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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:

Magnesium (Mg) 1 atom

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 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 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 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 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

Go back to 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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