Calcium in PDB 7lyu: Reelin Repeat 8
Protein crystallography data
The structure of Reelin Repeat 8, PDB code: 7lyu
was solved by
L.S.Turk,
D.Comoletti,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.12 /
3.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.171,
104.059,
67.615,
90,
104.11,
90
|
R / Rfree (%)
|
22.7 /
26.4
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Reelin Repeat 8
(pdb code 7lyu). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Reelin Repeat 8, PDB code: 7lyu:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 7lyu
Go back to
Calcium Binding Sites List in 7lyu
Calcium binding site 1 out
of 4 in the Reelin Repeat 8
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Reelin Repeat 8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca3501
b:105.0
occ:1.00
|
OG
|
A:SER3091
|
2.4
|
122.3
|
1.0
|
OD1
|
A:ASP3224
|
2.4
|
88.5
|
1.0
|
O
|
A:THR3062
|
2.5
|
86.4
|
1.0
|
CG
|
A:ASP3224
|
3.2
|
83.6
|
1.0
|
OD2
|
A:ASP3224
|
3.2
|
88.3
|
1.0
|
CB
|
A:SER3091
|
3.3
|
119.2
|
1.0
|
O
|
A:PHE3092
|
3.4
|
76.3
|
1.0
|
C
|
A:THR3062
|
3.5
|
89.1
|
1.0
|
CB
|
A:THR3062
|
3.6
|
99.5
|
1.0
|
CA
|
A:THR3062
|
3.9
|
91.2
|
1.0
|
OG1
|
A:THR3062
|
4.1
|
97.9
|
1.0
|
N
|
A:PHE3092
|
4.4
|
92.2
|
1.0
|
C
|
A:PHE3092
|
4.4
|
79.2
|
1.0
|
N
|
A:HIS3225
|
4.5
|
69.3
|
1.0
|
CB
|
A:HIS3225
|
4.6
|
91.1
|
1.0
|
CA
|
A:SER3091
|
4.6
|
120.5
|
1.0
|
CB
|
A:ASP3224
|
4.6
|
64.2
|
1.0
|
C
|
A:SER3091
|
4.7
|
111.5
|
1.0
|
N
|
A:PHE3063
|
4.7
|
78.3
|
1.0
|
CA
|
A:HIS3225
|
4.8
|
77.2
|
1.0
|
ND1
|
A:HIS3225
|
4.9
|
88.4
|
1.0
|
CG2
|
A:THR3062
|
4.9
|
100.5
|
1.0
|
CA
|
A:PHE3092
|
5.0
|
80.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 7lyu
Go back to
Calcium Binding Sites List in 7lyu
Calcium binding site 2 out
of 4 in the Reelin Repeat 8
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Reelin Repeat 8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca3502
b:78.7
occ:1.00
|
OD2
|
A:ASP3422
|
2.2
|
67.7
|
1.0
|
O
|
A:HIS3304
|
2.4
|
77.5
|
1.0
|
O
|
A:ASN3273
|
2.5
|
70.4
|
1.0
|
OD1
|
A:ASP3422
|
2.7
|
68.3
|
1.0
|
CG
|
A:ASP3422
|
2.8
|
66.8
|
1.0
|
O
|
A:ASP3306
|
3.0
|
86.0
|
1.0
|
OE2
|
A:GLU3275
|
3.5
|
111.8
|
1.0
|
C
|
A:ASN3273
|
3.6
|
67.4
|
1.0
|
C
|
A:HIS3304
|
3.6
|
79.0
|
1.0
|
C
|
A:ASP3306
|
3.9
|
83.1
|
1.0
|
C
|
A:GLY3305
|
4.1
|
81.1
|
1.0
|
CB
|
A:ASN3273
|
4.1
|
70.3
|
1.0
|
CA
|
A:ASN3273
|
4.2
|
71.2
|
1.0
|
N
|
A:ASP3306
|
4.2
|
87.4
|
1.0
|
CB
|
A:ASP3422
|
4.3
|
66.3
|
1.0
|
CA
|
A:GLY3305
|
4.3
|
73.6
|
1.0
|
CD
|
A:GLU3275
|
4.4
|
117.1
|
1.0
|
CG
|
A:GLU3275
|
4.4
|
108.1
|
1.0
|
O
|
A:GLY3305
|
4.4
|
88.7
|
1.0
|
N
|
A:GLY3305
|
4.5
|
73.3
|
1.0
|
N
|
A:HIS3304
|
4.5
|
73.0
|
1.0
|
CE1
|
A:HIS3423
|
4.5
|
75.3
|
1.0
|
ND1
|
A:HIS3423
|
4.6
|
75.8
|
1.0
|
O
|
A:PHE3274
|
4.7
|
82.6
|
1.0
|
N
|
A:PHE3274
|
4.7
|
63.3
|
1.0
|
N
|
A:SER3307
|
4.7
|
71.5
|
1.0
|
CA
|
A:HIS3304
|
4.7
|
77.4
|
1.0
|
CA
|
A:ASP3306
|
4.7
|
83.2
|
1.0
|
ND1
|
A:HIS3304
|
4.8
|
81.9
|
1.0
|
C
|
A:PHE3274
|
4.8
|
77.7
|
1.0
|
CA
|
A:SER3307
|
4.9
|
64.2
|
1.0
|
CE1
|
A:HIS3304
|
4.9
|
76.3
|
1.0
|
CB
|
A:PHE3274
|
5.0
|
66.9
|
1.0
|
|
Calcium binding site 3 out
of 4 in 7lyu
Go back to
Calcium Binding Sites List in 7lyu
Calcium binding site 3 out
of 4 in the Reelin Repeat 8
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Reelin Repeat 8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca3501
b:68.0
occ:1.00
|
OD2
|
B:ASP3422
|
2.5
|
59.9
|
1.0
|
O
|
B:HIS3304
|
2.6
|
65.9
|
1.0
|
OD1
|
B:ASP3422
|
2.6
|
57.2
|
1.0
|
O
|
B:ASP3306
|
2.6
|
77.0
|
0.5
|
O
|
B:ASP3306
|
2.6
|
68.0
|
0.5
|
CG
|
B:ASP3422
|
2.9
|
58.1
|
1.0
|
OE2
|
B:GLU3275
|
3.4
|
90.8
|
1.0
|
N
|
B:PHE3274
|
3.4
|
50.6
|
1.0
|
CG
|
B:GLU3275
|
3.6
|
76.0
|
1.0
|
CB
|
B:ASN3273
|
3.6
|
58.5
|
1.0
|
CD
|
B:GLU3275
|
3.7
|
87.6
|
1.0
|
C
|
B:HIS3304
|
3.8
|
74.0
|
1.0
|
C
|
B:ASP3306
|
3.8
|
77.5
|
0.5
|
C
|
B:ASP3306
|
3.8
|
94.2
|
0.5
|
C
|
B:ASN3273
|
3.9
|
51.8
|
1.0
|
CA
|
B:ASN3273
|
3.9
|
47.0
|
1.0
|
C
|
B:GLY3305
|
4.0
|
72.2
|
1.0
|
N
|
B:ASP3306
|
4.1
|
78.5
|
0.5
|
N
|
B:ASP3306
|
4.1
|
72.0
|
0.5
|
O
|
B:GLY3305
|
4.2
|
74.7
|
1.0
|
CA
|
B:GLY3305
|
4.3
|
74.1
|
1.0
|
CB
|
B:ASP3422
|
4.4
|
51.5
|
1.0
|
CA
|
B:PHE3274
|
4.4
|
55.5
|
1.0
|
C
|
B:PHE3274
|
4.4
|
59.5
|
1.0
|
N
|
B:GLY3305
|
4.5
|
76.9
|
1.0
|
N
|
B:GLU3275
|
4.5
|
58.2
|
1.0
|
CA
|
B:ASP3306
|
4.6
|
72.1
|
0.5
|
CA
|
B:ASP3306
|
4.6
|
72.1
|
0.5
|
NE2
|
B:HIS3423
|
4.6
|
72.1
|
1.0
|
CD2
|
B:HIS3423
|
4.7
|
67.1
|
1.0
|
CG
|
B:ASN3273
|
4.7
|
68.4
|
1.0
|
OE1
|
B:GLU3275
|
4.7
|
95.2
|
1.0
|
N
|
B:HIS3304
|
4.7
|
73.6
|
1.0
|
N
|
B:SER3307
|
4.7
|
66.5
|
1.0
|
O
|
B:ASN3273
|
4.8
|
61.2
|
1.0
|
CB
|
B:GLU3275
|
4.8
|
68.3
|
1.0
|
O
|
B:PHE3274
|
4.8
|
64.0
|
1.0
|
CB
|
B:PHE3274
|
4.8
|
48.9
|
1.0
|
ND1
|
B:HIS3304
|
4.9
|
85.3
|
1.0
|
CA
|
B:SER3307
|
4.9
|
56.6
|
1.0
|
CA
|
B:HIS3304
|
4.9
|
73.9
|
1.0
|
|
Calcium binding site 4 out
of 4 in 7lyu
Go back to
Calcium Binding Sites List in 7lyu
Calcium binding site 4 out
of 4 in the Reelin Repeat 8
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Reelin Repeat 8 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca3502
b:74.1
occ:1.00
|
OD1
|
B:ASP3224
|
2.3
|
63.6
|
1.0
|
OG
|
B:SER3091
|
2.3
|
87.1
|
1.0
|
O
|
B:THR3062
|
2.5
|
69.4
|
1.0
|
OD2
|
B:ASP3224
|
2.8
|
75.3
|
1.0
|
CG
|
B:ASP3224
|
2.9
|
65.7
|
1.0
|
O
|
B:PHE3092
|
2.9
|
88.3
|
1.0
|
CB
|
B:SER3091
|
3.1
|
80.7
|
1.0
|
C
|
B:THR3062
|
3.6
|
67.7
|
1.0
|
OD1
|
B:ASP3064
|
3.9
|
93.2
|
1.0
|
OD2
|
B:ASP3064
|
3.9
|
88.1
|
1.0
|
C
|
B:PHE3092
|
4.0
|
85.6
|
1.0
|
CD2
|
B:HIS3225
|
4.0
|
86.7
|
1.0
|
CA
|
B:THR3062
|
4.0
|
63.6
|
1.0
|
N
|
B:PHE3092
|
4.0
|
95.6
|
1.0
|
CB
|
B:THR3062
|
4.1
|
64.2
|
1.0
|
CG
|
B:ASP3064
|
4.2
|
96.9
|
1.0
|
C
|
B:SER3091
|
4.2
|
92.3
|
1.0
|
CA
|
B:SER3091
|
4.3
|
84.4
|
1.0
|
NE2
|
B:HIS3225
|
4.3
|
84.8
|
1.0
|
CB
|
B:ASP3224
|
4.3
|
50.5
|
1.0
|
N
|
B:HIS3225
|
4.4
|
64.9
|
1.0
|
CG
|
B:HIS3225
|
4.6
|
73.8
|
1.0
|
CA
|
B:PHE3092
|
4.6
|
85.2
|
1.0
|
N
|
B:PHE3063
|
4.7
|
67.9
|
1.0
|
CD2
|
B:PHE3063
|
4.8
|
61.7
|
1.0
|
O
|
B:SER3091
|
4.9
|
89.4
|
1.0
|
CB
|
B:PHE3063
|
5.0
|
64.2
|
1.0
|
CA
|
B:ASP3224
|
5.0
|
51.0
|
1.0
|
N
|
B:HIS3093
|
5.0
|
76.5
|
1.0
|
|
Reference:
L.S.Turk,
M.J.Currie,
R.C.J.Dobson,
D.Comoletti.
Structure of Reelin Repeat 8 and the Adjacent C-Terminal Region. Biophys.J. V. 121 2526 2022.
ISSN: ESSN 1542-0086
PubMed: 35659645
DOI: 10.1016/J.BPJ.2022.06.002
Page generated: Fri Jul 19 01:51:37 2024
|