Calcium in PDB 4okh: Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
Enzymatic activity of Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
All present enzymatic activity of Crystal Structure of Calpain-3 Penta-Ef-Hand Domain:
3.4.22.54;
Protein crystallography data
The structure of Crystal Structure of Calpain-3 Penta-Ef-Hand Domain, PDB code: 4okh
was solved by
S.Karunan Partha,
R.Ravulapalli,
R.L.Campbell,
J.S.Allingham,
P.L.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.85 /
2.45
|
|
Space group
|
P 41 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
107.000,
107.000,
96.710,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
19.8 /
26.9
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
11;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
(pdb code 4okh). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the
Crystal Structure of Calpain-3 Penta-Ef-Hand Domain, PDB code: 4okh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 1 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:53.2
occ:1.00
|
O
|
A:HOH1014
|
2.2
|
57.5
|
1.0
|
|
O
|
A:ALA662
|
2.3
|
55.5
|
1.0
|
|
O
|
A:GLU667
|
2.3
|
46.3
|
1.0
|
|
OE1
|
A:GLU672
|
2.4
|
44.4
|
1.0
|
|
OD1
|
A:ASP665
|
2.5
|
49.0
|
1.0
|
|
OE2
|
A:GLU672
|
2.5
|
47.1
|
1.0
|
|
CD
|
A:GLU672
|
2.8
|
45.4
|
1.0
|
|
CG
|
A:ASP665
|
3.3
|
48.3
|
1.0
|
|
OD2
|
A:ASP665
|
3.4
|
47.0
|
1.0
|
|
C
|
A:ALA662
|
3.4
|
55.2
|
1.0
|
|
C
|
A:GLU667
|
3.5
|
49.5
|
1.0
|
|
CA
|
A:ALA662
|
4.0
|
56.3
|
1.0
|
|
N
|
A:GLU667
|
4.3
|
49.9
|
1.0
|
|
N
|
A:ILE668
|
4.4
|
47.2
|
1.0
|
|
CG
|
A:GLU672
|
4.4
|
44.1
|
1.0
|
|
CA
|
A:ILE668
|
4.4
|
46.6
|
1.0
|
|
N
|
A:GLY663
|
4.4
|
55.9
|
1.0
|
|
O
|
A:ILE661
|
4.4
|
59.4
|
1.0
|
|
N
|
A:CYS669
|
4.5
|
44.7
|
1.0
|
|
CA
|
A:GLU667
|
4.6
|
50.5
|
1.0
|
|
CA
|
A:GLY663
|
4.7
|
56.1
|
1.0
|
|
CB
|
A:ASP665
|
4.7
|
50.9
|
1.0
|
|
CB
|
A:ALA662
|
4.9
|
55.0
|
1.0
|
|
C
|
A:GLY663
|
4.9
|
55.9
|
1.0
|
|
N
|
A:ASP665
|
4.9
|
55.6
|
1.0
|
|
C
|
A:ILE668
|
4.9
|
44.3
|
1.0
|
|
CD
|
A:LYS711
|
5.0
|
54.8
|
1.0
|
|
SG
|
A:CYS669
|
5.0
|
50.9
|
1.0
|
|
N
|
A:MET666
|
5.0
|
51.8
|
1.0
|
|
Calcium binding site 2 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 2 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca902
b:49.4
occ:1.00
|
OD1
|
A:ASP705
|
2.3
|
46.1
|
1.0
|
|
O
|
A:HOH1011
|
2.3
|
48.2
|
1.0
|
|
OG
|
A:SER709
|
2.3
|
52.3
|
1.0
|
|
O
|
A:LYS711
|
2.4
|
42.8
|
1.0
|
|
OE2
|
A:GLU716
|
2.4
|
49.7
|
1.0
|
|
OD1
|
A:ASP707
|
2.4
|
52.9
|
1.0
|
|
OE1
|
A:GLU716
|
2.6
|
48.1
|
1.0
|
|
CD
|
A:GLU716
|
2.8
|
48.9
|
1.0
|
|
CG
|
A:ASP707
|
3.3
|
56.3
|
1.0
|
|
CB
|
A:SER709
|
3.4
|
51.0
|
1.0
|
|
CG
|
A:ASP705
|
3.5
|
50.8
|
1.0
|
|
C
|
A:LYS711
|
3.6
|
44.0
|
1.0
|
|
OD2
|
A:ASP707
|
3.7
|
62.6
|
1.0
|
|
N
|
A:SER709
|
3.9
|
51.4
|
1.0
|
|
CA
|
A:SER709
|
4.2
|
49.6
|
1.0
|
|
OE1
|
A:GLU667
|
4.2
|
55.7
|
1.0
|
|
OE2
|
A:GLU667
|
4.2
|
58.4
|
1.0
|
|
N
|
A:ASN713
|
4.3
|
48.5
|
1.0
|
|
CA
|
A:LEU712
|
4.3
|
46.2
|
1.0
|
|
CA
|
A:ASP705
|
4.3
|
50.7
|
1.0
|
|
CB
|
A:ASP705
|
4.3
|
49.7
|
1.0
|
|
N
|
A:LYS711
|
4.3
|
48.3
|
1.0
|
|
CG
|
A:GLU716
|
4.4
|
47.0
|
1.0
|
|
N
|
A:LEU712
|
4.4
|
44.9
|
1.0
|
|
OD2
|
A:ASP705
|
4.4
|
55.4
|
1.0
|
|
N
|
A:ASP707
|
4.4
|
51.6
|
1.0
|
|
CD
|
A:GLU667
|
4.5
|
54.8
|
1.0
|
|
C
|
A:ASP705
|
4.5
|
49.7
|
1.0
|
|
N
|
A:THR706
|
4.6
|
51.9
|
1.0
|
|
N
|
A:GLY710
|
4.6
|
50.8
|
1.0
|
|
CA
|
A:LYS711
|
4.6
|
46.3
|
1.0
|
|
CB
|
A:ASP707
|
4.6
|
53.4
|
1.0
|
|
N
|
A:GLY708
|
4.7
|
53.7
|
1.0
|
|
C
|
A:LEU712
|
4.7
|
47.2
|
1.0
|
|
C
|
A:SER709
|
4.7
|
50.4
|
1.0
|
|
CA
|
A:ASP707
|
4.9
|
53.8
|
1.0
|
|
CG
|
A:ASN713
|
4.9
|
48.8
|
1.0
|
|
OD1
|
A:ASN713
|
4.9
|
48.5
|
1.0
|
|
C
|
A:ASP707
|
5.0
|
55.4
|
1.0
|
|
Calcium binding site 3 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 3 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca903
b:83.5
occ:1.00
|
OD1
|
A:ASP737
|
2.4
|
96.0
|
1.0
|
|
O
|
A:THR741
|
2.5
|
70.4
|
1.0
|
|
OG
|
A:SER739
|
2.6
|
69.6
|
1.0
|
|
O
|
A:HOH1012
|
2.7
|
59.1
|
1.0
|
|
OD1
|
A:ASP735
|
2.7
|
80.1
|
1.0
|
|
CG
|
A:ASP737
|
3.4
|
96.5
|
1.0
|
|
CB
|
A:SER739
|
3.5
|
76.1
|
1.0
|
|
C
|
A:THR741
|
3.6
|
64.3
|
1.0
|
|
OD2
|
A:ASP737
|
3.7
|
96.2
|
1.0
|
|
CG
|
A:ASP735
|
3.8
|
69.1
|
1.0
|
|
CA
|
A:ASP735
|
4.1
|
67.5
|
1.0
|
|
CA
|
A:ILE742
|
4.1
|
59.1
|
1.0
|
|
N
|
A:SER739
|
4.3
|
80.7
|
1.0
|
|
OG1
|
A:THR741
|
4.3
|
73.4
|
1.0
|
|
N
|
A:ILE742
|
4.3
|
59.2
|
1.0
|
|
CB
|
A:ASP735
|
4.4
|
67.4
|
1.0
|
|
CA
|
A:SER739
|
4.4
|
76.8
|
1.0
|
|
C
|
A:ASP735
|
4.5
|
70.8
|
1.0
|
|
N
|
A:THR741
|
4.7
|
69.5
|
1.0
|
|
N
|
A:ASP737
|
4.7
|
84.8
|
1.0
|
|
CA
|
A:THR741
|
4.7
|
67.2
|
1.0
|
|
O
|
A:TYR734
|
4.7
|
69.0
|
1.0
|
|
OE1
|
A:GLU746
|
4.7
|
60.9
|
1.0
|
|
OD2
|
A:ASP735
|
4.8
|
68.5
|
1.0
|
|
CB
|
A:ASP737
|
4.8
|
93.9
|
1.0
|
|
CG2
|
A:ILE742
|
4.8
|
58.5
|
1.0
|
|
N
|
A:THR736
|
4.9
|
75.7
|
1.0
|
|
C
|
A:ASP737
|
5.0
|
88.0
|
1.0
|
|
Calcium binding site 4 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 4 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca904
b:38.2
occ:1.00
|
O
|
A:ILE806
|
2.2
|
40.9
|
1.0
|
|
O
|
A:HOH1005
|
2.2
|
44.7
|
1.0
|
|
OD1
|
A:ASP800
|
2.3
|
38.4
|
1.0
|
|
O
|
A:HOH1008
|
2.3
|
34.7
|
1.0
|
|
OD1
|
A:ASP804
|
2.3
|
39.6
|
1.0
|
|
OD1
|
A:ASP802
|
2.4
|
41.8
|
1.0
|
|
OD2
|
A:ASP802
|
2.6
|
48.0
|
1.0
|
|
CG
|
A:ASP802
|
2.8
|
46.0
|
1.0
|
|
CG
|
A:ASP804
|
3.2
|
39.7
|
1.0
|
|
C
|
A:ILE806
|
3.4
|
38.4
|
1.0
|
|
CG
|
A:ASP800
|
3.5
|
38.0
|
1.0
|
|
OD2
|
A:ASP804
|
3.6
|
41.4
|
1.0
|
|
N
|
A:ILE806
|
4.0
|
37.2
|
1.0
|
|
CA
|
A:ILE806
|
4.2
|
38.1
|
1.0
|
|
N
|
A:ASP804
|
4.2
|
40.8
|
1.0
|
|
OD2
|
A:ASP800
|
4.3
|
39.1
|
1.0
|
|
CB
|
A:ASP800
|
4.3
|
37.1
|
1.0
|
|
CB
|
A:ASP802
|
4.3
|
47.2
|
1.0
|
|
CA
|
A:ASP800
|
4.4
|
38.5
|
1.0
|
|
CB
|
A:ASP804
|
4.4
|
39.9
|
1.0
|
|
N
|
A:ILE807
|
4.4
|
38.5
|
1.0
|
|
CB
|
A:ILE806
|
4.5
|
40.3
|
1.0
|
|
CA
|
A:ILE807
|
4.6
|
39.4
|
1.0
|
|
CG2
|
A:ILE807
|
4.6
|
39.1
|
1.0
|
|
CA
|
A:ASP804
|
4.7
|
39.3
|
1.0
|
|
N
|
A:GLY805
|
4.7
|
38.9
|
1.0
|
|
N
|
A:GLY803
|
4.7
|
43.5
|
1.0
|
|
C
|
A:ASP804
|
4.9
|
39.2
|
1.0
|
|
C
|
A:ASP800
|
5.0
|
41.9
|
1.0
|
|
Calcium binding site 5 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 5 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:58.7
occ:1.00
|
O
|
B:ALA662
|
2.3
|
60.8
|
1.0
|
|
O
|
B:HOH1010
|
2.4
|
47.8
|
1.0
|
|
O
|
B:HOH1011
|
2.4
|
56.8
|
1.0
|
|
O
|
B:GLU667
|
2.5
|
49.4
|
1.0
|
|
OD1
|
B:ASP665
|
2.5
|
66.9
|
1.0
|
|
OE1
|
B:GLU672
|
2.6
|
58.4
|
1.0
|
|
OE2
|
B:GLU672
|
2.9
|
71.0
|
1.0
|
|
CD
|
B:GLU672
|
3.1
|
61.3
|
1.0
|
|
OD2
|
B:ASP665
|
3.2
|
67.7
|
1.0
|
|
CG
|
B:ASP665
|
3.3
|
66.1
|
1.0
|
|
C
|
B:ALA662
|
3.4
|
58.6
|
1.0
|
|
C
|
B:GLU667
|
3.7
|
51.6
|
1.0
|
|
CA
|
B:ALA662
|
4.1
|
56.0
|
1.0
|
|
N
|
B:GLU667
|
4.3
|
53.0
|
1.0
|
|
N
|
B:GLY663
|
4.4
|
59.0
|
1.0
|
|
CA
|
B:ILE668
|
4.4
|
48.5
|
1.0
|
|
N
|
B:ILE668
|
4.6
|
48.8
|
1.0
|
|
CA
|
B:GLU667
|
4.6
|
54.8
|
1.0
|
|
CA
|
B:GLY663
|
4.6
|
62.2
|
1.0
|
|
CB
|
B:ALA662
|
4.6
|
52.3
|
1.0
|
|
CG
|
B:GLU672
|
4.6
|
58.5
|
1.0
|
|
CB
|
B:ASP665
|
4.8
|
66.0
|
1.0
|
|
N
|
B:CYS669
|
4.8
|
49.4
|
1.0
|
|
C
|
B:GLY663
|
4.9
|
68.1
|
1.0
|
|
Calcium binding site 6 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 6 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca902
b:48.2
occ:1.00
|
O
|
B:HOH1013
|
2.2
|
51.1
|
1.0
|
|
OD1
|
B:ASP705
|
2.3
|
45.8
|
1.0
|
|
OD1
|
B:ASP707
|
2.4
|
61.1
|
1.0
|
|
OE1
|
B:GLU716
|
2.5
|
53.5
|
1.0
|
|
OE2
|
B:GLU716
|
2.5
|
51.7
|
1.0
|
|
O
|
B:LYS711
|
2.5
|
47.6
|
1.0
|
|
OG
|
B:SER709
|
2.7
|
48.6
|
1.0
|
|
CD
|
B:GLU716
|
2.8
|
49.9
|
1.0
|
|
CG
|
B:ASP707
|
3.2
|
59.1
|
1.0
|
|
OD2
|
B:ASP707
|
3.5
|
61.4
|
1.0
|
|
CG
|
B:ASP705
|
3.5
|
46.0
|
1.0
|
|
CB
|
B:SER709
|
3.6
|
51.5
|
1.0
|
|
C
|
B:LYS711
|
3.7
|
46.5
|
1.0
|
|
N
|
B:SER709
|
4.0
|
54.8
|
1.0
|
|
CA
|
B:ASP705
|
4.2
|
46.0
|
1.0
|
|
N
|
B:ASN713
|
4.3
|
45.0
|
1.0
|
|
CB
|
B:ASP705
|
4.3
|
44.7
|
1.0
|
|
CA
|
B:SER709
|
4.3
|
51.9
|
1.0
|
|
CG
|
B:GLU716
|
4.3
|
49.5
|
1.0
|
|
CA
|
B:LEU712
|
4.3
|
43.5
|
1.0
|
|
OE1
|
B:GLU667
|
4.4
|
58.1
|
1.0
|
|
OD2
|
B:ASP705
|
4.4
|
47.5
|
1.0
|
|
N
|
B:ASP707
|
4.4
|
59.5
|
1.0
|
|
CB
|
B:ASP707
|
4.4
|
58.3
|
1.0
|
|
N
|
B:LYS711
|
4.5
|
46.9
|
1.0
|
|
N
|
B:LEU712
|
4.5
|
45.1
|
1.0
|
|
C
|
B:ASP705
|
4.5
|
51.6
|
1.0
|
|
CD
|
B:GLU667
|
4.6
|
59.5
|
1.0
|
|
N
|
B:GLY708
|
4.7
|
57.3
|
1.0
|
|
CA
|
B:ASP707
|
4.7
|
58.9
|
1.0
|
|
C
|
B:LEU712
|
4.7
|
45.2
|
1.0
|
|
N
|
B:GLY710
|
4.8
|
47.4
|
1.0
|
|
CA
|
B:LYS711
|
4.8
|
45.2
|
1.0
|
|
CG
|
B:ASN713
|
4.8
|
47.5
|
1.0
|
|
C
|
B:ASP707
|
4.8
|
55.4
|
1.0
|
|
C
|
B:SER709
|
4.8
|
50.6
|
1.0
|
|
ND2
|
B:ASN713
|
4.8
|
52.0
|
1.0
|
|
OE2
|
B:GLU667
|
4.9
|
58.2
|
1.0
|
|
O
|
B:ASP705
|
4.9
|
57.9
|
1.0
|
|
N
|
B:THR706
|
4.9
|
53.4
|
1.0
|
|
Calcium binding site 7 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 7 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca903
b:86.6
occ:1.00
|
OD1
|
B:ASP737
|
2.3
|
74.2
|
1.0
|
|
OG
|
B:SER739
|
2.5
|
72.9
|
1.0
|
|
O
|
B:THR741
|
2.6
|
68.1
|
1.0
|
|
OD1
|
B:ASP735
|
2.6
|
68.2
|
1.0
|
|
O
|
B:HOH1012
|
2.7
|
70.5
|
1.0
|
|
CG
|
B:ASP737
|
3.4
|
80.7
|
1.0
|
|
CB
|
B:SER739
|
3.4
|
72.6
|
1.0
|
|
C
|
B:THR741
|
3.7
|
65.7
|
1.0
|
|
OD2
|
B:ASP737
|
3.7
|
81.9
|
1.0
|
|
CG
|
B:ASP735
|
3.8
|
68.2
|
1.0
|
|
OG1
|
B:THR741
|
4.1
|
63.8
|
1.0
|
|
CA
|
B:ASP735
|
4.2
|
68.9
|
1.0
|
|
CA
|
B:ILE742
|
4.4
|
59.6
|
1.0
|
|
N
|
B:SER739
|
4.4
|
76.7
|
1.0
|
|
N
|
B:ILE742
|
4.4
|
64.8
|
1.0
|
|
CA
|
B:SER739
|
4.5
|
73.9
|
1.0
|
|
C
|
B:ASP735
|
4.5
|
73.5
|
1.0
|
|
CB
|
B:ASP735
|
4.5
|
66.6
|
1.0
|
|
N
|
B:THR741
|
4.5
|
61.6
|
1.0
|
|
CA
|
B:THR741
|
4.6
|
62.1
|
1.0
|
|
CB
|
B:ASP737
|
4.7
|
82.1
|
1.0
|
|
OE1
|
B:GLU746
|
4.7
|
70.8
|
1.0
|
|
N
|
B:ASP737
|
4.8
|
81.6
|
1.0
|
|
O
|
B:ASP735
|
4.8
|
77.8
|
1.0
|
|
OD2
|
B:ASP735
|
4.8
|
65.5
|
1.0
|
|
O
|
B:TYR734
|
4.8
|
73.2
|
1.0
|
|
N
|
B:THR736
|
4.9
|
77.7
|
1.0
|
|
CB
|
B:THR741
|
5.0
|
60.7
|
1.0
|
|
Calcium binding site 8 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 8 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca904
b:51.4
occ:1.00
|
OD1
|
B:ASP802
|
2.2
|
66.8
|
1.0
|
|
O
|
B:ILE806
|
2.2
|
50.9
|
1.0
|
|
OD1
|
B:ASP800
|
2.3
|
49.3
|
1.0
|
|
OD1
|
B:ASP804
|
2.3
|
52.0
|
1.0
|
|
O
|
B:HOH1009
|
2.3
|
65.5
|
1.0
|
|
O
|
B:HOH1007
|
2.4
|
53.5
|
1.0
|
|
CG
|
B:ASP802
|
3.1
|
62.4
|
1.0
|
|
CG
|
B:ASP804
|
3.3
|
51.2
|
1.0
|
|
OD2
|
B:ASP802
|
3.3
|
65.4
|
1.0
|
|
C
|
B:ILE806
|
3.4
|
46.5
|
1.0
|
|
CG
|
B:ASP800
|
3.4
|
48.0
|
1.0
|
|
OD2
|
B:ASP804
|
3.8
|
54.8
|
1.0
|
|
N
|
B:ILE806
|
3.9
|
42.8
|
1.0
|
|
O
|
B:HOH1001
|
4.1
|
58.5
|
1.0
|
|
CA
|
B:ILE806
|
4.2
|
43.2
|
1.0
|
|
N
|
B:ASP804
|
4.2
|
47.0
|
1.0
|
|
CA
|
B:ASP800
|
4.2
|
52.1
|
1.0
|
|
OD2
|
B:ASP800
|
4.2
|
54.5
|
1.0
|
|
CB
|
B:ASP800
|
4.3
|
49.1
|
1.0
|
|
CB
|
B:ASP804
|
4.4
|
48.7
|
1.0
|
|
N
|
B:ILE807
|
4.4
|
43.4
|
1.0
|
|
CB
|
B:ASP802
|
4.5
|
59.9
|
1.0
|
|
OCS
|
B:PEU905
|
4.6
|
57.4
|
1.0
|
|
C
|
B:ASP800
|
4.6
|
55.9
|
1.0
|
|
N
|
B:ASP802
|
4.6
|
55.6
|
1.0
|
|
N
|
B:GLY803
|
4.6
|
56.2
|
1.0
|
|
CB
|
B:ILE806
|
4.6
|
44.7
|
1.0
|
|
CA
|
B:ILE807
|
4.6
|
40.8
|
1.0
|
|
CA
|
B:ASP804
|
4.7
|
47.6
|
1.0
|
|
N
|
B:GLY805
|
4.8
|
46.0
|
1.0
|
|
N
|
B:LYS801
|
4.8
|
59.0
|
1.0
|
|
CA
|
B:ASP802
|
4.9
|
57.7
|
1.0
|
|
C
|
B:ASP804
|
5.0
|
46.0
|
1.0
|
|
CG2
|
B:ILE807
|
5.0
|
45.4
|
1.0
|
|
Calcium binding site 9 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 9 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:80.4
occ:1.00
|
OD1
|
C:ASP705
|
2.1
|
98.5
|
1.0
|
|
O
|
C:LYS711
|
2.3
|
86.9
|
1.0
|
|
O
|
C:HOH1007
|
2.3
|
79.2
|
1.0
|
|
OD1
|
C:ASP707
|
2.4
|
0.8
|
1.0
|
|
OG
|
C:SER709
|
2.5
|
85.8
|
1.0
|
|
OE1
|
C:GLU716
|
2.5
|
88.9
|
1.0
|
|
OE2
|
C:GLU716
|
2.6
|
89.4
|
1.0
|
|
CD
|
C:GLU716
|
2.9
|
90.7
|
1.0
|
|
CG
|
C:ASP707
|
3.2
|
0.5
|
1.0
|
|
CG
|
C:ASP705
|
3.3
|
97.5
|
1.0
|
|
OD2
|
C:ASP707
|
3.4
|
0.8
|
1.0
|
|
C
|
C:LYS711
|
3.5
|
83.5
|
1.0
|
|
CB
|
C:SER709
|
3.6
|
89.0
|
1.0
|
|
OE2
|
C:GLU667
|
3.8
|
0.2
|
1.0
|
|
N
|
C:LYS711
|
4.1
|
84.8
|
1.0
|
|
N
|
C:SER709
|
4.1
|
93.6
|
1.0
|
|
OD2
|
C:ASP705
|
4.1
|
98.5
|
1.0
|
|
CA
|
C:SER709
|
4.2
|
89.1
|
1.0
|
|
CB
|
C:ASP705
|
4.3
|
96.0
|
1.0
|
|
N
|
C:ASN713
|
4.4
|
81.6
|
1.0
|
|
N
|
C:GLY710
|
4.4
|
85.0
|
1.0
|
|
C
|
C:SER709
|
4.4
|
87.1
|
1.0
|
|
N
|
C:LEU712
|
4.4
|
80.3
|
1.0
|
|
CA
|
C:LEU712
|
4.4
|
77.4
|
1.0
|
|
CA
|
C:LYS711
|
4.4
|
85.0
|
1.0
|
|
CG
|
C:GLU716
|
4.4
|
89.0
|
1.0
|
|
CA
|
C:ASP705
|
4.5
|
96.3
|
1.0
|
|
CB
|
C:ASP707
|
4.6
|
0.5
|
1.0
|
|
N
|
C:ASP707
|
4.6
|
95.8
|
1.0
|
|
CD
|
C:GLU667
|
4.6
|
0.7
|
1.0
|
|
OE1
|
C:GLU667
|
4.7
|
0.2
|
1.0
|
|
CG
|
C:ASN713
|
4.8
|
90.7
|
1.0
|
|
OD1
|
C:ASN713
|
4.8
|
85.6
|
1.0
|
|
C
|
C:LEU712
|
4.8
|
79.3
|
1.0
|
|
C
|
C:ASP705
|
4.8
|
95.7
|
1.0
|
|
ND2
|
C:ASN713
|
5.0
|
93.1
|
1.0
|
|
CA
|
C:ASP707
|
5.0
|
99.2
|
1.0
|
|
N
|
C:THR706
|
5.0
|
96.4
|
1.0
|
|
N
|
C:GLY708
|
5.0
|
95.7
|
1.0
|
|
O
|
C:SER709
|
5.0
|
87.8
|
1.0
|
|
Calcium binding site 10 out
of 11 in 4okh
Go back to
Calcium Binding Sites List in 4okh
Calcium binding site 10 out
of 11 in the Crystal Structure of Calpain-3 Penta-Ef-Hand Domain
 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 Calpain-3 Penta-Ef-Hand Domain within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca902
b:76.6
occ:1.00
|
O
|
C:THR741
|
2.2
|
57.0
|
1.0
|
|
OD1
|
C:ASP735
|
2.4
|
58.2
|
1.0
|
|
OD2
|
C:ASP737
|
2.5
|
74.3
|
1.0
|
|
O
|
C:HOH1002
|
2.5
|
54.2
|
1.0
|
|
OD1
|
C:ASP737
|
2.8
|
75.0
|
1.0
|
|
OG
|
C:SER739
|
2.9
|
68.2
|
1.0
|
|
O
|
C:HOH1004
|
3.0
|
60.2
|
1.0
|
|
CG
|
C:ASP737
|
3.0
|
74.0
|
1.0
|
|
C
|
C:THR741
|
3.4
|
60.7
|
1.0
|
|
CG
|
C:ASP735
|
3.5
|
61.1
|
1.0
|
|
CB
|
C:SER739
|
3.8
|
73.1
|
1.0
|
|
CG2
|
C:THR741
|
4.1
|
74.8
|
1.0
|
|
CA
|
C:ASP735
|
4.2
|
61.1
|
1.0
|
|
CA
|
C:ILE742
|
4.2
|
51.8
|
1.0
|
|
N
|
C:ILE742
|
4.2
|
53.6
|
1.0
|
|
N
|
C:THR741
|
4.3
|
68.8
|
1.0
|
|
CB
|
C:ASP735
|
4.3
|
62.6
|
1.0
|
|
CA
|
C:THR741
|
4.3
|
67.2
|
1.0
|
|
N
|
C:SER739
|
4.4
|
70.7
|
1.0
|
|
OD2
|
C:ASP735
|
4.4
|
60.8
|
1.0
|
|
CB
|
C:ASP737
|
4.6
|
73.1
|
1.0
|
|
CA
|
C:SER739
|
4.7
|
72.3
|
1.0
|
|
CG2
|
C:ILE742
|
4.7
|
53.0
|
1.0
|
|
O
|
C:TYR734
|
4.8
|
55.2
|
1.0
|
|
CB
|
C:THR741
|
4.9
|
74.0
|
1.0
|
|
N
|
C:GLN738
|
5.0
|
70.5
|
1.0
|
|
Reference:
S.K.Partha,
R.Ravulapalli,
J.S.Allingham,
R.L.Campbell,
P.L.Davies.
Crystal Structure of Calpain-3 Penta-Ef-Hand (Pef) Domain - A Homodimerized Pef Family Member with Calcium Bound at the Fifth Ef-Hand. Febs J. V. 281 3138 2014.
ISSN: ISSN 1742-464X
PubMed: 24846670
DOI: 10.1111/FEBS.12849
Page generated: Sat Dec 12 05:02:21 2020
|
