieren, T.M.Jessell, B.Honig, S.R.Price, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 4.50
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 75.818, 75.818, 233.760, 90.00, 90.00, 90.00
R / Rfree (%) 27.1 / 34.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-8 EC1-3 (pdb code 2a62). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Mouse Cadherin-8 EC1-3, PDB code: 2a62:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2a62

Go back to Calcium Binding Sites List in 2a62
Calcium binding site 1 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca323

b:0.6
occ:1.00
 OD2 A:ASP132 1.9 0.2 1.0
O A:ASN102 2.2 0.2 1.0
OD1 A:ASN100 2.2 0.3 1.0
OD1 A:ASP132 2.5 0.8 1.0
CG A:ASP132 2.5 0.8 1.0
OD2 A:ASP187 2.9 0.9 1.0
OD2 A:ASP134 3.0 0.3 1.0
O A:SER141 3.1 1.0 1.0
C A:ASN102 3.2 0.3 1.0
CB A:ASP134 3.3 0.5 1.0
CG A:ASN100 3.3 0.3 1.0
OD1 A:ASP187 3.4 1.0 1.0
CG A:ASP187 3.5 0.9 1.0
CG A:ASP134 3.5 0.3 1.0
CB A:ASN102 3.8 0.5 1.0
CA A:ASN102 3.8 0.4 1.0
N A:ASN102 3.9 0.4 1.0
N A:ASP134 4.0 0.3 1.0
ND2 A:ASN100 4.0 0.5 1.0
CB A:ASP132 4.0 0.5 1.0
N A:ALA103 4.2 0.4 1.0
CA A:ASP134 4.2 0.6 1.0
C A:SER141 4.3 0.1 1.0
CD2 A:LEU195 4.3 0.6 1.0
CA A:ASN100 4.4 0.4 1.0
CB A:ASN100 4.4 0.3 1.0
N A:ALA133 4.5 0.9 1.0
C A:ASN100 4.6 0.3 1.0
OD1 A:ASP134 4.7 0.7 1.0
CA A:ALA103 4.7 0.6 1.0
CA A:ASP132 4.8 0.8 1.0
CB A:ASP187 4.8 0.9 1.0
C A:ALA103 4.9 0.6 1.0
O A:ASN100 4.9 0.3 1.0
ND2 A:ASN102 4.9 0.8 1.0
CG A:ASN102 4.9 0.8 1.0
O A:ALA103 4.9 0.9 1.0
C A:ASP132 4.9 0.9 1.0

Calcium binding site 2 out of 6 in 2a62

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Calcium binding site 2 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca324

b:0.2
occ:1.00
 OD1 A:ASP101 2.0 0.4 1.0
OD2 A:ASP98 2.0 0.1 1.0
ND2 A:ASN102 2.3 0.8 1.0
OE2 A:GLU11 2.3 0.8 1.0
O A:ILE99 2.3 0.7 1.0
OE2 A:GLU66 2.8 0.6 1.0
CG A:ASP101 3.2 0.8 1.0
CG A:ASP98 3.2 0.9 1.0
CD A:GLU11 3.3 0.9 1.0
OD1 A:ASP134 3.3 0.7 1.0
OD2 A:ASP134 3.3 0.3 1.0
CA A:CA325 3.4 0.1 1.0
CG A:ASN102 3.4 0.8 1.0
CD A:GLU66 3.4 0.6 1.0
C A:ILE99 3.5 0.6 1.0
CG A:ASP134 3.6 0.3 1.0
N A:ILE99 3.7 0.6 1.0
OD2 A:ASP101 3.7 0.8 1.0
OE1 A:GLU66 3.8 0.4 1.0
OE1 A:GLU11 3.8 0.2 1.0
OD1 A:ASP98 3.9 0.9 1.0
OD1 A:ASN102 3.9 0.2 1.0
N A:ASP101 4.0 0.3 1.0
CA A:ILE99 4.2 0.6 1.0
CG A:GLU11 4.3 0.9 1.0
CB A:ASP101 4.3 0.1 1.0
CA A:ASP98 4.4 1.0 1.0
CB A:ASP98 4.4 0.0 1.0
C A:ASP98 4.4 0.7 1.0
N A:ASN102 4.4 0.4 1.0
CG A:GLU66 4.5 0.8 1.0
CG2 A:ILE99 4.5 0.7 1.0
N A:ASN100 4.6 0.5 1.0
CB A:ASN102 4.6 0.5 1.0
CA A:ASP101 4.6 0.3 1.0
CA A:ASN100 4.9 0.4 1.0
C A:ASP101 4.9 0.4 1.0
CB A:ASP134 4.9 0.5 1.0
C A:ASN100 4.9 0.3 1.0

Calcium binding site 3 out of 6 in 2a62

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Calcium binding site 3 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca325

b:0.1
occ:1.00
 OE1 A:GLU66 2.1 0.4 1.0
OE2 A:GLU12 2.4 0.1 1.0
OD2 A:ASP64 2.4 0.2 1.0
OE2 A:GLU11 2.6 0.8 1.0
OD2 A:ASP101 2.6 0.8 1.0
OE2 A:GLU66 2.8 0.6 1.0
CD A:GLU66 2.8 0.6 1.0
OE1 A:GLU11 2.9 0.2 1.0
CD A:GLU11 3.1 0.9 1.0
OD1 A:ASP101 3.3 0.4 1.0
CD A:GLU12 3.3 0.2 1.0
CG A:ASP64 3.3 0.9 1.0
CG A:ASP101 3.3 0.8 1.0
CA A:CA324 3.4 0.2 1.0
CG A:GLU12 3.6 0.1 1.0
OD1 A:ASP64 3.9 0.9 1.0
OD1 A:ASN102 4.1 0.2 1.0
CA A:ASP64 4.2 0.4 1.0
CB A:ASP64 4.2 0.3 1.0
N A:ARG65 4.3 0.8 1.0
CG A:GLU66 4.3 0.8 1.0
ND2 A:ASN102 4.3 0.8 1.0
OE1 A:GLU12 4.4 0.5 1.0
CG A:GLU11 4.5 0.9 1.0
CG A:ASN102 4.6 0.8 1.0
C A:ASP64 4.7 0.5 1.0
CB A:ASP101 4.8 0.1 1.0
N A:GLU66 4.8 0.7 1.0
OD2 A:ASP98 4.8 0.1 1.0
O A:LEU63 4.9 0.4 1.0
CB A:GLU12 4.9 0.3 1.0
CB A:GLU66 5.0 0.9 1.0

Calcium binding site 4 out of 6 in 2a62

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Calcium binding site 4 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca326

b:0.5
occ:1.00
 OD2 A:ASP241 1.8 0.1 1.0
OD1 A:ASN209 1.9 0.7 1.0
O A:ASN211 2.2 0.5 1.0
OD1 A:ASP241 2.2 0.7 1.0
CG A:ASP241 2.3 0.7 1.0
OD1 A:ASN298 2.5 0.0 1.0
O A:ASN247 2.9 0.8 1.0
CG A:ASN209 2.9 0.0 1.0
C A:ASN211 3.3 0.4 1.0
CG A:ASN298 3.4 0.1 1.0
CB A:ASP243 3.5 0.8 1.0
ND2 A:ASN209 3.6 0.0 1.0
CB A:ASN211 3.7 0.5 1.0
O A:ASN209 3.7 0.3 1.0
CB A:ASP241 3.8 1.0 1.0
CA A:ASN211 3.8 0.5 1.0
OD2 A:ASP243 3.9 0.9 1.0
N A:ASN211 3.9 0.5 1.0
ND2 A:ASN298 4.0 0.5 1.0
CG A:ASP243 4.0 0.4 1.0
CB A:ASN209 4.1 0.1 1.0
C A:ASN247 4.1 0.8 1.0
C A:ASN209 4.1 0.1 1.0
CA A:ASN209 4.2 0.1 1.0
N A:PRO212 4.4 0.5 1.0
O A:ASP243 4.4 0.2 1.0
CB A:ASN298 4.5 0.9 1.0
C A:PRO212 4.6 0.6 1.0
CA A:PRO212 4.7 0.6 1.0
CA A:ASP243 4.7 1.0 1.0
O A:PRO212 4.7 0.5 1.0
CB A:ASN247 4.7 0.7 1.0
CA A:ASP241 4.7 0.0 1.0
N A:ASP243 4.8 0.0 1.0
CA A:ASN247 4.9 0.7 1.0

Calcium binding site 5 out of 6 in 2a62

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Calcium binding site 5 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


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 Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca327

b:0.6
occ:1.00
 CA A:CA328 1.8 0.9 1.0
OD1 A:ASP210 2.1 0.5 1.0
O A:ASP207 2.1 0.5 1.0
OD2 A:ASP207 2.2 0.7 1.0
O A:VAL208 2.4 0.4 1.0
OD2 A:ASP243 2.9 0.9 1.0
OE1 A:GLU117 3.0 0.8 1.0
C A:ASP207 3.1 0.5 1.0
CG A:ASP243 3.1 0.4 1.0
C A:VAL208 3.2 0.2 1.0
CG A:ASP210 3.3 0.1 1.0
CG A:ASP207 3.3 0.7 1.0
OD1 A:ASP243 3.4 0.1 1.0
CG1 A:VAL208 3.5 0.0 1.0
N A:ASP210 3.5 0.9 1.0
CD A:GLU117 3.7 0.1 1.0
CA A:VAL208 3.8 0.1 1.0
OE2 A:GLU117 3.8 0.8 1.0
N A:VAL208 3.8 0.8 1.0
CB A:ASP243 3.9 0.8 1.0
CB A:VAL208 3.9 0.2 1.0
CA A:ASP207 4.0 0.4 1.0
OD2 A:ASP210 4.1 0.2 1.0
NH2 A:ARG173 4.1 0.5 1.0
N A:ASN209 4.1 0.2 1.0
OD1 A:ASP207 4.1 0.4 1.0
CB A:ASP210 4.2 0.6 1.0
CB A:ASP207 4.2 0.6 1.0
OE1 A:GLU174 4.3 0.8 1.0
OE2 A:GLU174 4.3 0.3 1.0
CA A:ASP210 4.3 0.7 1.0
CA A:ASN209 4.3 0.1 1.0
C A:ASN209 4.3 0.1 1.0
CD A:GLU174 4.4 0.8 1.0
CA A:ASP243 4.5 1.0 1.0
C A:ASP210 4.7 0.6 1.0
CZ A:ARG173 4.9 0.5 1.0

Calcium binding site 6 out of 6 in 2a62

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Calcium binding site 6 out of 6 in the Crystal Structure of Mouse Cadherin-8 EC1-3


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 Mouse Cadherin-8 EC1-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca328

b:0.9
occ:1.00
 CA A:CA327 1.8 0.6 1.0
OE1 A:GLU117 2.3 0.8 1.0
OD2 A:ASP207 2.5 0.7 1.0
OD1 A:ASP210 2.6 0.5 1.0
NH2 A:ARG173 2.7 0.5 1.0
OE2 A:GLU174 2.7 0.3 1.0
CD A:GLU174 3.0 0.8 1.0
OD1 A:ASP243 3.0 0.1 1.0
CD A:GLU117 3.2 0.1 1.0
OE1 A:GLU174 3.2 0.8 1.0
O A:ASP207 3.3 0.5 1.0
CG A:ASP243 3.3 0.4 1.0
OE2 A:GLU117 3.4 0.8 1.0
CZ A:ARG173 3.5 0.5 1.0
OD2 A:ASP243 3.6 0.9 1.0
CG A:ASP210 3.7 0.1 1.0
CG A:ASP207 3.7 0.7 1.0
NE A:ARG173 3.7 0.5 1.0
CG A:GLU174 3.8 0.1 1.0
O A:VAL208 4.0 0.4 1.0
OD2 A:ASP210 4.0 0.2 1.0
CB A:ASP243 4.1 0.8 1.0
C A:ASP207 4.2 0.5 1.0
CA A:ASP243 4.3 1.0 1.0
OD1 A:ASP207 4.4 0.4 1.0
OD2 A:ASP172 4.5 0.2 1.0
CA A:ASP207 4.6 0.4 1.0
NH1 A:ARG173 4.6 0.6 1.0
CG A:GLU117 4.6 0.8 1.0
CB A:ARG173 4.8 0.8 1.0
CB A:ASP207 4.8 0.6 1.0
N A:GLU174 4.8 0.1 1.0
N A:ASP210 4.9 0.9 1.0
C A:VAL208 4.9 0.2 1.0
CB A:ASP210 5.0 0.6 1.0

Reference:

S.D.Patel, C.Ciatto, C.P.Chen, F.Bahna, M.Rajebhosale, N.Arkus, I.Schieren, T.M.Jessell, B.Honig, S.R.Price, L.Shapiro. Type II Cadherin Ectodomain Structures: Implications For Classical Cadherin Specificity. Cell(Cambridge,Mass.) V. 124 1255 2006.
ISSN: ISSN 0092-8674
PubMed: 16564015
DOI: 10.1016/J.CELL.2005.12.046
Page generated: Fri Jul 12 08:35:34 2024

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