Calcium in PDB 5ulu: Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
Protein crystallography data
The structure of Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N, PDB code: 5ulu
was solved by
A.Jaiganesh,
M.Sotomayor,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.34 /
2.85
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.238,
65.386,
114.651,
90.00,
98.62,
90.00
|
R / Rfree (%)
|
19.5 /
24.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
(pdb code 5ulu). 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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N, PDB code: 5ulu:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 5ulu
Go back to
Calcium Binding Sites List in 5ulu
Calcium binding site 1 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2301
b:79.5
occ:1.00
|
O
|
A:HOH2403
|
2.1
|
66.5
|
1.0
|
OE2
|
A:GLU2007
|
2.3
|
82.3
|
1.0
|
O
|
A:HOH2404
|
2.4
|
85.0
|
1.0
|
OE2
|
A:GLU1947
|
2.5
|
72.2
|
1.0
|
OD1
|
A:ASP2005
|
2.6
|
95.9
|
1.0
|
OD2
|
A:ASP2041
|
2.7
|
81.1
|
1.0
|
OD1
|
A:ASP2041
|
2.9
|
81.0
|
1.0
|
CG
|
A:ASP2041
|
3.1
|
81.4
|
1.0
|
CG
|
A:ASP2005
|
3.3
|
93.3
|
1.0
|
CD
|
A:GLU1947
|
3.4
|
75.2
|
1.0
|
CD
|
A:GLU2007
|
3.4
|
85.2
|
1.0
|
OE1
|
A:GLU1947
|
3.7
|
69.2
|
1.0
|
OD2
|
A:ASP2005
|
3.8
|
0.5
|
1.0
|
CA
|
A:CA2302
|
3.9
|
81.9
|
1.0
|
ND2
|
A:ASN2042
|
4.0
|
83.3
|
1.0
|
CG
|
A:GLU2007
|
4.0
|
87.7
|
1.0
|
CB
|
A:GLU2007
|
4.1
|
89.8
|
1.0
|
N
|
A:GLU2007
|
4.3
|
90.3
|
1.0
|
CB
|
A:ASP2005
|
4.3
|
89.9
|
1.0
|
CA
|
A:ASP2005
|
4.4
|
90.5
|
1.0
|
CB
|
A:ASP2041
|
4.4
|
83.2
|
1.0
|
N
|
A:ARG2006
|
4.5
|
83.2
|
1.0
|
OE1
|
A:GLU2007
|
4.5
|
85.7
|
1.0
|
ND2
|
A:ASN1948
|
4.6
|
77.1
|
1.0
|
C
|
A:ASP2005
|
4.7
|
88.9
|
1.0
|
CG
|
A:GLU1947
|
4.8
|
78.3
|
1.0
|
OD1
|
A:ASN1948
|
4.8
|
79.8
|
1.0
|
CA
|
A:GLU2007
|
4.9
|
88.8
|
1.0
|
|
Calcium binding site 2 out
of 6 in 5ulu
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Calcium Binding Sites List in 5ulu
Calcium binding site 2 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2302
b:81.9
occ:1.00
|
OE1
|
A:GLU1947
|
2.1
|
69.2
|
1.0
|
O
|
A:ASP2039
|
2.3
|
88.7
|
1.0
|
OD1
|
A:ASP2038
|
2.3
|
76.9
|
1.0
|
OD1
|
A:ASP2074
|
2.3
|
83.2
|
1.0
|
OE2
|
A:GLU2007
|
2.4
|
82.3
|
1.0
|
OD1
|
A:ASP2041
|
2.6
|
81.0
|
1.0
|
OE1
|
A:GLU2007
|
2.6
|
85.7
|
1.0
|
CD
|
A:GLU2007
|
2.8
|
85.2
|
1.0
|
CD
|
A:GLU1947
|
3.2
|
75.2
|
1.0
|
C
|
A:ASP2039
|
3.4
|
88.5
|
1.0
|
CG
|
A:ASP2074
|
3.5
|
84.5
|
1.0
|
CG
|
A:ASP2038
|
3.5
|
81.9
|
1.0
|
CG
|
A:ASP2041
|
3.6
|
81.4
|
1.0
|
N
|
A:ASP2039
|
3.6
|
85.6
|
1.0
|
OE2
|
A:GLU1947
|
3.7
|
72.2
|
1.0
|
CA
|
A:CA2301
|
3.9
|
79.5
|
1.0
|
ND2
|
A:ASN2042
|
4.0
|
83.3
|
1.0
|
OD2
|
A:ASP2041
|
4.0
|
81.1
|
1.0
|
CA
|
A:ASP2039
|
4.0
|
90.2
|
1.0
|
N
|
A:ASP2041
|
4.1
|
81.5
|
1.0
|
CB
|
A:ASP2074
|
4.2
|
87.9
|
1.0
|
CG
|
A:GLU2007
|
4.2
|
87.7
|
1.0
|
OD2
|
A:ASP2038
|
4.2
|
82.8
|
1.0
|
CB
|
A:ASP2039
|
4.3
|
95.2
|
1.0
|
OD2
|
A:ASP2074
|
4.4
|
82.3
|
1.0
|
NE
|
A:ARG2006
|
4.5
|
0.3
|
1.0
|
C
|
A:ASP2038
|
4.5
|
82.7
|
1.0
|
CG
|
A:GLU1947
|
4.5
|
78.3
|
1.0
|
N
|
A:ASN2040
|
4.5
|
90.3
|
1.0
|
CA
|
A:ASP2074
|
4.5
|
89.2
|
1.0
|
CA
|
A:ASP2038
|
4.5
|
82.9
|
1.0
|
CB
|
A:ASP2038
|
4.6
|
83.8
|
1.0
|
CB
|
A:ASP2041
|
4.8
|
83.2
|
1.0
|
CA
|
A:ASN2040
|
4.8
|
88.8
|
1.0
|
NH2
|
A:ARG2006
|
4.8
|
0.7
|
1.0
|
CB
|
A:ARG2006
|
4.8
|
84.6
|
1.0
|
CA
|
A:ASP2041
|
4.9
|
81.4
|
1.0
|
O
|
A:HOH2404
|
4.9
|
85.0
|
1.0
|
C
|
A:ASN2040
|
5.0
|
87.6
|
1.0
|
|
Calcium binding site 3 out
of 6 in 5ulu
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Calcium Binding Sites List in 5ulu
Calcium binding site 3 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2303
b:83.4
occ:1.00
|
OD1
|
A:ASN2040
|
2.1
|
88.4
|
1.0
|
O
|
A:ASN2042
|
2.2
|
81.5
|
1.0
|
OD2
|
A:ASP2074
|
2.2
|
82.3
|
1.0
|
OD1
|
A:ASP2072
|
2.4
|
82.3
|
1.0
|
OD2
|
A:ASP2072
|
2.4
|
84.9
|
1.0
|
O
|
A:ASN2078
|
2.5
|
88.4
|
1.0
|
OD1
|
A:ASN2125
|
2.5
|
82.7
|
1.0
|
CG
|
A:ASP2072
|
2.8
|
83.3
|
1.0
|
CG
|
A:ASN2040
|
3.3
|
90.9
|
1.0
|
CG
|
A:ASP2074
|
3.4
|
84.5
|
1.0
|
C
|
A:ASN2042
|
3.4
|
80.1
|
1.0
|
CG
|
A:ASN2125
|
3.4
|
84.8
|
1.0
|
C
|
A:ASN2078
|
3.7
|
91.0
|
1.0
|
ND2
|
A:ASN2125
|
3.7
|
85.8
|
1.0
|
CB
|
A:ASP2074
|
3.9
|
87.9
|
1.0
|
ND2
|
A:ASN2040
|
3.9
|
91.7
|
1.0
|
N
|
A:ASN2042
|
4.0
|
75.4
|
1.0
|
CA
|
A:ASN2042
|
4.1
|
81.2
|
1.0
|
CB
|
A:ASN2042
|
4.3
|
87.5
|
1.0
|
CD
|
A:PRO2044
|
4.3
|
76.6
|
1.0
|
CB
|
A:ASP2072
|
4.4
|
84.0
|
1.0
|
OD1
|
A:ASP2074
|
4.4
|
83.2
|
1.0
|
N
|
A:TRP2043
|
4.5
|
79.0
|
1.0
|
CD1
|
A:LEU2131
|
4.5
|
75.1
|
1.0
|
CB
|
A:ASN2040
|
4.5
|
89.7
|
1.0
|
CA
|
A:ASN2078
|
4.5
|
89.0
|
1.0
|
N
|
A:GLY2079
|
4.6
|
95.3
|
1.0
|
CA
|
A:ASN2040
|
4.6
|
88.8
|
1.0
|
CB
|
A:ASN2125
|
4.6
|
84.8
|
1.0
|
CA
|
A:GLY2079
|
4.6
|
95.0
|
1.0
|
CB
|
A:ASN2078
|
4.7
|
87.0
|
1.0
|
CA
|
A:TRP2043
|
4.8
|
77.2
|
1.0
|
C
|
A:ASN2040
|
4.8
|
87.6
|
1.0
|
N
|
A:ASP2074
|
4.8
|
86.3
|
1.0
|
N
|
A:PRO2044
|
4.9
|
77.5
|
1.0
|
C
|
A:TRP2043
|
4.9
|
78.2
|
1.0
|
N
|
A:ASP2041
|
4.9
|
81.5
|
1.0
|
CA
|
A:ASP2074
|
5.0
|
89.2
|
1.0
|
|
Calcium binding site 4 out
of 6 in 5ulu
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Calcium Binding Sites List in 5ulu
Calcium binding site 4 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2304
b:99.5
occ:1.00
|
OD1
|
A:ASP2110
|
2.0
|
0.2
|
1.0
|
OD2
|
A:ASP2146
|
2.2
|
95.4
|
1.0
|
OE2
|
A:GLU2112
|
2.4
|
91.3
|
1.0
|
OD1
|
A:ASP2146
|
2.5
|
94.7
|
1.0
|
OE2
|
A:GLU2057
|
2.5
|
95.0
|
1.0
|
CG
|
A:ASP2146
|
2.7
|
93.7
|
1.0
|
CG
|
A:ASP2110
|
3.1
|
0.5
|
1.0
|
O
|
A:HOH2407
|
3.3
|
77.4
|
1.0
|
CD
|
A:GLU2057
|
3.5
|
93.5
|
1.0
|
CD
|
A:GLU2112
|
3.6
|
86.8
|
1.0
|
OD2
|
A:ASP2110
|
3.7
|
0.6
|
1.0
|
OE1
|
A:GLU2057
|
3.7
|
93.7
|
1.0
|
CA
|
A:CA2305
|
3.9
|
91.0
|
1.0
|
OD1
|
A:ASN2058
|
4.0
|
98.6
|
1.0
|
CB
|
A:ASP2146
|
4.2
|
94.0
|
1.0
|
CB
|
A:ASP2110
|
4.2
|
0.1
|
1.0
|
OG
|
A:SER2147
|
4.3
|
95.6
|
1.0
|
OE1
|
A:GLU2112
|
4.3
|
87.2
|
1.0
|
N
|
A:ARG2111
|
4.4
|
92.7
|
1.0
|
CA
|
A:ASP2110
|
4.4
|
99.2
|
1.0
|
CG
|
A:GLU2112
|
4.5
|
87.2
|
1.0
|
N
|
A:GLU2112
|
4.5
|
90.5
|
1.0
|
CB
|
A:GLU2112
|
4.5
|
89.0
|
1.0
|
ND2
|
A:ASN2058
|
4.7
|
0.4
|
1.0
|
CG
|
A:GLU2057
|
4.8
|
93.0
|
1.0
|
C
|
A:ASP2110
|
4.8
|
97.0
|
1.0
|
CG
|
A:ASN2058
|
4.8
|
0.6
|
1.0
|
C
|
A:ASP2146
|
4.9
|
94.7
|
1.0
|
O
|
A:ASP2146
|
4.9
|
99.4
|
1.0
|
|
Calcium binding site 5 out
of 6 in 5ulu
Go back to
Calcium Binding Sites List in 5ulu
Calcium binding site 5 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2305
b:91.0
occ:1.00
|
OE1
|
A:GLU2112
|
2.0
|
87.2
|
1.0
|
O
|
A:ILE2144
|
2.1
|
89.8
|
1.0
|
OE1
|
A:GLU2057
|
2.2
|
93.7
|
1.0
|
OD1
|
A:ASP2179
|
2.3
|
93.4
|
1.0
|
OD1
|
A:ASP2143
|
2.4
|
91.4
|
1.0
|
OD1
|
A:ASP2146
|
2.6
|
94.7
|
1.0
|
CD
|
A:GLU2112
|
2.7
|
86.8
|
1.0
|
OE2
|
A:GLU2112
|
2.7
|
91.3
|
1.0
|
CD
|
A:GLU2057
|
3.3
|
93.5
|
1.0
|
C
|
A:ILE2144
|
3.3
|
92.7
|
1.0
|
CG
|
A:ASP2143
|
3.4
|
91.6
|
1.0
|
CG
|
A:ASP2179
|
3.5
|
95.7
|
1.0
|
CG
|
A:ASP2146
|
3.5
|
93.7
|
1.0
|
OE2
|
A:GLU2057
|
3.7
|
95.0
|
1.0
|
N
|
A:ASP2146
|
3.9
|
91.0
|
1.0
|
N
|
A:ILE2144
|
3.9
|
92.7
|
1.0
|
CA
|
A:CA2304
|
3.9
|
99.5
|
1.0
|
OD2
|
A:ASP2143
|
3.9
|
87.5
|
1.0
|
OD2
|
A:ASP2146
|
4.1
|
95.4
|
1.0
|
CG
|
A:GLU2112
|
4.1
|
87.2
|
1.0
|
CB
|
A:ASP2179
|
4.1
|
90.9
|
1.0
|
CA
|
A:ILE2144
|
4.2
|
93.2
|
1.0
|
N
|
A:ASN2145
|
4.3
|
93.9
|
1.0
|
CA
|
A:ASN2145
|
4.4
|
92.2
|
1.0
|
NE
|
A:ARG2111
|
4.4
|
96.6
|
1.0
|
CB
|
A:ASP2146
|
4.4
|
94.0
|
1.0
|
CA
|
A:ASP2179
|
4.4
|
85.8
|
1.0
|
OD2
|
A:ASP2179
|
4.5
|
96.5
|
1.0
|
CB
|
A:ARG2111
|
4.6
|
93.8
|
1.0
|
CB
|
A:ASP2143
|
4.6
|
92.2
|
1.0
|
CG
|
A:GLU2057
|
4.6
|
93.0
|
1.0
|
CA
|
A:ASP2146
|
4.6
|
93.0
|
1.0
|
C
|
A:ASN2145
|
4.7
|
97.4
|
1.0
|
CA
|
A:ASP2143
|
4.7
|
91.1
|
1.0
|
C
|
A:ASP2143
|
4.8
|
93.2
|
1.0
|
OG
|
A:SER2147
|
4.8
|
95.6
|
1.0
|
CB
|
A:ILE2144
|
4.8
|
94.8
|
1.0
|
N
|
A:SER2147
|
4.9
|
94.5
|
1.0
|
NH2
|
A:ARG2111
|
5.0
|
94.5
|
1.0
|
|
Calcium binding site 6 out
of 6 in 5ulu
Go back to
Calcium Binding Sites List in 5ulu
Calcium binding site 6 out
of 6 in the Crystal Structure of Mouse Cadherin-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N
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-23 EC19-21 (S2087P) with Non- Syndromic Deafness (DFNB12) Associated Mutation D2148N within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca2306
b:91.6
occ:1.00
|
OD1
|
A:ASN2145
|
2.2
|
91.3
|
1.0
|
OD2
|
A:ASP2239
|
2.2
|
90.8
|
1.0
|
OD2
|
A:ASP2177
|
2.2
|
83.6
|
1.0
|
O
|
A:SER2147
|
2.4
|
92.9
|
1.0
|
OD2
|
A:ASP2179
|
2.6
|
96.5
|
1.0
|
OD1
|
A:ASP2177
|
2.8
|
95.0
|
1.0
|
CG
|
A:ASP2177
|
2.8
|
87.5
|
1.0
|
CG
|
A:ASN2145
|
3.3
|
92.2
|
1.0
|
CG
|
A:ASP2239
|
3.3
|
91.6
|
1.0
|
C
|
A:SER2147
|
3.5
|
95.4
|
1.0
|
CB
|
A:ASP2239
|
3.7
|
90.0
|
1.0
|
OG
|
A:SER2242
|
3.7
|
95.0
|
1.0
|
ND2
|
A:ASN2145
|
3.7
|
94.5
|
1.0
|
CG
|
A:ASP2179
|
3.7
|
95.7
|
1.0
|
N
|
A:SER2147
|
3.8
|
94.5
|
1.0
|
CA
|
A:SER2147
|
4.1
|
94.1
|
1.0
|
CB
|
A:ASP2177
|
4.3
|
86.7
|
1.0
|
CB
|
A:SER2242
|
4.3
|
96.3
|
1.0
|
CB
|
A:ASP2179
|
4.4
|
90.9
|
1.0
|
OD1
|
A:ASP2239
|
4.4
|
89.4
|
1.0
|
C
|
A:ASN2145
|
4.4
|
97.4
|
1.0
|
CB
|
A:SER2147
|
4.4
|
90.9
|
1.0
|
N
|
A:ARG2148
|
4.5
|
98.7
|
1.0
|
CB
|
A:ASN2145
|
4.5
|
91.9
|
1.0
|
N
|
A:ASP2146
|
4.6
|
91.0
|
1.0
|
O
|
A:ASN2145
|
4.6
|
99.7
|
1.0
|
CD
|
A:PRO2149
|
4.6
|
89.0
|
1.0
|
O
|
A:HIS2247
|
4.7
|
97.5
|
1.0
|
CA
|
A:ASN2145
|
4.7
|
92.2
|
1.0
|
OD1
|
A:ASP2179
|
4.7
|
93.4
|
1.0
|
CA
|
A:SER2242
|
4.8
|
98.2
|
1.0
|
C
|
A:ASP2146
|
4.9
|
94.7
|
1.0
|
N
|
A:PRO2149
|
4.9
|
88.1
|
1.0
|
CA
|
A:ARG2148
|
5.0
|
96.7
|
1.0
|
|
Reference:
A.Jaiganesh,
P.De-La-Torre,
A.A.Patel,
D.J.Termine,
F.Velez-Cortes,
C.Chen,
M.Sotomayor.
Zooming in on Cadherin-23: Structural Diversity and Potential Mechanisms of Inherited Deafness. Structure V. 26 1210 2018.
ISSN: ISSN 1878-4186
PubMed: 30033219
DOI: 10.1016/J.STR.2018.06.003
Page generated: Mon Jul 15 12:04:57 2024
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