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Calcium in PDB 7nmi: Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone

Protein crystallography data

The structure of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone, PDB code: 7nmi was solved by P.Ecsedi, L.Nyitray, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.92, 86.77, 113.42, 90, 90, 90
R / Rfree (%) 19.4 / 22.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone (pdb code 7nmi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone, PDB code: 7nmi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 7nmi

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Calcium binding site 1 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:66.8
occ:1.00
 O B:SER24 2.3 38.7 1.0
O B:GLU22 2.4 42.4 1.0
O B:SER19 2.5 43.9 1.0
O B:THR27 2.5 39.8 1.0
O B:HOH766 2.6 40.2 1.0
OE2 B:GLU32 2.6 79.6 1.0
OE1 B:GLU32 3.2 91.0 1.0
CD B:GLU32 3.3 84.5 1.0
N B:SER24 3.4 37.5 1.0
C B:SER24 3.4 47.2 1.0
C B:SER19 3.5 52.9 1.0
C B:GLU22 3.6 45.5 1.0
C B:THR27 3.6 42.1 1.0
C B:GLY23 3.8 41.9 1.0
CA B:SER19 3.9 47.4 1.0
CA B:SER24 3.9 45.4 1.0
CA B:GLY23 4.2 36.8 1.0
CB B:SER19 4.2 48.5 1.0
N B:THR29 4.3 44.2 1.0
CG2 B:THR29 4.3 39.3 1.0
N B:GLY23 4.4 42.4 1.0
OG1 B:THR27 4.4 46.9 1.0
CA B:LEU28 4.4 35.7 1.0
N B:LEU28 4.4 38.9 1.0
O B:GLY23 4.5 41.2 1.0
N B:THR27 4.5 50.2 1.0
N B:GLU22 4.5 50.6 1.0
N B:THR25 4.6 49.6 1.0
CB B:SER24 4.6 50.2 1.0
CA B:THR27 4.6 48.7 1.0
N B:GLY20 4.7 50.3 1.0
CA B:GLU22 4.7 50.4 1.0
C B:LEU28 4.7 41.2 1.0
CG B:GLU32 4.8 71.1 1.0
CA B:THR25 4.9 47.8 1.0
CG B:GLU22 5.0 57.7 1.0

Calcium binding site 2 out of 9 in 7nmi

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Calcium binding site 2 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:36.7
occ:1.00
 O B:GLN68 2.3 37.2 1.0
OD1 B:ASN64 2.3 38.0 1.0
OD1 B:ASP62 2.3 41.6 1.0
OD1 B:ASP66 2.4 39.9 1.0
O B:HOH768 2.5 34.9 1.0
OE2 B:GLU73 2.5 40.4 1.0
OE1 B:GLU73 2.6 37.6 1.0
CD B:GLU73 2.9 36.5 1.0
CG B:ASN64 3.3 41.3 1.0
CG B:ASP66 3.3 41.2 1.0
C B:GLN68 3.4 34.2 1.0
CG B:ASP62 3.5 44.3 1.0
OD2 B:ASP66 3.7 38.8 1.0
ND2 B:ASN64 3.8 41.0 1.0
CA B:ASP62 4.1 37.5 1.0
N B:GLN68 4.2 38.3 1.0
N B:ASP66 4.3 43.1 1.0
CB B:ASP62 4.3 41.1 1.0
N B:ASN64 4.3 45.0 1.0
N B:VAL69 4.3 35.3 1.0
CA B:GLN68 4.3 38.8 1.0
OD2 B:ASP70 4.3 47.1 1.0
OD2 B:ASP62 4.4 42.5 1.0
CA B:VAL69 4.4 35.8 1.0
N B:ASP70 4.4 31.8 1.0
CG B:GLU73 4.4 31.3 1.0
C B:ASP62 4.4 38.9 1.0
N B:GLY65 4.4 42.8 1.0
N B:ALA63 4.5 39.4 1.0
CB B:ASN64 4.6 43.9 1.0
CB B:ASP66 4.6 37.4 1.0
O B:HOH782 4.7 56.4 1.0
CA B:ASN64 4.8 49.2 1.0
CB B:GLN68 4.8 42.6 1.0
CG B:ASP70 4.8 42.4 1.0
C B:ASN64 4.8 46.4 1.0
CA B:ASP66 4.8 39.1 1.0
C B:VAL69 4.9 36.9 1.0
N B:ALA67 4.9 41.6 1.0

Calcium binding site 3 out of 9 in 7nmi

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Calcium binding site 3 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:46.7
occ:1.00
 O B:HOH884 2.4 49.5 1.0
O B:VAL223 2.4 41.4 1.0
O B:GLY222 2.4 44.6 1.0
O B:HOH823 2.5 48.8 1.0
OE1 B:GLU225 2.5 39.6 1.0
O B:HOH904 2.6 50.9 1.0
OE2 B:GLU225 2.6 44.4 1.0
O B:HOH901 2.7 48.3 1.0
CD B:GLU225 2.9 38.2 1.0
C B:GLY222 3.3 45.9 1.0
C B:VAL223 3.5 41.5 1.0
N B:VAL223 4.1 46.4 1.0
CA B:VAL223 4.1 40.1 1.0
CA B:GLY222 4.3 44.9 1.0
CB B:VAL223 4.3 42.4 1.0
O B:HOH800 4.3 53.2 1.0
CG B:GLU225 4.4 38.9 1.0
N B:ASP224 4.6 46.4 1.0
O B:HOH851 4.6 54.1 1.0
N B:GLU225 4.7 41.2 1.0
O B:HOH711 4.8 43.4 1.0
CA B:ASP224 4.9 40.0 1.0
CG1 B:VAL223 5.0 38.6 1.0

Calcium binding site 4 out of 9 in 7nmi

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Calcium binding site 4 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:46.4
occ:1.00
 O B:LYS260 2.3 44.2 1.0
O B:HOH898 2.3 47.2 1.0
O B:LEU263 2.4 41.7 1.0
O B:HOH733 2.4 48.6 1.0
O B:HOH803 2.4 48.1 1.0
OE1 B:GLU268 2.4 46.5 1.0
O B:HOH907 2.5 49.0 1.0
CD B:GLU268 3.4 42.6 1.0
C B:LYS260 3.5 43.9 1.0
C B:LEU263 3.5 39.5 1.0
OE2 B:GLU268 3.8 45.0 1.0
CA B:SER264 4.1 40.5 1.0
O B:SER261 4.2 47.5 1.0
N B:SER264 4.3 38.1 1.0
C B:SER261 4.4 46.2 1.0
CA B:LYS260 4.4 44.3 1.0
N B:SER261 4.4 40.7 1.0
CA B:SER261 4.4 44.3 1.0
N B:LEU263 4.5 39.3 1.0
CB B:SER264 4.6 36.5 1.0
CG B:LYS260 4.6 48.4 1.0
CA B:LEU263 4.6 40.7 1.0
CG B:GLU268 4.8 34.4 1.0

Calcium binding site 5 out of 9 in 7nmi

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Calcium binding site 5 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:41.8
occ:1.00
 O B:GLY292 2.3 42.4 1.0
O B:GLY294 2.4 41.7 1.0
O B:HOH877 2.5 50.3 1.0
O B:MET290 2.5 47.4 1.0
OD1 B:ASP334 2.6 50.6 1.0
OD2 B:ASP334 2.9 54.9 1.0
CG B:ASP334 3.1 50.3 1.0
C B:GLY292 3.5 48.2 1.0
C B:GLY294 3.6 48.5 1.0
C B:MET290 3.6 41.2 1.0
N B:GLY294 3.8 49.2 1.0
N B:GLY292 4.1 42.4 1.0
C B:LEU293 4.2 45.5 1.0
CA B:GLY294 4.2 42.8 1.0
CA B:MET290 4.3 31.2 1.0
C B:LYS291 4.4 47.6 1.0
CA B:GLY292 4.4 49.5 1.0
N B:LEU293 4.5 46.3 1.0
CA B:LEU293 4.6 45.2 1.0
CB B:ASP334 4.6 46.3 1.0
OG1 B:THR295 4.6 47.7 1.0
N B:LYS291 4.6 41.1 1.0
N B:THR295 4.7 41.7 1.0
O B:HOH922 4.7 53.6 1.0
O B:LEU293 4.7 49.0 1.0
CA B:LYS291 4.8 46.4 1.0
CB B:MET290 4.8 35.5 1.0
O B:LYS291 4.8 54.0 1.0
CA B:THR295 5.0 43.3 1.0

Calcium binding site 6 out of 9 in 7nmi

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Calcium binding site 6 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca607

b:53.9
occ:1.00
 O B:THR295 2.4 43.3 1.0
OE2 B:GLU297 2.5 53.2 1.0
O B:HOH834 2.5 59.7 1.0
O B:HOH845 2.6 51.4 1.0
CD B:GLU297 3.2 51.3 1.0
OE1 B:GLU297 3.3 56.5 1.0
C B:THR295 3.5 41.5 1.0
O B:HOH714 3.8 69.5 1.0
N B:THR295 4.1 41.7 1.0
CA B:THR295 4.3 43.3 1.0
N B:GLU297 4.5 34.7 1.0
CB B:THR295 4.6 47.4 1.0
N B:ASP296 4.6 40.0 1.0
CG B:GLU297 4.7 42.8 1.0
CA B:ASP296 4.8 34.1 1.0
O B:HOH816 4.9 47.5 1.0

Calcium binding site 7 out of 9 in 7nmi

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Calcium binding site 7 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca608

b:47.1
occ:1.00
 O B:GLY379 2.3 50.0 1.0
O B:ARG377 2.3 56.4 1.0
O B:HOH788 2.4 54.6 1.0
O B:GLY374 2.4 46.4 1.0
OE1 B:GLU419 2.4 46.5 1.0
O B:HOH853 2.4 50.5 1.0
OE2 B:GLU419 2.5 45.8 1.0
CD B:GLU419 2.8 43.1 1.0
C B:GLY374 3.4 48.0 1.0
C B:GLY379 3.4 54.9 1.0
C B:ARG377 3.5 55.0 1.0
N B:GLY379 3.6 58.7 1.0
O B:HOH796 3.9 55.0 1.0
C B:LYS378 3.9 53.0 1.0
CA B:GLY379 4.1 56.8 1.0
CA B:LYS378 4.1 52.6 1.0
CA B:GLY374 4.1 46.5 1.0
O B:HOH712 4.2 49.8 1.0
OG1 B:THR380 4.2 52.6 1.0
N B:VAL375 4.3 52.1 1.0
N B:LYS378 4.3 54.0 1.0
CG B:GLU419 4.3 37.0 1.0
CA B:VAL375 4.4 49.6 1.0
N B:ARG377 4.5 58.5 1.0
CG B:ARG377 4.5 53.0 1.0
CA B:ARG377 4.5 56.9 1.0
N B:THR380 4.6 47.1 1.0
O B:HOH819 4.6 59.9 1.0
O B:LYS378 4.6 51.1 1.0
C B:VAL375 4.6 49.6 1.0
O B:VAL375 4.7 51.0 1.0
CA B:THR380 4.8 50.1 1.0

Calcium binding site 8 out of 9 in 7nmi

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Calcium binding site 8 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca609

b:34.4
occ:1.00
 O B:GLY452 2.4 32.5 1.0
O B:MET450 2.4 31.8 1.0
OD2 B:ASP494 2.5 39.0 1.0
O B:GLY454 2.5 34.5 1.0
OD1 B:ASP494 2.6 39.3 1.0
CG B:ASP494 2.8 31.4 1.0
C B:MET450 3.5 32.4 1.0
C B:GLY452 3.6 41.7 1.0
C B:GLY454 3.7 35.4 1.0
N B:GLY454 4.1 35.2 1.0
CA B:MET450 4.2 35.7 1.0
N B:GLY452 4.2 31.0 1.0
C B:LYS451 4.2 33.3 1.0
C B:LYS453 4.2 30.1 1.0
CB B:ASP494 4.3 33.7 1.0
O B:HOH735 4.3 40.2 1.0
CA B:GLY454 4.4 31.5 1.0
O B:LYS451 4.4 37.3 1.0
OG1 B:THR455 4.4 35.8 1.0
CA B:LYS453 4.5 33.9 1.0
N B:LYS453 4.5 40.5 1.0
N B:LYS451 4.5 33.8 1.0
CA B:GLY452 4.5 31.5 1.0
N B:THR455 4.7 38.2 1.0
O B:LYS453 4.8 31.9 1.0
CB B:MET450 4.8 36.2 1.0
CA B:LYS451 4.8 38.1 1.0
O B:HOH772 4.8 32.5 1.0
CA B:THR455 4.9 36.1 1.0
CA B:ASP494 4.9 34.6 1.0

Calcium binding site 9 out of 9 in 7nmi

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Calcium binding site 9 out of 9 in the Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Transactivation Domain of P53 in Complex with S100P, Using Annexin A2 As Crystallization Chaperone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca610

b:49.5
occ:1.00
 O B:HOH780 2.3 45.0 1.0
OD1 B:ASN167 2.4 53.6 1.0
O B:GLN171 2.4 52.8 1.0
OD1 B:ASP169 2.5 53.7 1.0
OE1 B:GLU176 2.5 48.5 1.0
OE2 B:GLU176 2.5 46.4 1.0
OD1 B:ASP165 2.6 59.5 1.0
CD B:GLU176 2.8 49.5 1.0
CG B:ASP169 3.4 54.7 1.0
CG B:ASN167 3.4 55.1 1.0
C B:GLN171 3.5 54.3 1.0
CG B:ASP165 3.6 61.1 1.0
OD2 B:ASP169 3.8 52.8 1.0
ND2 B:ASN167 4.0 56.5 1.0
CA B:ASP165 4.0 46.4 1.0
N B:GLN171 4.2 51.1 1.0
N B:VAL172 4.3 46.6 1.0
CB B:ASP165 4.3 51.3 1.0
N B:ASP169 4.3 50.8 1.0
CA B:VAL172 4.3 47.8 1.0
N B:ASN167 4.4 51.0 1.0
CG B:GLU176 4.4 42.3 1.0
C B:ASP165 4.4 52.0 1.0
CA B:GLN171 4.4 51.9 1.0
N B:ASP173 4.4 44.9 1.0
OD2 B:ASP173 4.4 45.5 1.0
N B:ALA166 4.4 52.2 1.0
OD2 B:ASP165 4.5 72.9 1.0
N B:GLY168 4.5 59.6 1.0
CB B:ASP169 4.6 51.3 1.0
CB B:ASN167 4.6 54.7 1.0
O B:HOH830 4.8 46.4 1.0
CB B:GLN171 4.8 47.1 1.0
CG B:ASP173 4.8 40.4 1.0
CA B:ASP169 4.8 52.3 1.0
C B:VAL172 4.9 48.9 1.0
CA B:ASN167 4.9 53.5 1.0
O B:ASP165 4.9 59.2 1.0
C B:ASN167 4.9 60.1 1.0

Reference:

P.Ecsedi, L.Nyitray. Transactivation Domain of P53 in Complex with S100P Using Annexin A2 As A Crystallization Chaperone To Be Published.
Page generated: Wed Jul 9 23:42:39 2025

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