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Calcium in PDB 5lq2: Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution

Protein crystallography data

The structure of Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution, PDB code: 5lq2 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) 86.51 / 3.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.370, 99.200, 173.020, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 23.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution (pdb code 5lq2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution, PDB code: 5lq2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5lq2

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Calcium binding site 1 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:0.2
occ:1.00
 O A:HOH502 2.8 85.1 1.0
OE1 A:GLU125 2.8 0.6 1.0
O A:THR123 2.8 91.3 1.0
OE2 A:GLU125 3.1 0.1 1.0
CD A:GLU125 3.4 0.4 1.0
C A:THR123 4.0 0.8 1.0
N A:THR123 4.2 0.8 1.0
C A:GLY122 4.5 0.4 1.0
CA A:GLY122 4.6 0.9 1.0
CA A:THR123 4.8 0.1 1.0
CG A:GLU125 4.9 95.8 1.0

Calcium binding site 2 out of 10 in 5lq2

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Calcium binding site 2 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:91.5
occ:1.00
 O A:ARG205 2.1 76.0 1.0
OE1 A:GLU247 2.2 89.8 1.0
OE2 A:GLU247 2.3 92.1 1.0
CD A:GLU247 2.5 88.8 1.0
O A:GLY207 2.6 79.8 1.0
O A:GLY202 2.7 75.9 1.0
C A:ARG205 3.2 72.8 1.0
N A:GLY207 3.3 71.5 1.0
C A:GLY207 3.6 73.4 1.0
C A:LYS206 3.8 71.1 1.0
CA A:LYS206 3.8 75.6 1.0
C A:GLY202 3.9 82.2 1.0
CA A:GLY207 3.9 75.2 1.0
N A:LYS206 3.9 74.4 1.0
CG A:GLU247 3.9 79.7 1.0
O A:VAL203 4.0 76.0 1.0
OG1 A:THR208 4.3 86.2 1.0
CA A:ARG205 4.3 76.9 1.0
C A:VAL203 4.4 70.0 1.0
N A:ARG205 4.4 78.4 1.0
CA A:VAL203 4.4 74.0 1.0
O A:LYS206 4.6 76.9 1.0
N A:VAL203 4.6 77.8 1.0
CG A:ARG205 4.7 79.7 1.0
CB A:ARG205 4.7 77.4 1.0
N A:THR208 4.8 72.8 1.0
CB A:GLU247 5.0 71.1 1.0
CA A:GLY202 5.0 88.2 1.0

Calcium binding site 3 out of 10 in 5lq2

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Calcium binding site 3 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:65.3
occ:1.00
 OD2 A:ASP322 2.2 61.3 1.0
O A:GLY282 2.3 56.0 1.0
OD1 A:ASP322 2.3 73.0 1.0
O A:MET278 2.4 62.4 1.0
O A:GLY280 2.5 66.7 1.0
CG A:ASP322 2.6 64.3 1.0
C A:GLY282 3.4 61.6 1.0
C A:MET278 3.5 65.7 1.0
N A:GLY282 3.7 65.6 1.0
C A:GLY280 3.7 64.2 1.0
OG1 A:THR283 3.9 93.6 1.0
CA A:GLY282 4.0 65.0 1.0
CA A:MET278 4.1 66.7 1.0
CB A:ASP322 4.1 62.2 1.0
N A:GLY280 4.2 70.2 1.0
C A:LYS281 4.2 65.2 1.0
C A:LYS279 4.4 63.1 1.0
N A:THR283 4.4 68.2 1.0
CA A:GLY280 4.5 66.1 1.0
N A:LYS279 4.7 62.4 1.0
O A:LYS281 4.7 70.0 1.0
N A:LYS281 4.7 64.3 1.0
CA A:THR283 4.7 71.5 1.0
CA A:LYS281 4.7 68.7 1.0
O A:LYS279 4.7 62.5 1.0
CB A:MET278 4.8 65.2 1.0
CA A:ASP322 4.9 64.3 1.0
CB A:THR283 4.9 82.7 1.0

Calcium binding site 4 out of 10 in 5lq2

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Calcium binding site 4 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:0.7
occ:1.00
 OE2 A:GLU53 2.3 0.7 1.0
O A:GLY50 2.8 0.4 1.0
OE1 A:GLU53 2.9 0.7 1.0
CD A:GLU53 3.0 1.0 1.0
C A:GLY50 3.6 0.1 1.0
O A:VAL51 3.8 98.5 1.0
CA A:GLY50 4.0 0.8 1.0
CG A:GLU53 4.4 0.1 1.0
N A:VAL51 4.7 0.8 1.0
C A:VAL51 4.9 98.2 1.0

Calcium binding site 5 out of 10 in 5lq2

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Calcium binding site 5 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:30.0
occ:1.00
 OE1 A:GLU96 2.5 97.8 1.0
O A:LEU91 2.7 87.9 1.0
O A:LYS88 2.8 93.0 1.0
OE2 A:GLU96 3.0 93.8 1.0
CD A:GLU96 3.0 91.0 1.0
C A:LEU91 3.9 95.1 1.0
C A:LYS88 3.9 95.9 1.0
CA A:SER92 4.2 93.0 1.0
CG A:GLU96 4.5 85.4 1.0
N A:SER92 4.5 95.4 1.0
CG A:LYS88 4.6 96.2 1.0
CB A:SER92 4.8 96.7 1.0
CA A:LYS88 4.8 94.5 1.0
N A:SER89 4.9 98.0 1.0
CA A:SER89 5.0 92.8 1.0

Calcium binding site 6 out of 10 in 5lq2

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Calcium binding site 6 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca401

b:0.8
occ:1.00
 O B:GLY50 2.5 0.7 1.0
OE1 B:GLU53 2.7 0.7 1.0
OE2 B:GLU53 2.7 0.1 1.0
O B:VAL51 2.7 0.8 1.0
CD B:GLU53 2.9 0.7 1.0
C B:GLY50 3.4 0.2 1.0
C B:VAL51 3.8 0.6 1.0
CA B:GLY50 4.1 0.1 1.0
N B:VAL51 4.2 0.3 1.0
CG B:GLU53 4.3 0.5 1.0
CA B:VAL51 4.5 0.4 1.0
N B:GLU53 4.8 0.3 1.0
N B:ASP52 4.8 0.8 1.0
CB B:VAL51 4.9 0.2 1.0

Calcium binding site 7 out of 10 in 5lq2

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Calcium binding site 7 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:0.7
occ:1.00
 OE1 B:GLU96 2.3 0.1 1.0
O B:LYS88 2.8 0.8 1.0
O B:LEU91 2.8 0.8 1.0
CD B:GLU96 3.4 0.5 1.0
OE2 B:GLU96 3.9 97.2 1.0
CA B:SER92 3.9 0.7 1.0
C B:LEU91 3.9 0.4 1.0
C B:LYS88 4.0 0.4 1.0
CB B:SER92 4.3 0.3 1.0
N B:SER92 4.4 0.8 1.0
CG B:GLU96 4.6 0.8 1.0
CG B:LYS88 4.7 0.5 1.0
CA B:LYS88 4.9 0.9 1.0
CB B:GLU96 4.9 0.6 1.0
N B:SER89 4.9 1.0 1.0
CA B:SER89 5.0 0.1 1.0

Calcium binding site 8 out of 10 in 5lq2

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Calcium binding site 8 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:76.0
occ:1.00
 O B:GLY280 2.3 67.8 1.0
OD1 B:ASP322 2.3 89.6 1.0
OD2 B:ASP322 2.3 73.6 1.0
O B:GLY282 2.4 70.5 1.0
O B:MET278 2.5 69.5 1.0
CG B:ASP322 2.7 78.6 1.0
C B:GLY280 3.5 77.8 1.0
C B:GLY282 3.6 75.5 1.0
C B:MET278 3.6 71.1 1.0
N B:GLY282 3.8 72.4 1.0
C B:LYS281 4.0 67.5 1.0
OG1 B:THR283 4.1 88.1 1.0
CB B:ASP322 4.2 71.5 1.0
N B:GLY280 4.2 86.4 1.0
CA B:GLY282 4.2 76.8 1.0
CA B:MET278 4.3 69.3 1.0
C B:LYS279 4.3 74.8 1.0
N B:LYS281 4.4 78.4 1.0
CA B:LYS281 4.4 75.8 1.0
CA B:GLY280 4.5 84.3 1.0
O B:LYS281 4.5 63.2 1.0
O B:LYS279 4.5 78.9 1.0
N B:THR283 4.7 81.7 1.0
N B:LYS279 4.7 69.1 1.0
CA B:THR283 4.9 78.6 1.0
CB B:MET278 4.9 74.5 1.0
CA B:ASP322 4.9 77.7 1.0
CA B:LYS279 5.0 67.1 1.0

Calcium binding site 9 out of 10 in 5lq2

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Calcium binding site 9 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:0.7
occ:1.00
 OE1 B:GLU247 2.1 0.8 1.0
O B:ARG205 2.2 0.1 1.0
OE2 B:GLU247 2.3 0.1 1.0
O B:GLY207 2.4 0.3 1.0
CD B:GLU247 2.5 0.5 1.0
O B:GLY202 2.8 0.9 1.0
C B:ARG205 3.2 0.9 1.0
N B:GLY207 3.2 0.3 1.0
C B:GLY207 3.3 0.8 1.0
CA B:LYS206 3.4 0.9 1.0
C B:LYS206 3.6 0.7 1.0
N B:LYS206 3.7 0.5 1.0
CA B:GLY207 3.8 0.2 1.0
CG B:GLU247 3.9 0.9 1.0
C B:GLY202 3.9 0.7 1.0
OG1 B:THR208 4.1 0.2 1.0
CG B:ARG205 4.3 0.0 1.0
CA B:ARG205 4.4 0.1 1.0
N B:THR208 4.4 0.7 1.0
O B:VAL203 4.5 0.6 1.0
O B:LYS206 4.6 0.2 1.0
CA B:VAL203 4.7 0.6 1.0
N B:ARG205 4.8 0.7 1.0
CB B:LYS206 4.8 0.8 1.0
CA B:THR208 4.8 0.7 1.0
N B:VAL203 4.8 0.2 1.0
CB B:ARG205 4.8 0.9 1.0
C B:VAL203 4.8 0.3 1.0
CB B:GLU247 4.8 95.5 1.0
CA B:GLY202 4.8 0.1 1.0

Calcium binding site 10 out of 10 in 5lq2

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Calcium binding site 10 out of 10 in the Crystal Structure of TYR24 Phosphorylated Annexin A2 at 3.4 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 TYR24 Phosphorylated Annexin A2 at 3.4 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:30.0
occ:1.00
 OE2 B:GLU125 2.6 0.5 1.0
CD B:GLU125 2.9 0.3 1.0
O B:THR123 3.1 0.3 1.0
OE1 B:GLU125 3.2 0.4 1.0
CG B:GLU125 3.7 0.5 1.0
C B:THR123 4.4 0.6 1.0
CB B:GLU125 4.5 0.2 1.0
N B:THR123 4.6 0.3 1.0
C B:GLY122 4.7 0.1 1.0
O B:ASP124 4.8 0.8 1.0
CA B:GLY122 4.8 0.8 1.0
O B:LEU121 5.0 0.2 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 07:45:17 2024

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