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Calcium in PDB 5lpx: Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2

Protein crystallography data

The structure of Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2, PDB code: 5lpx was solved by P.Ecsedi, G.Gogl, B.Kiss, L.Nyitray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.05 / 1.90
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.950, 58.760, 182.090, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 18.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 (pdb code 5lpx). 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 Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2, PDB code: 5lpx:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5lpx

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Calcium binding site 1 out of 5 in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2


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 Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:41.5
occ:1.00
 OE2 A:GLU53 2.4 36.9 1.0
O A:HOH722 2.4 45.7 1.0
O A:VAL51 2.4 37.5 1.0
O A:GLY50 2.5 45.1 1.0
OE1 A:GLU53 2.5 36.1 1.0
O A:HOH799 2.5 50.3 1.0
O A:HOH850 2.6 46.7 1.0
O A:HOH842 2.6 44.8 1.0
CD A:GLU53 2.8 34.5 1.0
C A:GLY50 3.4 43.4 1.0
C A:VAL51 3.6 40.4 1.0
N A:VAL51 4.1 38.0 1.0
CA A:VAL51 4.2 37.2 1.0
CB A:VAL51 4.2 36.0 1.0
CG A:GLU53 4.3 32.3 1.0
O A:HOH549 4.3 45.7 1.0
CA A:GLY50 4.4 42.6 1.0
O A:HOH810 4.5 47.2 1.0
N A:GLU53 4.6 31.6 1.0
O A:HOH831 4.6 66.0 1.0
N A:ASP52 4.7 37.4 1.0
CA A:ASP52 4.9 30.7 1.0
O A:HOH543 4.9 33.7 1.0
CG1 A:VAL51 5.0 30.3 1.0

Calcium binding site 2 out of 5 in 5lpx

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Calcium binding site 2 out of 5 in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2


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 Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:48.6
occ:1.00
 O A:LYS88 2.4 39.1 1.0
OE1 A:GLU96 2.4 37.6 1.0
O A:LEU91 2.4 33.9 1.0
O A:HOH801 2.5 57.9 1.0
O A:HOH813 2.5 45.4 1.0
O A:HOH863 2.6 49.7 1.0
O A:HOH885 3.1 71.1 1.0
CD A:GLU96 3.3 41.3 1.0
C A:LEU91 3.6 34.4 1.0
C A:LYS88 3.6 40.1 1.0
OE2 A:GLU96 3.8 47.4 1.0
CA A:SER92 4.1 33.3 1.0
N A:SER92 4.3 32.9 1.0
O A:SER89 4.4 42.9 1.0
CB A:SER92 4.5 37.5 1.0
CG A:GLU96 4.5 30.9 1.0
N A:LEU91 4.5 32.5 1.0
C A:SER89 4.5 42.7 1.0
CA A:LYS88 4.5 38.8 1.0
CA A:SER89 4.5 42.9 1.0
N A:SER89 4.5 39.6 1.0
CG A:LYS88 4.5 48.5 1.0
CA A:LEU91 4.6 30.4 1.0
O A:HOH873 4.8 51.6 1.0
O A:HOH804 4.9 52.2 1.0
CB A:GLU96 4.9 30.1 1.0

Calcium binding site 3 out of 5 in 5lpx

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Calcium binding site 3 out of 5 in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2


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 Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:35.1
occ:1.00
 O A:MET118 2.4 31.0 1.0
O A:GLY122 2.4 33.5 1.0
O A:GLY120 2.5 38.6 1.0
OD2 A:ASP162 2.5 36.0 1.0
O A:HOH536 2.5 37.5 1.0
O A:HOH699 2.5 41.9 1.0
OD1 A:ASP162 2.7 40.3 1.0
CG A:ASP162 2.9 34.8 1.0
C A:MET118 3.4 36.5 1.0
C A:GLY122 3.6 43.4 1.0
C A:GLY120 3.7 37.0 1.0
O A:HOH875 3.8 67.1 1.0
O A:LEU121 4.0 49.1 1.0
C A:LEU121 4.1 42.5 1.0
CA A:MET118 4.1 33.3 1.0
OG1 A:THR123 4.2 40.0 1.0
C A:LYS119 4.2 35.5 1.0
O A:LYS119 4.2 40.6 1.0
N A:GLY120 4.3 38.4 1.0
N A:GLY122 4.3 41.0 1.0
CB A:ASP162 4.4 36.1 1.0
N A:LYS119 4.4 33.5 1.0
CA A:GLY122 4.5 44.6 1.0
N A:THR123 4.5 40.3 1.0
N A:LEU121 4.5 33.5 1.0
CB A:MET118 4.5 34.6 1.0
CA A:LEU121 4.6 41.0 1.0
CA A:GLY120 4.6 37.9 1.0
CA A:LYS119 4.7 33.9 1.0
CA A:THR123 4.7 39.4 1.0
O A:HOH600 4.9 49.5 1.0

Calcium binding site 4 out of 5 in 5lpx

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Calcium binding site 4 out of 5 in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2


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 Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:35.7
occ:1.00
 O A:GLY207 2.3 36.6 1.0
O A:ARG205 2.4 38.9 1.0
O A:GLY202 2.4 34.8 1.0
O A:HOH840 2.4 37.2 1.0
OE1 A:GLU247 2.4 30.2 1.0
O A:HOH715 2.4 42.5 1.0
OE2 A:GLU247 2.5 41.1 1.0
CD A:GLU247 2.8 37.0 1.0
C A:GLY202 3.3 30.8 1.0
C A:GLY207 3.4 39.4 1.0
C A:ARG205 3.5 43.1 1.0
N A:GLY207 3.8 42.3 1.0
CA A:GLY207 4.1 42.7 1.0
CA A:GLY202 4.1 30.5 1.0
C A:LYS206 4.1 46.1 1.0
N A:VAL203 4.2 30.7 1.0
CA A:VAL203 4.3 31.6 1.0
O A:HOH566 4.3 43.2 1.0
OG1 A:THR208 4.3 36.1 1.0
CG A:GLU247 4.3 32.2 1.0
N A:ARG205 4.4 40.9 1.0
O A:HOH533 4.4 45.7 1.0
N A:LYS206 4.4 41.8 1.0
CG A:ARG205 4.5 40.7 1.0
CA A:ARG205 4.5 41.4 1.0
O A:HOH845 4.5 69.7 1.0
CA A:LYS206 4.5 47.3 1.0
N A:THR208 4.5 36.0 1.0
C A:VAL203 4.5 39.3 1.0
O A:VAL203 4.6 37.0 1.0
O A:HOH703 4.7 54.7 1.0
O A:LYS206 4.7 45.8 1.0
O A:HOH614 4.8 53.6 1.0
O A:HOH861 4.8 58.9 1.0
CA A:THR208 4.8 36.5 1.0

Calcium binding site 5 out of 5 in 5lpx

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Calcium binding site 5 out of 5 in the Crystal Structure of Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2


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 Pkc Phosphorylation-Mimicking Mutant (S26E) Annexin A2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:25.6
occ:1.00
 O A:MET278 2.4 23.6 1.0
O A:GLY282 2.4 26.4 1.0
O A:GLY280 2.4 25.4 1.0
OD1 A:ASP322 2.5 25.1 1.0
OD2 A:ASP322 2.5 25.1 1.0
CG A:ASP322 2.8 22.4 1.0
C A:MET278 3.4 24.1 1.0
C A:GLY282 3.6 26.1 1.0
C A:GLY280 3.6 26.9 1.0
N A:GLY282 3.9 25.9 1.0
CA A:MET278 4.0 23.2 1.0
N A:GLY280 4.1 26.2 1.0
C A:LYS281 4.2 28.3 1.0
CA A:GLY282 4.2 26.5 1.0
O A:HOH770 4.3 37.9 1.0
C A:LYS279 4.3 24.3 1.0
CB A:ASP322 4.3 22.1 1.0
CA A:GLY280 4.4 25.1 1.0
OG1 A:THR283 4.4 26.1 1.0
N A:LYS279 4.5 23.8 1.0
CB A:MET278 4.5 20.1 1.0
N A:LYS281 4.6 24.5 1.0
N A:THR283 4.6 24.3 1.0
O A:LYS281 4.6 27.6 1.0
O A:LYS279 4.6 24.6 1.0
CA A:LYS281 4.7 22.3 1.0
O A:HOH605 4.7 23.6 1.0
CA A:THR283 4.8 24.9 1.0
CA A:LYS279 4.8 22.5 1.0
O A:HOH701 4.9 33.7 1.0
CA A:ASP322 5.0 26.5 1.0

Reference:

P.Ecsedi, B.Kiss, G.Gogl, L.Radnai, L.Buday, K.Koprivanacz, K.Liliom, I.Leveles, B.Vertessy, N.Jeszenoi, C.Hetenyi, G.Schlosser, G.Katona, L.Nyitray. Regulation of the Equilibrium Between Closed and Open Conformations of Annexin A2 By N-Terminal Phosphorylation and S100A4-Binding. Structure V. 25 1195 2017.
ISSN: ISSN 1878-4186
PubMed: 28669632
DOI: 10.1016/J.STR.2017.06.001
Page generated: Mon Jul 15 07:44:41 2024

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