Calcium in PDB 6t58: Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone

The structure of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone, PDB code: 6t58 was solved by P.Ecsedi, G.Gogl, L.Nyitray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	95.960, 62.770, 106.020, 90.00, 90.26, 90.00
R / Rfree (%)	23 / 27.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone (pdb code 6t58). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone, PDB code: 6t58:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:59.0 occ:1.00 OD1 A:ASP128 2.1 81.2 1.0 OE1 A:GLU135 2.2 81.9 1.0 O A:GLU130 2.5 65.4 1.0 CG A:ASP128 2.8 70.5 1.0 OD2 A:ASP128 2.9 68.8 1.0 CD A:GLU135 3.0 67.7 1.0 OE2 A:GLU135 3.1 72.8 1.0 CB A:ASN126 3.2 72.1 1.0 OD1 A:ASP124 3.3 71.2 1.0 CG A:ASP124 3.7 68.8 1.0 C A:GLU130 3.7 57.9 1.0 N A:ASN126 3.9 75.2 1.0 OD2 A:ASP124 4.0 68.2 1.0 CA A:ASN126 4.1 70.7 1.0 ND2 A:ASN126 4.2 73.9 1.0 CB A:ASP128 4.2 75.3 1.0 CG A:ASN126 4.3 76.0 1.0 N A:ASP132 4.3 64.7 1.0 N A:ASP128 4.3 65.4 1.0 CA A:VAL131 4.3 54.0 1.0 CA A:ASP124 4.4 69.5 1.0 CG A:GLU135 4.4 59.0 1.0 N A:VAL131 4.5 53.2 1.0 N A:ARG127 4.5 68.8 1.0 C A:ASN126 4.5 67.4 1.0 CB A:ASP124 4.5 67.7 1.0 CG A:ASP132 4.6 58.5 1.0 N A:GLU130 4.6 61.8 1.0 OD2 A:ASP132 4.6 62.9 1.0 N A:SER125 4.6 85.5 1.0 CA A:GLU130 4.7 59.7 1.0 C A:ASP124 4.7 85.1 1.0 C A:VAL131 4.7 65.1 1.0 OD1 A:ASP132 4.7 58.2 1.0 CA A:ASP128 4.8 72.8 1.0 CB A:ASP132 4.9 57.1 1.0

Calcium binding site 2 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:59.1 occ:1.00 OE1 A:GLU473 2.2 79.4 1.0 O A:GLY433 2.2 81.6 1.0 OE2 A:GLU473 2.6 76.1 1.0 CD A:GLU473 2.7 67.3 1.0 O A:ARG431 2.7 72.9 1.0 O A:GLY428 2.8 52.0 1.0 N A:GLY433 3.0 49.8 1.0 C A:GLY433 3.1 60.2 1.0 CA A:GLY433 3.5 53.1 1.0 C A:ARG431 3.6 71.8 1.0 C A:LYS432 3.7 65.1 1.0 C A:GLY428 3.9 47.9 1.0 CA A:LYS432 4.0 67.9 1.0 OG1 A:THR434 4.1 46.2 1.0 CG A:GLU473 4.2 39.7 1.0 N A:LYS432 4.2 75.0 1.0 N A:THR434 4.3 55.8 1.0 CG A:ARG431 4.6 55.9 1.0 O A:VAL429 4.6 66.0 1.0 CA A:VAL429 4.7 46.8 1.0 O A:LYS432 4.7 69.8 1.0 CA A:ARG431 4.7 63.3 1.0 N A:ARG431 4.7 52.4 1.0 N A:VAL429 4.8 45.8 1.0 C A:VAL429 4.8 51.3 1.0 CA A:THR434 4.8 51.2 1.0 CA A:GLY428 4.9 46.9 1.0 CB A:GLU473 4.9 38.9 1.0

Calcium binding site 3 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca605 b:58.0 occ:1.00 O A:GLY276 2.6 61.4 1.0 OE1 A:GLU279 2.7 63.4 1.0 O A:VAL277 2.8 58.4 1.0 OE2 A:GLU279 2.9 55.8 1.0 CD A:GLU279 3.1 59.6 1.0 C A:GLY276 3.3 61.5 1.0 C A:VAL277 3.9 59.1 1.0 CA A:GLY276 3.9 63.6 1.0 N A:VAL277 4.1 61.8 1.0 CA A:VAL277 4.5 60.1 1.0 O A:LYS275 4.5 65.4 1.0 CG A:GLU279 4.6 53.2 1.0 CB A:VAL277 4.8 58.5 1.0 N A:ASP278 5.0 59.3 1.0 N A:GLU279 5.0 55.2 1.0

Calcium binding site 4 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca606 b:64.5 occ:1.00 OD1 A:ASP388 2.2 68.6 1.0 O A:GLY348 2.4 66.9 1.0 O A:GLY346 2.7 80.5 1.0 O A:MET344 2.9 64.4 1.0 CG A:ASP388 3.0 63.0 1.0 OD2 A:ASP388 3.1 61.4 1.0 O A:LEU347 3.4 99.8 1.0 C A:GLY346 3.5 82.3 1.0 C A:GLY348 3.6 69.3 1.0 C A:LEU347 3.7 94.9 1.0 N A:GLY346 4.0 83.0 1.0 N A:GLY348 4.1 83.5 1.0 C A:MET344 4.1 60.2 1.0 CA A:GLY348 4.2 78.8 1.0 N A:LEU347 4.3 95.8 1.0 OG1 A:THR349 4.3 81.5 1.0 CA A:GLY346 4.3 83.7 1.0 CA A:LEU347 4.3 94.4 1.0 CB A:ASP388 4.4 56.2 1.0 N A:THR349 4.6 66.0 1.0 CA A:MET344 4.9 50.6 1.0 C A:LYS345 4.9 78.9 1.0 CA A:ASP388 4.9 59.3 1.0 CA A:THR349 4.9 62.2 1.0

Calcium binding site 5 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca607 b:0.4 occ:1.00 OD1 A:ASN224 2.2 0.9 1.0 OD1 A:ASP222 2.3 1.0 1.0 OE2 A:GLU233 2.4 0.6 1.0 CA A:ASP222 2.7 0.9 1.0 CG A:ASP222 2.8 0.6 1.0 C A:ASP222 2.9 0.3 1.0 OE1 A:GLU233 3.0 0.2 1.0 N A:SER223 3.0 0.7 1.0 OD1 A:ASP226 3.1 0.3 1.0 CD A:GLU233 3.1 0.0 1.0 CG A:ASN224 3.1 0.0 1.0 N A:ARG225 3.2 0.6 1.0 CB A:ASP222 3.3 0.1 1.0 N A:ASN224 3.3 0.5 1.0 O A:GLU228 3.3 0.5 1.0 O A:ASP222 3.6 0.0 1.0 OD2 A:ASP222 3.7 0.5 1.0 N A:ASP226 3.8 0.8 1.0 ND2 A:ASN224 3.8 1.0 1.0 C A:SER223 3.9 0.0 1.0 C A:ASN224 3.9 0.8 1.0 CA A:ASN224 3.9 0.9 1.0 O A:LEU221 3.9 1.0 1.0 N A:ASP222 3.9 0.2 1.0 CG A:ASP226 4.0 0.1 1.0 CA A:SER223 4.0 0.2 0.0 CA A:ARG225 4.1 0.0 1.0 CB A:ASN224 4.1 0.9 1.0 C A:LEU221 4.4 0.0 1.0 C A:ARG225 4.5 0.6 1.0 C A:GLU228 4.5 0.7 1.0 N A:ASN227 4.5 0.5 1.0 CG A:GLU233 4.6 1.0 1.0 OD2 A:ASP226 4.6 0.0 1.0 OG A:SER223 4.6 0.5 1.0 CA A:ASP226 4.7 0.0 1.0 O A:SER223 4.8 0.7 1.0 CB A:ASP226 4.9 0.5 1.0 O A:ASN224 4.9 0.5 1.0 CB A:SER223 5.0 0.5 1.0

Calcium binding site 6 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca608 b:78.8 occ:1.00 O A:THR349 2.6 60.5 1.0 OE2 A:GLU351 2.7 75.8 1.0 OE1 A:GLU351 2.7 81.7 1.0 CD A:GLU351 3.0 72.2 1.0 C A:THR349 3.8 55.4 1.0 N A:THR349 4.0 66.0 1.0 CA A:THR349 4.4 62.2 1.0 CG A:GLU351 4.5 57.5 1.0 CB A:THR349 4.7 67.4 1.0 N A:GLU351 4.8 63.5 1.0 N A:ASP350 4.9 48.2 1.0

Calcium binding site 7 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca609 b:0.1 occ:1.00 O A:LYS187 2.3 0.3 1.0 OE1 A:GLU192 2.4 0.1 1.0 O A:ASP184 2.4 0.5 1.0 O A:GLU182 2.6 0.7 1.0 N A:ASP184 2.9 0.7 1.0 C A:ASP184 3.3 0.9 1.0 C A:GLY183 3.3 0.2 1.0 CD A:GLU192 3.3 0.0 1.0 C A:GLU182 3.5 0.7 1.0 C A:LYS187 3.5 0.2 1.0 CA A:GLY183 3.5 0.5 1.0 O A:SER179 3.5 0.6 1.0 CA A:ASP184 3.6 0.5 1.0 N A:ASN189 3.7 0.6 1.0 CB A:ASN189 3.7 0.6 1.0 OE2 A:GLU192 3.8 0.4 1.0 N A:GLY183 3.9 1.0 1.0 CB A:ASP184 4.1 0.4 1.0 O A:GLY183 4.2 0.3 1.0 N A:LYS187 4.2 0.9 1.0 CA A:ASN189 4.2 0.7 1.0 CA A:LYS187 4.3 0.5 1.0 C A:LEU188 4.4 0.5 1.0 N A:LEU188 4.5 0.0 1.0 CB A:LYS187 4.5 0.1 1.0 CG A:GLU192 4.5 0.9 1.0 N A:LYS185 4.6 0.3 1.0 CA A:LEU188 4.6 0.7 1.0 C A:SER179 4.6 0.2 1.0 N A:GLU182 4.7 0.6 1.0 CA A:GLU182 4.7 0.3 1.0

Calcium binding site 8 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca610 b:45.1 occ:1.00 O A:GLY508 2.1 60.1 1.0 OD1 A:ASP548 2.3 59.9 1.0 OD2 A:ASP548 2.3 55.2 1.0 CG A:ASP548 2.6 50.1 1.0 O A:GLY506 2.7 53.9 1.0 O A:MET504 3.0 36.9 1.0 C A:GLY508 3.1 44.9 1.0 N A:GLY508 3.5 42.1 1.0 CA A:GLY508 3.6 41.6 1.0 C A:MET504 3.8 44.1 1.0 C A:GLY506 3.9 44.3 1.0 CB A:ASP548 4.0 38.8 1.0 OG1 A:THR509 4.1 42.2 1.0 N A:THR509 4.2 41.9 1.0 CA A:MET504 4.3 37.2 1.0 C A:LYS507 4.3 42.1 1.0 C A:LYS505 4.4 46.9 1.0 N A:GLY506 4.4 49.9 1.0 O A:LYS505 4.5 43.0 1.0 CA A:THR509 4.6 39.6 1.0 N A:LYS505 4.7 38.9 1.0 CA A:ASP548 4.7 40.4 1.0 CA A:GLY506 4.8 54.1 1.0 N A:LYS507 4.8 41.3 1.0 CA A:LYS507 4.8 42.7 1.0 CA A:LYS505 5.0 36.1 1.0 CB A:THR509 5.0 38.0 1.0 CB A:MET504 5.0 44.4 1.0

Calcium binding site 9 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca611 b:48.4 occ:1.00 OD2 B:ASP296 2.4 64.8 1.0 O A:LYS314 2.5 65.5 1.0 OE1 A:GLU322 2.6 57.5 1.0 OD1 B:ASP296 2.9 65.5 1.0 CG B:ASP296 3.0 65.2 1.0 O A:LEU317 3.0 52.3 1.0 CD A:GLU322 3.6 55.1 1.0 C A:LYS314 3.7 55.2 1.0 OE2 A:GLU322 3.9 54.1 1.0 O B:GLU292 4.1 61.3 1.0 C A:LEU317 4.2 51.6 1.0 CA A:SER315 4.4 58.1 1.0 CB B:GLU292 4.4 64.1 1.0 CB B:ASP296 4.4 65.8 1.0 N A:SER315 4.5 56.4 1.0 N A:LEU317 4.6 59.8 1.0 C A:SER315 4.6 58.0 1.0 CG A:LYS314 4.6 68.2 1.0 CA A:LYS314 4.6 52.9 1.0 C B:GLU292 4.6 61.8 1.0 O A:SER315 4.8 59.2 1.0 CG A:GLU322 4.8 51.7 1.0 OE1 B:GLU292 4.9 76.0 1.0 CA A:LEU317 4.9 51.9 1.0 CA B:GLU292 5.0 62.1 1.0 N A:ALA316 5.0 56.7 1.0

Calcium binding site 10 out of 16 in the Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca612 b:53.9 occ:1.00 O A:ASP86 2.4 55.0 1.0 OE1 A:GLU94 2.4 53.8 1.0 O A:LYS89 2.5 53.8 1.0 O A:GLU84 2.5 54.4 1.0 O A:SER81 2.7 55.7 1.0 OE2 A:GLU94 2.8 54.4 1.0 CD A:GLU94 2.9 55.3 1.0 C A:ASP86 3.5 55.9 1.0 C A:GLU84 3.7 54.7 1.0 C A:LYS89 3.7 55.4 1.0 C A:SER81 3.7 56.4 1.0 N A:ASP86 3.9 54.6 1.0 C A:GLY85 4.1 55.1 1.0 OE1 A:GLU130 4.2 60.0 1.0 CA A:SER81 4.2 55.8 1.0 CA A:ASP86 4.2 55.6 1.0 N A:ASN91 4.2 51.6 1.0 ND2 A:ASN91 4.3 51.7 1.0 CG A:GLU94 4.4 53.8 1.0 CA A:LEU90 4.4 54.2 1.0 N A:GLU84 4.4 56.3 1.0 N A:LEU90 4.5 54.3 1.0 CA A:GLY85 4.5 54.3 1.0 N A:GLY85 4.5 54.7 1.0 N A:LYS87 4.6 57.5 1.0 CB A:ASP86 4.6 65.4 1.0 CA A:GLU84 4.6 55.5 1.0 C A:LEU90 4.6 53.9 1.0 N A:LYS89 4.6 58.6 1.0 O A:GLY85 4.6 65.3 1.0 CA A:LYS89 4.7 58.6 1.0 CG A:ASN91 4.8 51.5 1.0 CA A:LYS87 4.8 58.3 1.0 CB A:SER81 4.8 56.0 1.0 N A:GLY82 4.9 59.3 1.0 O A:TYR80 4.9 56.4 1.0 CB A:ASN91 4.9 50.9 1.0

P.Ecsedi, G.Gogl, H.Hof, B.Kiss, V.Harmat, L.Nyitray. Structure Determination of the Transactivation Domain of P53 in Complex with S100A4 Using Annexin A2 As A Crystallization Chaperone Structure 2020.
ISSN: ISSN 0969-2126
DOI: 10.1016/J.STR.2020.05.001