Atomistry » Calcium » PDB 7nif-7o1w » 7nmi
Atomistry »
  Calcium »
    PDB 7nif-7o1w »
      7nmi »

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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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

Go back to Calcium Binding Sites List in 7nmi
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: Fri Jul 19 02:19:15 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy