Calcium in PDB 5lpu: Crystal Structure of Annexin A2 Complexed with S100A4

The structure of Crystal Structure of Annexin A2 Complexed with S100A4, PDB code: 5lpu 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)	49.37 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	71.740, 61.240, 148.160, 90.00, 88.69, 90.00
R / Rfree (%)	18.1 / 20.7

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>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Annexin A2 Complexed with S100A4 (pdb code 5lpu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Annexin A2 Complexed with S100A4, PDB code: 5lpu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:0.4 occ:1.00 OE1 A:GLU53 2.2 97.6 1.0 O A:VAL51 2.5 81.5 1.0 O A:GLY50 2.6 85.8 1.0 O A:HOH633 2.6 86.5 1.0 OE2 A:GLU53 2.9 97.9 1.0 CD A:GLU53 2.9 91.8 1.0 O A:HOH694 3.1 88.9 1.0 C A:GLY50 3.6 84.1 1.0 C A:VAL51 3.7 76.1 1.0 N A:VAL51 4.3 82.6 1.0 CA A:VAL51 4.4 76.0 1.0 CG A:GLU53 4.4 74.3 1.0 CB A:VAL51 4.5 67.0 1.0 CA A:GLY50 4.6 86.1 1.0 N A:GLU53 4.6 64.2 1.0 N A:ASP52 4.8 76.6 1.0 CB A:GLU53 4.9 68.0 1.0 CA A:ASP52 5.0 73.6 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:97.8 occ:1.00 O A:LEU91 2.0 54.3 1.0 O A:LYS88 2.1 57.3 1.0 O A:HOH664 2.7 69.1 1.0 OE1 A:GLU96 2.8 70.8 1.0 OE2 A:GLU96 3.0 74.2 1.0 CD A:GLU96 3.0 67.2 1.0 O A:HOH689 3.2 84.1 1.0 C A:LEU91 3.2 60.1 1.0 C A:LYS88 3.4 60.7 1.0 N A:SER92 4.0 62.1 1.0 CA A:SER92 4.1 56.7 1.0 N A:LEU91 4.1 59.2 1.0 CA A:LEU91 4.2 54.5 1.0 C A:SER89 4.2 63.6 1.0 O A:SER89 4.2 66.5 1.0 CG A:GLU96 4.2 56.9 1.0 CA A:SER89 4.2 59.6 1.0 N A:SER89 4.2 56.5 1.0 CA A:LYS88 4.3 58.2 1.0 CB A:SER92 4.5 64.7 1.0 CG A:LYS88 4.6 65.8 1.0 O A:LEU87 4.7 59.2 1.0 N A:ALA90 4.8 63.0 1.0 CB A:GLU96 4.8 54.6 1.0 C A:ALA90 4.9 63.8 1.0 CB A:LEU91 5.0 52.2 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:0.2 occ:1.00 O A:MET118 2.5 57.7 1.0 O A:GLY120 2.7 91.7 1.0 OD1 A:ASP162 2.8 67.3 1.0 OD2 A:ASP162 2.8 74.4 1.0 CG A:ASP162 2.8 63.9 1.0 OG1 A:THR123 3.4 76.8 1.0 C A:GLY120 3.5 99.7 1.0 C A:MET118 3.7 56.4 1.0 CB A:ASP162 3.9 49.8 1.0 CA A:LEU121 4.0 99.9 1.0 N A:LEU121 4.1 0.7 1.0 C A:LEU121 4.2 96.5 1.0 O A:LEU121 4.2 95.5 1.0 N A:GLY120 4.3 90.6 1.0 CA A:MET118 4.4 45.4 1.0 C A:LYS119 4.5 86.2 1.0 CA A:GLY120 4.5 95.3 1.0 CB A:THR123 4.7 63.2 1.0 N A:THR123 4.7 68.8 1.0 N A:LYS119 4.7 65.9 1.0 CA A:ASP162 4.7 50.1 1.0 CB A:MET118 4.8 42.6 1.0 N A:GLY122 4.8 88.2 1.0 CA A:THR123 4.9 58.5 1.0 CA A:LYS119 4.9 78.8 1.0 O A:LYS119 4.9 88.7 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:53.8 occ:1.00 O A:ARG205 2.4 62.0 1.0 O A:GLY207 2.4 50.3 1.0 O A:HOH676 2.5 55.4 1.0 OE2 A:GLU247 2.5 49.0 1.0 O A:HOH617 2.5 70.7 1.0 OE1 A:GLU247 2.5 46.5 1.0 O A:GLY202 2.5 50.2 1.0 CD A:GLU247 2.8 49.7 1.0 C A:GLY202 3.3 49.0 1.0 C A:GLY207 3.4 52.6 1.0 C A:ARG205 3.5 59.7 1.0 N A:GLY207 3.6 60.3 1.0 CA A:GLY207 4.0 57.5 1.0 N A:VAL203 4.1 42.5 1.0 C A:LYS206 4.1 61.5 1.0 CA A:GLY202 4.1 47.0 1.0 CA A:VAL203 4.2 46.7 1.0 CG A:GLU247 4.3 47.6 1.0 OG1 A:THR208 4.3 52.0 1.0 CA A:LYS206 4.4 61.9 1.0 N A:ARG205 4.4 55.2 1.0 N A:LYS206 4.4 60.3 1.0 C A:VAL203 4.4 52.5 1.0 O A:VAL203 4.4 51.0 1.0 CG A:ARG205 4.5 50.7 1.0 CA A:ARG205 4.5 57.3 1.0 N A:THR208 4.5 48.9 1.0 CA A:THR208 4.8 45.7 1.0 O A:LYS206 4.8 60.9 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:40.0 occ:1.00 O A:GLY282 2.4 47.9 1.0 O A:MET278 2.4 38.9 1.0 OD1 A:ASP322 2.5 51.4 1.0 O A:GLY280 2.5 45.9 1.0 OD2 A:ASP322 2.5 39.2 1.0 CG A:ASP322 2.8 47.9 1.0 C A:MET278 3.5 38.5 1.0 C A:GLY282 3.5 42.5 1.0 C A:GLY280 3.7 48.5 1.0 N A:GLY282 4.0 45.8 1.0 CA A:MET278 4.1 35.3 1.0 N A:GLY280 4.1 42.4 1.0 CA A:GLY282 4.2 41.7 1.0 C A:LYS281 4.3 45.9 1.0 C A:LYS279 4.3 43.0 1.0 CB A:ASP322 4.3 45.1 1.0 CA A:GLY280 4.5 43.3 1.0 OG1 A:THR283 4.5 50.5 1.0 N A:LYS279 4.5 39.0 1.0 O A:LYS279 4.6 45.8 1.0 N A:THR283 4.6 39.2 1.0 O A:HOH599 4.6 60.4 1.0 CB A:MET278 4.6 36.5 1.0 N A:LYS281 4.6 44.0 1.0 O A:LYS281 4.7 42.5 1.0 CA A:LYS281 4.8 43.8 1.0 CA A:THR283 4.8 41.4 1.0 O A:HOH586 4.9 44.8 1.0 CA A:LYS279 4.9 40.0 1.0 CA A:ASP322 5.0 47.9 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:0.8 occ:1.00 O B:HOH528 2.5 92.9 1.0 O B:LEU91 2.5 95.5 1.0 OE1 B:GLU96 2.6 0.8 1.0 O B:LYS88 2.6 0.5 1.0 O B:HOH524 3.0 75.8 1.0 CD B:GLU96 3.4 0.1 1.0 OE2 B:GLU96 3.7 0.2 1.0 C B:LEU91 3.7 96.6 1.0 C B:LYS88 3.8 0.2 1.0 CE B:LYS88 4.1 0.5 1.0 CA B:SER92 4.3 98.3 1.0 CD B:LYS88 4.3 0.0 1.0 O B:SER89 4.4 0.4 1.0 N B:SER92 4.4 97.6 1.0 CG B:GLU96 4.5 93.9 1.0 CB B:SER92 4.5 1.0 1.0 C B:SER89 4.6 0.6 1.0 CA B:SER89 4.6 0.8 1.0 N B:SER89 4.7 0.3 1.0 N B:LEU91 4.7 95.6 1.0 CA B:LYS88 4.8 95.8 1.0 CA B:LEU91 4.8 96.2 1.0 CG B:LYS88 4.9 0.3 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca402 b:0.6 occ:1.00 OD2 B:ASP162 2.3 0.4 1.0 O B:GLY120 2.5 0.5 1.0 O B:GLY122 2.6 0.7 1.0 O B:MET118 2.8 0.1 1.0 OG1 B:THR123 3.0 0.9 1.0 CG B:ASP162 3.1 0.4 1.0 OD1 B:ASP162 3.1 0.7 1.0 C B:GLY122 3.6 0.6 1.0 C B:MET118 3.7 1.0 1.0 C B:GLY120 3.7 0.6 1.0 O B:LEU121 3.8 0.1 1.0 C B:LEU121 3.9 0.5 1.0 O B:LYS119 3.9 0.0 1.0 C B:LYS119 4.2 0.8 1.0 CB B:THR123 4.2 0.4 1.0 N B:GLY122 4.3 0.9 1.0 CA B:MET118 4.4 0.6 1.0 CA B:LEU121 4.4 0.5 1.0 N B:THR123 4.5 0.6 1.0 CA B:THR123 4.5 0.7 1.0 CA B:GLY122 4.5 0.6 1.0 N B:LEU121 4.5 0.2 1.0 CB B:ASP162 4.5 0.0 1.0 N B:GLY120 4.6 0.8 1.0 N B:LYS119 4.6 0.4 1.0 CA B:GLY120 4.7 0.1 1.0 CA B:LYS119 4.8 1.0 1.0 CG2 B:THR123 4.9 0.3 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:0.3 occ:1.00 O B:VAL51 2.6 94.5 1.0 O B:HOH527 2.6 95.2 1.0 O B:HOH526 2.7 92.2 1.0 O B:GLY50 2.7 0.0 1.0 C B:VAL51 3.8 91.6 1.0 C B:GLY50 3.8 0.8 1.0 CG B:GLU53 3.9 97.0 1.0 CD B:GLU53 4.0 0.1 1.0 OE2 B:GLU53 4.1 0.7 1.0 CA B:VAL51 4.5 97.6 1.0 N B:GLU53 4.5 84.1 1.0 N B:VAL51 4.5 0.2 1.0 CB B:VAL51 4.6 0.4 1.0 OE1 B:GLU53 4.6 0.3 1.0 CB B:GLU53 4.7 88.5 1.0 CA B:GLY50 4.8 0.2 1.0 N B:ASP52 4.8 85.9 1.0 CA B:ASP52 5.0 87.9 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca404 b:0.2 occ:1.00 OE1 B:GLU247 2.2 0.3 1.0 O B:GLY202 2.6 0.0 1.0 OE2 B:GLU247 2.6 0.9 1.0 CD B:GLU247 2.7 0.0 1.0 O B:ARG205 2.8 0.2 1.0 O B:GLY207 2.9 0.2 1.0 O B:HOH525 3.0 90.3 1.0 C B:GLY202 3.4 0.0 1.0 O B:VAL203 3.7 0.6 1.0 CA B:VAL203 3.9 0.6 1.0 C B:ARG205 3.9 0.6 1.0 O B:LYS206 4.0 0.2 1.0 N B:VAL203 4.0 0.1 1.0 C B:VAL203 4.0 0.4 1.0 C B:GLY207 4.0 1.0 1.0 C B:LYS206 4.2 0.5 1.0 CG B:GLU247 4.2 0.9 1.0 CA B:GLY202 4.4 0.5 1.0 N B:GLY207 4.5 0.3 1.0 CA B:GLY207 4.6 0.0 1.0 CA B:LYS206 4.7 0.5 1.0 N B:ARG205 4.7 0.1 1.0 N B:LYS206 4.7 1.0 1.0 CA B:ARG205 4.8 0.4 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of Annexin A2 Complexed with S100A4


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 Annexin A2 Complexed with S100A4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca405 b:72.6 occ:1.00 OD1 B:ASP322 2.4 0.8 1.0 O B:GLY282 2.5 80.5 1.0 OD2 B:ASP322 2.5 87.8 1.0 O B:HOH505 2.5 62.0 1.0 O B:GLY280 2.6 83.0 1.0 O B:MET278 2.7 89.4 1.0 CG B:ASP322 2.7 92.5 1.0 C B:MET278 3.5 86.6 1.0 C B:GLY282 3.7 79.8 1.0 C B:GLY280 3.8 91.2 1.0 CB B:ASP322 4.1 89.1 1.0 CA B:MET278 4.1 80.5 1.0 N B:GLY282 4.2 88.6 1.0 O B:LYS279 4.3 78.2 1.0 C B:LYS279 4.3 88.2 1.0 OG1 B:THR283 4.3 79.8 1.0 N B:GLY280 4.4 91.6 1.0 N B:LYS279 4.5 83.6 1.0 C B:LYS281 4.5 89.6 1.0 CA B:GLY282 4.5 82.6 1.0 CB B:MET278 4.6 78.3 1.0 CA B:GLY280 4.7 89.0 1.0 N B:THR283 4.7 81.7 1.0 N B:LYS281 4.8 89.9 1.0 CA B:THR283 4.8 82.5 1.0 CA B:LYS281 4.9 90.6 1.0 O B:LYS281 4.9 93.1 1.0 CA B:LYS279 4.9 87.1 1.0

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