Atomistry » Calcium » PDB 7zci-8a0l » 7zvn
Atomistry »
  Calcium »
    PDB 7zci-8a0l »
      7zvn »

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

Go back to 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

Go back to 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

Go back to 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

Go back to 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

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy