Calcium in PDB 1avh: Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
Protein crystallography data
The structure of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins, PDB code: 1avh
was solved by
R.Huber,
R.Berendes,
A.Burger,
M.Schneider,
A.Karshikov,
H.Luecke,
J.Roemisch,
E.Paques,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
N/A /
2.30
|
Space group
|
P 63
|
Cell size a, b, c (Å), α, β, γ (°)
|
98.800,
98.800,
129.000,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.4 /
n/a
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
(pdb code 1avh). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the
Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins, PDB code: 1avh:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
Calcium binding site 1 out
of 5 in 1avh
Go back to
Calcium Binding Sites List in 1avh
Calcium binding site 1 out
of 5 in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca321
b:34.6
occ:1.00
|
O
|
A:LEU100
|
3.0
|
53.7
|
1.0
|
O
|
A:GLY104
|
3.2
|
44.0
|
1.0
|
O
|
A:GLY102
|
3.2
|
56.5
|
1.0
|
CA
|
A:GLY104
|
3.6
|
44.8
|
1.0
|
OD2
|
A:ASP144
|
3.7
|
53.7
|
1.0
|
C
|
A:GLY104
|
3.8
|
60.2
|
1.0
|
N
|
A:GLY104
|
4.1
|
66.6
|
1.0
|
C
|
A:LEU100
|
4.1
|
41.9
|
1.0
|
C
|
A:GLY102
|
4.3
|
69.9
|
1.0
|
O
|
A:LYS101
|
4.4
|
32.3
|
1.0
|
C
|
A:ALA103
|
4.5
|
87.5
|
1.0
|
C
|
A:LYS101
|
4.6
|
57.5
|
1.0
|
CG
|
A:ASP144
|
4.7
|
41.4
|
1.0
|
O
|
A:ALA103
|
4.7
|
61.0
|
1.0
|
O
|
A:ALA99
|
4.7
|
33.3
|
1.0
|
CA
|
A:LEU100
|
4.7
|
32.5
|
1.0
|
N
|
A:GLY102
|
4.9
|
41.4
|
1.0
|
N
|
A:LYS101
|
5.0
|
40.6
|
1.0
|
|
Calcium binding site 2 out
of 5 in 1avh
Go back to
Calcium Binding Sites List in 1avh
Calcium binding site 2 out
of 5 in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca322
b:41.9
occ:0.00
|
O
|
A:GLY30
|
2.8
|
47.1
|
1.0
|
OE1
|
A:GLU72
|
2.9
|
31.5
|
1.0
|
O
|
A:GLY32
|
2.9
|
34.3
|
1.0
|
OE2
|
A:GLU72
|
3.0
|
40.0
|
1.0
|
N
|
A:GLY32
|
3.3
|
42.1
|
1.0
|
CD
|
A:GLU72
|
3.3
|
44.8
|
1.0
|
O
|
A:MET28
|
3.6
|
46.2
|
1.0
|
C
|
A:GLY32
|
3.7
|
35.8
|
1.0
|
OG1
|
A:THR33
|
3.8
|
19.4
|
1.0
|
C
|
A:GLY30
|
4.0
|
48.7
|
1.0
|
CA
|
A:LEU31
|
4.0
|
67.9
|
1.0
|
CA
|
A:GLY32
|
4.0
|
51.4
|
1.0
|
C
|
A:LEU31
|
4.1
|
64.5
|
1.0
|
CD1
|
A:LEU31
|
4.1
|
74.1
|
1.0
|
N
|
A:LEU31
|
4.5
|
32.5
|
1.0
|
C
|
A:MET28
|
4.7
|
29.3
|
1.0
|
N
|
A:THR33
|
4.7
|
14.5
|
1.0
|
CG
|
A:GLU72
|
4.8
|
36.2
|
1.0
|
CG
|
A:LEU31
|
4.9
|
89.5
|
1.0
|
|
Calcium binding site 3 out
of 5 in 1avh
Go back to
Calcium Binding Sites List in 1avh
Calcium binding site 3 out
of 5 in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca323
b:50.7
occ:0.00
|
OD2
|
A:ASP303
|
2.7
|
44.5
|
1.0
|
O
|
A:GLY261
|
2.7
|
44.1
|
1.0
|
O
|
A:GLY263
|
3.0
|
48.1
|
1.0
|
O
|
A:MET259
|
3.0
|
28.8
|
1.0
|
CG
|
A:ASP303
|
3.4
|
52.1
|
1.0
|
OD1
|
A:ASP303
|
3.6
|
40.9
|
1.0
|
C
|
A:GLY263
|
3.8
|
62.1
|
1.0
|
C
|
A:MET259
|
3.8
|
30.3
|
1.0
|
C
|
A:GLY261
|
3.9
|
50.9
|
1.0
|
OG1
|
A:THR264
|
4.0
|
37.6
|
1.0
|
N
|
A:GLY261
|
4.2
|
61.0
|
1.0
|
CA
|
A:MET259
|
4.4
|
19.6
|
1.0
|
N
|
A:GLY263
|
4.4
|
60.3
|
1.0
|
C
|
A:LYS260
|
4.5
|
78.3
|
1.0
|
N
|
A:THR264
|
4.6
|
34.2
|
1.0
|
CA
|
A:GLY261
|
4.7
|
51.0
|
1.0
|
N
|
A:LYS260
|
4.7
|
43.3
|
1.0
|
CA
|
A:GLY263
|
4.7
|
64.8
|
1.0
|
CB
|
A:ASP303
|
4.8
|
20.6
|
1.0
|
CB
|
A:MET259
|
4.8
|
39.2
|
1.0
|
CA
|
A:LYS260
|
4.9
|
37.9
|
1.0
|
N
|
A:ALA262
|
4.9
|
56.2
|
1.0
|
CA
|
A:THR264
|
4.9
|
24.4
|
1.0
|
C
|
A:ALA262
|
5.0
|
65.6
|
1.0
|
|
Calcium binding site 4 out
of 5 in 1avh
Go back to
Calcium Binding Sites List in 1avh
Calcium binding site 4 out
of 5 in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca321
b:31.4
occ:1.00
|
OE1
|
B:GLU72
|
2.8
|
38.6
|
1.0
|
O
|
B:GLY32
|
2.8
|
53.1
|
1.0
|
N
|
B:GLY32
|
2.9
|
38.6
|
1.0
|
OG1
|
B:THR33
|
3.0
|
40.3
|
1.0
|
C
|
B:GLY32
|
3.2
|
89.9
|
1.0
|
O
|
B:MET28
|
3.2
|
34.6
|
1.0
|
OE2
|
B:GLU72
|
3.3
|
48.7
|
1.0
|
O
|
B:GLY30
|
3.3
|
52.4
|
1.0
|
CD
|
B:GLU72
|
3.4
|
46.1
|
1.0
|
CA
|
B:GLY32
|
3.5
|
59.8
|
1.0
|
C
|
B:LEU31
|
3.8
|
82.7
|
1.0
|
C
|
B:GLY30
|
3.9
|
68.9
|
1.0
|
N
|
B:THR33
|
3.9
|
57.2
|
1.0
|
C
|
B:MET28
|
4.0
|
32.0
|
1.0
|
CA
|
B:LEU31
|
4.0
|
81.5
|
1.0
|
O
|
B:HOH722
|
4.0
|
45.1
|
1.0
|
N
|
B:LEU31
|
4.2
|
56.8
|
1.0
|
CB
|
B:THR33
|
4.3
|
53.6
|
1.0
|
CA
|
B:THR33
|
4.4
|
29.7
|
1.0
|
N
|
B:GLY30
|
4.5
|
64.2
|
1.0
|
C
|
B:LYS29
|
4.6
|
88.4
|
1.0
|
CA
|
B:MET28
|
4.6
|
16.6
|
1.0
|
CA
|
B:GLY30
|
4.7
|
69.3
|
1.0
|
O
|
B:LYS29
|
4.8
|
54.1
|
1.0
|
O
|
B:LEU31
|
4.8
|
54.6
|
1.0
|
CG
|
B:GLU72
|
4.9
|
46.4
|
1.0
|
N
|
B:LYS29
|
4.9
|
49.1
|
1.0
|
|
Calcium binding site 5 out
of 5 in 1avh
Go back to
Calcium Binding Sites List in 1avh
Calcium binding site 5 out
of 5 in the Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins
 Mono view
 Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca322
b:35.5
occ:1.00
|
OD2
|
B:ASP303
|
2.6
|
40.2
|
1.0
|
O
|
B:GLY263
|
2.7
|
32.0
|
1.0
|
OD1
|
B:ASP303
|
2.7
|
38.3
|
1.0
|
O
|
B:GLY261
|
2.9
|
34.7
|
1.0
|
O
|
B:MET259
|
3.0
|
38.8
|
1.0
|
CG
|
B:ASP303
|
3.0
|
38.0
|
1.0
|
C
|
B:MET259
|
3.6
|
18.9
|
1.0
|
C
|
B:GLY261
|
3.8
|
25.8
|
1.0
|
N
|
B:GLY261
|
3.8
|
34.3
|
1.0
|
C
|
B:GLY263
|
3.8
|
45.5
|
1.0
|
CA
|
B:MET259
|
4.1
|
24.2
|
1.0
|
N
|
B:GLY263
|
4.3
|
46.6
|
1.0
|
C
|
B:LYS260
|
4.4
|
57.6
|
1.0
|
CA
|
B:GLY261
|
4.4
|
51.1
|
1.0
|
N
|
B:LYS260
|
4.5
|
46.8
|
1.0
|
OG1
|
B:THR264
|
4.5
|
35.9
|
1.0
|
CB
|
B:ASP303
|
4.6
|
41.5
|
1.0
|
O
|
B:HOH893
|
4.6
|
34.4
|
1.0
|
CA
|
B:GLY263
|
4.6
|
42.8
|
1.0
|
C
|
B:ALA262
|
4.7
|
33.2
|
1.0
|
CA
|
B:LYS260
|
4.7
|
45.9
|
1.0
|
N
|
B:ALA262
|
4.7
|
42.3
|
1.0
|
CB
|
B:MET259
|
4.8
|
6.0
|
1.0
|
N
|
B:THR264
|
4.8
|
44.4
|
1.0
|
CA
|
B:ALA262
|
4.9
|
29.5
|
1.0
|
|
Reference:
R.Huber,
R.Berendes,
A.Burger,
M.Schneider,
A.Karshikov,
H.Luecke,
J.Romisch,
E.Paques.
Crystal and Molecular Structure of Human Annexin V After Refinement. Implications For Structure, Membrane Binding and Ion Channel Formation of the Annexin Family of Proteins. J.Mol.Biol. V. 223 683 1992.
ISSN: ISSN 0022-2836
PubMed: 1311770
DOI: 10.1016/0022-2836(92)90984-R
Page generated: Thu Jul 11 06:07:04 2024
|