Calcium in PDB 7zvn: Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
Protein crystallography data
The structure of Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution, PDB code: 7zvn
was solved by
M.Hyjek-Skladanowska,
B.Anderson,
V.Mykhaylyk,
C.Orr,
A.Wagner,
K.Skowronek,
P.Seth,
M.Nowotny,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
43.75 /
1.87
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
55.621,
57.502,
70.478,
90,
90.24,
90
|
R / Rfree (%)
|
16.7 /
19.8
|
Other elements in 7zvn:
The structure of Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
(pdb code 7zvn). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the
Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution, PDB code: 7zvn:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
Calcium binding site 1 out
of 7 in 7zvn
Go back to
Calcium Binding Sites List in 7zvn
Calcium binding site 1 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca409
b:42.9
occ:1.00
|
O
|
A:HOH667
|
2.3
|
45.7
|
1.0
|
O
|
A:HOH759
|
2.4
|
43.0
|
1.0
|
O
|
A:HOH717
|
2.4
|
48.6
|
1.0
|
O
|
A:VAL51
|
2.4
|
38.3
|
1.0
|
O
|
A:GLY50
|
2.4
|
39.9
|
1.0
|
O
|
A:HOH725
|
2.4
|
51.0
|
1.0
|
OE1
|
A:GLU53
|
2.6
|
38.3
|
1.0
|
OE2
|
A:GLU53
|
2.6
|
34.9
|
1.0
|
CD
|
A:GLU53
|
2.9
|
39.5
|
1.0
|
C
|
A:GLY50
|
3.3
|
39.5
|
1.0
|
C
|
A:VAL51
|
3.5
|
37.0
|
1.0
|
N
|
A:VAL51
|
4.1
|
45.5
|
1.0
|
CA
|
A:VAL51
|
4.2
|
45.0
|
1.0
|
CA
|
A:GLY50
|
4.2
|
44.6
|
1.0
|
CB
|
A:VAL51
|
4.3
|
36.2
|
1.0
|
CG
|
A:GLU53
|
4.4
|
31.8
|
1.0
|
N
|
A:GLU53
|
4.6
|
34.4
|
1.0
|
N
|
A:ASP52
|
4.6
|
36.4
|
1.0
|
O
|
A:HOH669
|
4.7
|
47.4
|
1.0
|
CA
|
A:ASP52
|
5.0
|
28.7
|
1.0
|
|
Calcium binding site 2 out
of 7 in 7zvn
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Calcium Binding Sites List in 7zvn
Calcium binding site 2 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca410
b:25.9
occ:1.00
|
O
|
A:MET118
|
2.3
|
25.3
|
1.0
|
O
|
A:GLY120
|
2.4
|
23.0
|
1.0
|
O
|
A:HOH680
|
2.4
|
26.2
|
1.0
|
OD1
|
A:ASP162
|
2.4
|
28.6
|
1.0
|
O
|
A:HOH672
|
2.5
|
31.4
|
1.0
|
O
|
A:GLY122
|
2.5
|
28.1
|
1.0
|
OD2
|
A:ASP162
|
2.6
|
29.7
|
1.0
|
CG
|
A:ASP162
|
2.9
|
28.5
|
1.0
|
C
|
A:MET118
|
3.4
|
35.8
|
1.0
|
C
|
A:GLY120
|
3.6
|
32.7
|
1.0
|
C
|
A:GLY122
|
3.7
|
28.6
|
1.0
|
C
|
A:LEU121
|
4.1
|
27.4
|
1.0
|
C
|
A:LYS119
|
4.1
|
21.8
|
1.0
|
O
|
A:LYS119
|
4.1
|
28.8
|
1.0
|
CA
|
A:MET118
|
4.2
|
25.9
|
1.0
|
N
|
A:GLY122
|
4.2
|
28.5
|
1.0
|
N
|
A:GLY120
|
4.2
|
30.4
|
1.0
|
OG1
|
A:THR123
|
4.2
|
36.5
|
1.0
|
O
|
A:LEU121
|
4.3
|
30.4
|
1.0
|
CB
|
A:ASP162
|
4.4
|
28.8
|
1.0
|
N
|
A:LYS119
|
4.4
|
24.8
|
1.0
|
O
|
A:HOH702
|
4.4
|
55.0
|
1.0
|
CA
|
A:LEU121
|
4.4
|
25.8
|
1.0
|
N
|
A:LEU121
|
4.5
|
26.4
|
1.0
|
CA
|
A:GLY122
|
4.5
|
39.8
|
1.0
|
CA
|
A:GLY120
|
4.5
|
27.6
|
1.0
|
N
|
A:THR123
|
4.6
|
27.3
|
1.0
|
CA
|
A:LYS119
|
4.7
|
28.8
|
1.0
|
O
|
A:HOH589
|
4.7
|
41.0
|
1.0
|
CB
|
A:MET118
|
4.8
|
27.9
|
1.0
|
CA
|
A:THR123
|
4.8
|
26.3
|
1.0
|
CA
|
A:ASP162
|
5.0
|
28.4
|
1.0
|
|
Calcium binding site 3 out
of 7 in 7zvn
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Calcium Binding Sites List in 7zvn
Calcium binding site 3 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca411
b:24.1
occ:1.00
|
O
|
A:ARG205
|
2.3
|
22.8
|
1.0
|
O
|
A:GLY202
|
2.3
|
23.7
|
1.0
|
O
|
A:GLY207
|
2.3
|
28.2
|
1.0
|
O
|
A:HOH739
|
2.4
|
31.3
|
1.0
|
OE1
|
A:GLU247
|
2.4
|
22.0
|
1.0
|
OE2
|
A:GLU247
|
2.5
|
25.9
|
1.0
|
O
|
A:HOH630
|
2.5
|
29.1
|
1.0
|
CD
|
A:GLU247
|
2.8
|
24.3
|
1.0
|
C
|
A:GLY202
|
3.3
|
28.7
|
1.0
|
C
|
A:GLY207
|
3.4
|
22.7
|
1.0
|
C
|
A:ARG205
|
3.5
|
23.0
|
1.0
|
N
|
A:GLY207
|
3.8
|
25.8
|
1.0
|
N
|
A:VAL203
|
4.1
|
21.6
|
1.0
|
CA
|
A:VAL203
|
4.1
|
21.4
|
1.0
|
O
|
A:VAL203
|
4.1
|
21.6
|
1.0
|
C
|
A:LYS206
|
4.1
|
24.9
|
0.5
|
CA
|
A:GLY207
|
4.1
|
25.6
|
1.0
|
C
|
A:LYS206
|
4.1
|
24.9
|
0.5
|
CA
|
A:GLY202
|
4.1
|
23.4
|
1.0
|
O
|
A:HOH524
|
4.2
|
45.9
|
1.0
|
C
|
A:VAL203
|
4.2
|
21.3
|
1.0
|
N
|
A:ARG205
|
4.3
|
23.8
|
1.0
|
CG
|
A:GLU247
|
4.3
|
22.9
|
1.0
|
CG
|
A:ARG205
|
4.3
|
24.8
|
1.0
|
CA
|
A:LYS206
|
4.4
|
25.0
|
0.5
|
O
|
A:HOH566
|
4.4
|
35.5
|
1.0
|
CA
|
A:LYS206
|
4.4
|
25.0
|
0.5
|
OG1
|
A:THR208
|
4.4
|
29.3
|
1.0
|
N
|
A:LYS206
|
4.4
|
23.9
|
0.5
|
N
|
A:LYS206
|
4.4
|
23.9
|
0.5
|
CA
|
A:ARG205
|
4.4
|
26.5
|
1.0
|
N1
|
D:AS13
|
4.5
|
26.2
|
1.0
|
N
|
A:THR208
|
4.5
|
28.0
|
1.0
|
O
|
D:HOH113
|
4.6
|
42.8
|
1.0
|
O
|
A:LYS206
|
4.7
|
25.8
|
0.5
|
O
|
A:LYS206
|
4.8
|
25.8
|
0.5
|
CA
|
A:THR208
|
4.8
|
25.9
|
1.0
|
C2
|
D:AS13
|
4.9
|
22.2
|
1.0
|
O
|
A:HOH745
|
5.0
|
39.5
|
1.0
|
|
Calcium binding site 4 out
of 7 in 7zvn
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Calcium Binding Sites List in 7zvn
Calcium binding site 4 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca412
b:42.6
occ:1.00
|
O
|
A:LYS88
|
2.3
|
44.3
|
1.0
|
O
|
A:LEU91
|
2.3
|
37.0
|
1.0
|
O
|
A:HOH720
|
2.3
|
47.0
|
1.0
|
OE1
|
A:GLU96
|
2.3
|
43.5
|
1.0
|
O
|
A:HOH591
|
2.5
|
40.8
|
1.0
|
O
|
A:HOH756
|
2.6
|
43.6
|
1.0
|
CD
|
A:GLU96
|
3.3
|
43.2
|
1.0
|
C
|
A:LYS88
|
3.5
|
47.7
|
1.0
|
C
|
A:LEU91
|
3.5
|
33.9
|
1.0
|
OE2
|
A:GLU96
|
3.8
|
45.0
|
1.0
|
CA
|
A:SER92
|
4.1
|
28.0
|
1.0
|
N
|
A:SER92
|
4.2
|
36.0
|
1.0
|
O
|
A:SER89
|
4.3
|
46.9
|
1.0
|
CA
|
A:LYS88
|
4.3
|
35.9
|
1.0
|
CB
|
A:SER92
|
4.3
|
32.1
|
1.0
|
N
|
A:SER89
|
4.4
|
44.3
|
1.0
|
C
|
A:SER89
|
4.4
|
43.1
|
1.0
|
CA
|
A:SER89
|
4.4
|
39.3
|
1.0
|
CG
|
A:LYS88
|
4.5
|
48.2
|
1.0
|
N
|
A:LEU91
|
4.5
|
28.7
|
1.0
|
CG
|
A:GLU96
|
4.5
|
31.4
|
1.0
|
CA
|
A:LEU91
|
4.6
|
34.5
|
1.0
|
O
|
A:LEU87
|
5.0
|
37.5
|
1.0
|
|
Calcium binding site 5 out
of 7 in 7zvn
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Calcium Binding Sites List in 7zvn
Calcium binding site 5 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca413
b:20.8
occ:1.00
|
O
|
A:MET278
|
2.3
|
18.3
|
1.0
|
O
|
A:GLY280
|
2.4
|
15.4
|
1.0
|
O
|
A:GLY282
|
2.4
|
24.3
|
1.0
|
OD1
|
A:ASP322
|
2.5
|
21.0
|
1.0
|
OD2
|
A:ASP322
|
2.5
|
21.4
|
1.0
|
CG
|
A:ASP322
|
2.8
|
27.6
|
1.0
|
C
|
A:MET278
|
3.4
|
20.3
|
1.0
|
C
|
A:GLY282
|
3.5
|
24.2
|
1.0
|
C
|
A:GLY280
|
3.6
|
24.1
|
1.0
|
N
|
A:GLY282
|
3.9
|
23.4
|
1.0
|
CA
|
A:MET278
|
4.0
|
20.3
|
1.0
|
N
|
A:GLY280
|
4.1
|
23.2
|
1.0
|
C
|
A:LYS281
|
4.2
|
23.2
|
1.0
|
CA
|
A:GLY282
|
4.2
|
25.0
|
1.0
|
C
|
A:LYS279
|
4.3
|
22.0
|
1.0
|
CB
|
A:ASP322
|
4.3
|
21.2
|
1.0
|
OG1
|
A:THR283
|
4.4
|
25.9
|
1.0
|
CA
|
A:GLY280
|
4.5
|
25.6
|
1.0
|
N
|
A:LYS279
|
4.5
|
17.5
|
1.0
|
O
|
A:HOH598
|
4.5
|
32.5
|
1.0
|
N
|
A:LYS281
|
4.6
|
23.9
|
1.0
|
CB
|
A:MET278
|
4.6
|
18.4
|
1.0
|
N
|
A:THR283
|
4.6
|
25.2
|
1.0
|
O
|
A:LYS279
|
4.6
|
22.9
|
1.0
|
CA
|
A:LYS281
|
4.7
|
23.1
|
1.0
|
O
|
A:LYS281
|
4.7
|
21.5
|
1.0
|
C1
|
A:GOL405
|
4.8
|
31.6
|
1.0
|
O
|
A:HOH611
|
4.8
|
21.8
|
1.0
|
CA
|
A:LYS279
|
4.8
|
20.3
|
1.0
|
CA
|
A:THR283
|
4.9
|
23.7
|
1.0
|
CA
|
A:ASP322
|
5.0
|
22.0
|
1.0
|
|
Calcium binding site 6 out
of 7 in 7zvn
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Calcium Binding Sites List in 7zvn
Calcium binding site 6 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca414
b:30.2
occ:1.00
|
O
|
A:THR123
|
2.3
|
22.8
|
1.0
|
O
|
A:HOH674
|
2.4
|
46.8
|
1.0
|
O
|
A:HOH780
|
2.4
|
66.0
|
1.0
|
O
|
A:HOH681
|
2.4
|
37.4
|
1.0
|
OE1
|
A:GLU125
|
2.5
|
38.5
|
1.0
|
O
|
A:HOH683
|
2.6
|
42.4
|
1.0
|
O
|
A:HOH740
|
2.7
|
47.2
|
1.0
|
O
|
A:HOH503
|
2.7
|
47.1
|
1.0
|
O
|
A:HOH818
|
2.8
|
44.5
|
1.0
|
OE2
|
A:GLU125
|
3.0
|
48.9
|
1.0
|
CD
|
A:GLU125
|
3.1
|
35.0
|
1.0
|
C
|
A:THR123
|
3.5
|
34.1
|
1.0
|
N
|
A:THR123
|
4.0
|
27.3
|
1.0
|
CA
|
A:THR123
|
4.3
|
26.3
|
1.0
|
O
|
A:HOH636
|
4.3
|
43.7
|
1.0
|
N
|
A:ASP124
|
4.5
|
24.2
|
1.0
|
N
|
A:GLU125
|
4.5
|
22.8
|
1.0
|
CG
|
A:GLU125
|
4.6
|
31.9
|
1.0
|
CB
|
A:THR123
|
4.6
|
31.7
|
1.0
|
O
|
A:HOH744
|
4.6
|
48.8
|
1.0
|
O
|
A:HOH665
|
4.7
|
36.8
|
1.0
|
CA
|
A:ASP124
|
4.7
|
23.1
|
1.0
|
|
Calcium binding site 7 out
of 7 in 7zvn
Go back to
Calcium Binding Sites List in 7zvn
Calcium binding site 7 out
of 7 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution
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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 1.87 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca415
b:33.0
occ:0.50
|
OE1
|
A:GLU253
|
2.2
|
49.5
|
1.0
|
O
|
A:HOH686
|
2.3
|
42.0
|
1.0
|
O
|
A:HOH666
|
2.4
|
44.1
|
1.0
|
O
|
A:ARG245
|
2.4
|
30.8
|
1.0
|
O
|
A:VAL248
|
2.4
|
25.3
|
1.0
|
CD
|
A:GLU253
|
3.3
|
33.6
|
1.0
|
C
|
A:ARG245
|
3.4
|
31.5
|
1.0
|
C
|
A:VAL248
|
3.6
|
23.7
|
1.0
|
OE2
|
A:GLU253
|
3.7
|
43.3
|
1.0
|
CA
|
A:ARG245
|
3.9
|
23.6
|
1.0
|
CA
|
A:LYS249
|
4.1
|
21.3
|
1.0
|
N
|
A:LYS249
|
4.3
|
25.6
|
1.0
|
O
|
A:HOH761
|
4.4
|
51.7
|
1.0
|
CG
|
A:GLU253
|
4.4
|
25.8
|
1.0
|
O
|
A:ILE244
|
4.4
|
22.0
|
1.0
|
CB
|
A:LYS249
|
4.5
|
30.6
|
1.0
|
N
|
A:VAL248
|
4.5
|
22.9
|
1.0
|
N
|
A:LYS246
|
4.6
|
26.9
|
1.0
|
CA
|
A:VAL248
|
4.7
|
23.2
|
1.0
|
O
|
A:HOH608
|
4.7
|
46.8
|
1.0
|
CB
|
A:ARG245
|
4.7
|
27.2
|
1.0
|
C
|
A:LYS246
|
4.9
|
28.6
|
1.0
|
CB
|
A:GLU253
|
4.9
|
21.8
|
1.0
|
CA
|
A:LYS246
|
4.9
|
26.1
|
1.0
|
O
|
A:HOH737
|
5.0
|
41.4
|
1.0
|
|
Reference:
M.Hyjek-Skladanowska,
B.A.Anderson,
V.Mykhaylyk,
C.Orr,
A.Wagner,
J.T.Poznanski,
K.Skowronek,
P.Seth,
M.Nowotny.
Structures of Annexin A2-Ps Dna Complexes Show Dominance of Hydrophobic Interactions in Phosphorothioate Binding. Nucleic Acids Res. 2022.
ISSN: ESSN 1362-4962
PubMed: 36124719
DOI: 10.1093/NAR/GKAC774
Page generated: Fri Jul 19 06:37:21 2024
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