Calcium in PDB 7zvx: Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution, PDB code: 7zvx 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) 35.85 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.23, 60.36, 128.43, 90, 97.17, 90
R / Rfree (%) 18.5 / 24.2

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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution (pdb code 7zvx). 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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution, PDB code: 7zvx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 7zvx

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Calcium binding site 1 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:87.9
occ:1.00
 OD1 A:ASP162 2.4 71.5 1.0
O A:GLY122 2.4 66.1 1.0
O A:MET118 2.9 69.1 1.0
O A:GLY120 2.9 72.2 1.0
O A:LYS119 3.2 66.9 1.0
C A:GLY122 3.2 67.3 1.0
C A:MET118 3.3 62.8 1.0
CG A:ASP162 3.3 68.5 1.0
OG1 A:THR123 3.6 66.8 1.0
C A:GLY120 3.6 68.7 1.0
O A:LEU121 3.6 85.4 1.0
O A:HOH510 3.6 75.8 1.0
C A:LEU121 3.6 78.1 1.0
C A:LYS119 3.6 65.5 1.0
OD2 A:ASP162 3.8 73.2 1.0
N A:LYS119 3.9 60.4 1.0
N A:GLY122 3.9 77.2 1.0
N A:THR123 4.0 63.1 1.0
CA A:MET118 4.0 48.8 1.0
CA A:GLY122 4.1 71.7 1.0
N A:LEU121 4.1 70.8 1.0
CA A:THR123 4.2 62.0 1.0
CA A:LEU121 4.2 84.4 1.0
CA A:LYS119 4.2 56.0 1.0
N A:GLY120 4.2 68.9 1.0
CB A:ASP162 4.4 49.7 1.0
CA A:GLY120 4.5 68.8 1.0
CB A:THR123 4.5 63.4 1.0
CB A:MET118 4.9 43.2 1.0

Calcium binding site 2 out of 11 in 7zvx

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Calcium binding site 2 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:49.0
occ:1.00
 O A:GLY280 2.5 31.0 1.0
O A:MET278 2.5 40.2 1.0
O A:GLY282 2.5 39.3 1.0
OD2 A:ASP322 2.6 45.5 1.0
OD1 A:ASP322 2.6 53.2 1.0
CG A:ASP322 3.0 45.0 1.0
C A:MET278 3.5 34.0 1.0
C A:GLY282 3.5 38.5 1.0
C A:GLY280 3.7 32.1 1.0
N A:GLY282 3.9 34.1 1.0
CA A:MET278 4.0 35.3 1.0
CA A:GLY282 4.1 27.2 1.0
O A:HOH529 4.3 40.8 1.0
N A:GLY280 4.3 35.1 1.0
C A:LYS281 4.3 41.6 1.0
OG1 A:THR283 4.3 43.5 1.0
C A:LYS279 4.4 38.0 1.0
C1 A:EDO412 4.4 36.6 1.0
CA A:GLY280 4.5 30.1 1.0
CB A:ASP322 4.5 35.7 1.0
N A:LYS279 4.5 34.2 1.0
N A:LYS281 4.6 34.9 1.0
N A:THR283 4.6 38.0 1.0
O A:HOH519 4.6 34.9 1.0
CB A:MET278 4.7 36.1 1.0
O A:LYS279 4.7 45.6 1.0
O A:LYS281 4.7 42.4 1.0
CA A:LYS281 4.8 32.8 1.0
O A:HOH555 4.8 35.5 1.0
CA A:LYS279 4.9 34.4 1.0
CA A:THR283 5.0 36.5 1.0

Calcium binding site 3 out of 11 in 7zvx

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Calcium binding site 3 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:76.8
occ:1.00
 O A:LEU91 2.6 43.1 1.0
O A:LYS88 2.7 47.0 1.0
O A:HOH592 2.8 61.3 1.0
OE1 A:GLU96 3.4 60.9 1.0
O A:HOH599 3.5 34.5 1.0
C A:LEU91 3.8 39.0 1.0
C A:LYS88 3.9 41.2 1.0
O A:SER89 4.1 44.7 0.5
O A:SER89 4.2 45.5 0.5
C A:SER89 4.3 43.1 0.5
CA A:SER89 4.3 41.0 0.5
CA A:SER89 4.3 41.1 0.5
C A:SER89 4.3 42.9 0.5
CA A:SER92 4.3 32.3 1.0
CB A:SER92 4.4 38.5 1.0
CD A:GLU96 4.5 60.6 1.0
N A:SER92 4.5 45.3 1.0
N A:SER89 4.6 39.6 0.5
N A:SER89 4.6 39.6 0.5
N A:LEU91 4.7 38.1 1.0
CA A:LEU91 4.9 34.5 1.0
CA A:LYS88 5.0 40.2 1.0

Calcium binding site 4 out of 11 in 7zvx

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Calcium binding site 4 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:87.1
occ:1.00
 O A:ARG245 3.0 52.1 1.0
O A:VAL248 4.0 51.1 1.0
OE1 A:GLU253 4.1 57.9 1.0
C A:ARG245 4.2 48.7 1.0
CD A:GLU253 4.4 55.1 1.0
CB A:LYS249 4.4 43.1 1.0
OE2 A:GLU253 4.5 64.9 1.0
CA A:LYS249 4.8 43.9 1.0
CA A:ARG245 4.9 40.8 1.0

Calcium binding site 5 out of 11 in 7zvx

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Calcium binding site 5 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:89.3
occ:1.00
 OE1 A:GLU247 2.9 60.2 1.0
OE2 A:GLU247 3.2 59.6 1.0
O A:GLY207 3.3 66.5 1.0
CD A:GLU247 3.4 63.2 1.0
N A:GLY207 3.7 52.9 1.0
O A:ARG205 3.8 68.8 1.0
C A:GLY207 4.1 60.7 1.0
O A:GLY202 4.2 64.6 1.0
CA A:GLY207 4.3 59.3 1.0
CA A:LYS206 4.5 67.1 1.0
C A:LYS206 4.6 64.7 1.0
OG1 A:THR208 4.6 59.5 1.0
C A:ARG205 4.8 60.4 1.0
CG A:GLU247 4.9 46.5 1.0

Calcium binding site 6 out of 11 in 7zvx

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Calcium binding site 6 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:75.8
occ:1.00
 O B:LEU91 2.6 36.9 1.0
O B:LYS88 2.8 48.7 1.0
O B:HOH577 3.0 51.5 1.0
O B:HOH612 3.3 38.5 1.0
OE1 B:GLU96 3.3 51.7 1.0
O B:SER89 3.7 57.1 1.0
C B:LEU91 3.8 37.4 1.0
C B:LYS88 4.0 45.0 1.0
C B:SER89 4.1 40.6 1.0
CB B:SER92 4.3 43.7 1.0
CA B:SER92 4.3 34.7 1.0
CA B:SER89 4.3 42.4 1.0
N B:SER92 4.5 37.5 1.0
CD B:GLU96 4.5 51.2 1.0
N B:LEU91 4.7 37.5 1.0
N B:SER89 4.7 42.3 1.0
CA B:LEU91 4.9 32.5 1.0
N B:ALA90 4.9 42.3 1.0

Calcium binding site 7 out of 11 in 7zvx

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Calcium binding site 7 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 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 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:91.4
occ:1.00
 OD1 B:ASP162 2.4 56.7 1.0
O B:MET118 2.6 74.0 1.0
O B:GLY120 2.7 73.6 1.0
O B:GLY122 2.8 61.0 1.0
CG B:ASP162 3.5 65.9 1.0
C B:GLY120 3.5 74.9 1.0
C B:MET118 3.6 52.3 1.0
OD2 B:ASP162 3.8 80.4 1.0
C B:GLY122 3.8 68.3 1.0
C B:LEU121 4.0 82.2 1.0
O B:LEU121 4.0 77.8 1.0
OG1 B:THR123 4.0 65.0 1.0
C B:LYS119 4.1 72.7 1.0
O B:LYS119 4.1 71.3 1.0
N B:GLY120 4.2 76.2 1.0
N B:LEU121 4.2 74.1 1.0
CA B:MET118 4.3 54.0 1.0
CA B:LEU121 4.3 89.0 1.0
N B:GLY122 4.4 80.2 1.0
CA B:GLY120 4.4 75.2 1.0
N B:LYS119 4.5 62.5 1.0
CA B:LYS119 4.6 66.7 1.0
N B:THR123 4.7 62.5 1.0
CA B:GLY122 4.7 72.6 1.0
CB B:ASP162 4.7 49.1 1.0
CA B:THR123 4.9 57.5 1.0

Calcium binding site 8 out of 11 in 7zvx

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Calcium binding site 8 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution


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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:76.0
occ:1.00
 O B:GLY207 2.3 42.5 1.0
OE1 B:GLU247 2.5 60.1 1.0
O B:ARG205 2.7 61.1 1.0
O B:GLY202 2.7 57.0 1.0
CD B:GLU247 3.2 61.1 1.0
OE2 B:GLU247 3.3 65.1 1.0
C B:GLY207 3.3 55.2 1.0
N B:GLY207 3.5 36.4 1.0
C B:ARG205 3.5 60.4 1.0
C B:GLY202 3.6 43.1 1.0
C B:LYS206 3.8 53.1 1.0
CA B:GLY207 3.9 40.4 1.0
CA B:LYS206 4.0 55.4 1.0
CG B:ARG205 4.0 55.5 1.0
N B:LYS206 4.1 53.2 1.0
CA B:GLY202 4.4 43.3 1.0
OG1 B:THR208 4.4 49.4 1.0
N B:THR208 4.4 51.2 1.0
N B:ARG205 4.4 48.9 1.0
CA B:ARG205 4.5 52.2 1.0
O B:LYS206 4.5 54.7 1.0
N B:VAL203 4.5 39.7 1.0
CA B:VAL203 4.6 39.5 1.0
CG B:GLU247 4.6 40.6 1.0
CA B:THR208 4.7 45.6 1.0
C B:VAL203 4.8 47.8 1.0
O B:VAL203 4.8 54.3 1.0
CB B:ARG205 4.9 54.0 1.0

Calcium binding site 9 out of 11 in 7zvx

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Calcium binding site 9 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution


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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:95.8
occ:1.00
 OE2 B:GLU253 2.8 73.5 1.0
NZ B:LYS249 3.0 63.0 1.0
OE1 B:GLU253 3.0 51.6 1.0
CD B:GLU253 3.0 55.7 1.0
O B:ARG245 3.7 44.5 1.0
CA B:ARG245 4.0 42.6 1.0
CB B:ARG245 4.0 28.9 1.0
CG B:ARG245 4.0 45.2 1.0
CG B:GLU253 4.1 34.7 1.0
CE B:LYS249 4.2 59.8 1.0
C B:ARG245 4.3 46.9 1.0
CD B:LYS249 4.4 66.5 1.0
O B:VAL248 4.4 44.8 1.0
CD B:ARG245 4.7 45.9 1.0

Calcium binding site 10 out of 11 in 7zvx

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Calcium binding site 10 out of 11 in the Crystal Structure of Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution


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 Human Annexin A2 in Complex with Full Phosphorothioate 5-10 2'-Methoxyethyl Dna Gapmer Antisense Oligonucleotide Solved at 2.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:38.5
occ:1.00
 O B:GLY282 2.4 36.0 1.0
O B:GLY280 2.4 40.6 1.0
O B:MET278 2.6 39.3 1.0
OD2 B:ASP322 2.7 45.6 1.0
OD1 B:ASP322 2.8 41.2 1.0
CG B:ASP322 3.1 41.7 1.0
C B:GLY282 3.4 35.5 1.0
C B:MET278 3.5 28.2 1.0
C B:GLY280 3.5 31.1 1.0
N B:GLY282 3.8 36.4 1.0
N B:GLY280 4.0 41.7 1.0
CA B:GLY282 4.1 28.4 1.0
CA B:MET278 4.1 31.1 1.0
C B:LYS281 4.2 37.8 1.0
O B:HOH536 4.2 41.7 1.0
OG1 B:THR283 4.2 43.2 1.0
C1 B:EDO412 4.3 36.2 1.0
CA B:GLY280 4.3 26.9 1.0
C B:LYS279 4.3 30.5 1.0
N B:LYS279 4.4 29.1 1.0
N B:THR283 4.5 37.3 1.0
N B:LYS281 4.5 34.1 1.0
CB B:ASP322 4.6 27.4 1.0
O B:LYS281 4.6 37.3 1.0
CA B:LYS281 4.7 29.6 1.0
CA B:LYS279 4.8 30.3 1.0
O B:LYS279 4.8 35.1 1.0
CA B:THR283 4.8 30.9 1.0
CB B:MET278 4.8 28.4 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: Tue Apr 4 19:22:06 2023

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