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Calcium in PDB 7p73: The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1

Protein crystallography data

The structure of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7p73 was solved by G.Gogl, A.Cousido-Siah, G.Trave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.68 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.45, 63.99, 146.95, 90, 90, 90
R / Rfree (%) 16.8 / 19.2

Calcium Binding Sites:

The binding sites of Calcium atom in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 (pdb code 7p73). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1, PDB code: 7p73:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 7p73

Go back to Calcium Binding Sites List in 7p73
Calcium binding site 1 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:37.6
occ:1.00
 O A:GLY133 2.3 33.9 1.0
O A:HOH855 2.3 44.8 1.0
O A:VAL134 2.3 34.8 1.0
O A:HOH782 2.4 40.5 1.0
OE1 A:GLU136 2.4 33.2 1.0
O A:HOH802 2.4 51.4 1.0
OE2 A:GLU136 2.6 36.8 1.0
CD A:GLU136 2.8 41.1 1.0
C A:GLY133 3.3 37.2 1.0
C A:VAL134 3.5 33.8 1.0
N A:VAL134 4.0 34.7 1.0
CA A:VAL134 4.1 28.9 1.0
CB A:VAL134 4.2 27.5 1.0
CA A:GLY133 4.3 42.0 1.0
CG A:GLU136 4.3 35.5 1.0
O A:HOH642 4.4 46.3 1.0
O A:HOH932 4.6 47.3 1.0
N A:ASP135 4.6 33.9 1.0
N A:GLU136 4.6 32.8 1.0
O A:HOH659 4.9 41.9 1.0
CG1 A:VAL134 4.9 30.9 1.0
CA A:ASP135 5.0 32.7 1.0

Calcium binding site 2 out of 7 in 7p73

Go back to Calcium Binding Sites List in 7p73
Calcium binding site 2 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:26.8
occ:1.00
 O A:LYS171 2.3 24.9 1.0
OE1 A:GLU179 2.4 34.6 1.0
O A:LEU174 2.4 27.6 1.0
O A:HOH660 2.4 44.5 1.0
CD A:GLU179 3.3 34.1 1.0
C A:LEU174 3.5 30.7 1.0
C A:LYS171 3.6 29.4 1.0
OE2 A:GLU179 3.7 41.3 1.0
CA A:SER175 4.2 27.8 1.0
N A:SER175 4.3 28.9 1.0
O A:SER172 4.4 33.9 1.0
CB A:SER175 4.4 30.7 1.0
C A:SER172 4.5 31.3 1.0
CA A:SER172 4.5 28.2 1.0
N A:SER172 4.5 24.4 1.0
CA A:LYS171 4.5 30.9 1.0
N A:LEU174 4.5 26.0 1.0
CG A:GLU179 4.6 27.8 1.0
CA A:LEU174 4.6 25.4 1.0
O A:HOH957 4.7 47.0 1.0
CG A:LYS171 4.8 38.5 1.0

Calcium binding site 3 out of 7 in 7p73

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Calcium binding site 3 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:27.8
occ:1.00
 O A:MET201 2.3 31.0 1.0
O A:GLY203 2.4 33.7 1.0
O A:GLY205 2.4 31.0 1.0
OD1 A:ASP245 2.4 29.0 1.0
O A:HOH928 2.4 32.5 1.0
OD2 A:ASP245 2.6 29.4 1.0
CG A:ASP245 2.8 30.7 1.0
C A:MET201 3.4 28.2 1.0
C A:GLY205 3.6 35.6 1.0
C A:GLY203 3.6 35.3 1.0
N A:GLY205 3.9 36.5 1.0
CA A:MET201 4.1 21.6 1.0
C A:LEU204 4.2 34.8 1.0
N A:GLY203 4.2 37.1 1.0
CB A:ASP245 4.3 24.0 1.0
CA A:GLY205 4.3 38.6 1.0
OG1 A:THR206 4.3 34.9 1.0
C A:LYS202 4.4 34.0 1.0
O1 A:GOL509 4.4 45.0 1.0
O A:HOH830 4.4 38.3 1.0
CA A:LEU204 4.5 31.7 1.0
N A:LEU204 4.5 35.5 1.0
N A:LYS202 4.5 31.4 1.0
CA A:GLY203 4.5 37.9 1.0
N A:THR206 4.6 27.8 1.0
CB A:MET201 4.6 25.1 1.0
O A:HOH720 4.7 60.0 1.0
O A:HOH863 4.7 46.9 1.0
O A:LEU204 4.7 40.4 1.0
CA A:LYS202 4.7 33.2 1.0
CA A:THR206 4.8 23.7 1.0
O A:LYS202 4.9 37.8 1.0
C1 A:GOL509 4.9 56.8 1.0
CA A:ASP245 4.9 29.7 1.0

Calcium binding site 4 out of 7 in 7p73

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Calcium binding site 4 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:32.3
occ:1.00
 O A:GLY290 2.4 34.8 1.0
O A:HOH912 2.4 34.1 1.0
O A:GLY285 2.4 29.0 1.0
O A:ARG288 2.4 35.0 1.0
O A:HOH787 2.4 40.5 1.0
OE1 A:GLU330 2.5 31.7 1.0
OE2 A:GLU330 2.5 34.9 1.0
CD A:GLU330 2.8 31.3 1.0
C A:GLY285 3.3 26.2 1.0
C A:GLY290 3.4 34.6 1.0
C A:ARG288 3.5 41.3 1.0
N A:GLY290 3.7 31.7 1.0
CA A:GLY290 4.1 35.9 1.0
C A:LYS289 4.1 37.8 1.0
CA A:GLY285 4.1 29.7 1.0
N A:VAL286 4.2 24.3 1.0
CA A:VAL286 4.3 28.9 1.0
OG1 A:THR291 4.3 38.8 1.0
CA A:LYS289 4.3 37.5 1.0
O A:HOH643 4.3 40.3 1.0
N A:ARG288 4.4 33.5 1.0
CG A:GLU330 4.4 28.1 1.0
O A:HOH705 4.4 45.5 1.0
N A:LYS289 4.4 37.7 1.0
O A:HOH870 4.4 52.8 1.0
C A:VAL286 4.5 34.5 1.0
CG A:ARG288 4.5 35.4 1.0
O A:VAL286 4.5 37.3 1.0
CA A:ARG288 4.5 37.0 1.0
N A:THR291 4.5 32.0 1.0
O A:LYS289 4.8 34.5 1.0
CA A:THR291 4.9 31.3 1.0

Calcium binding site 5 out of 7 in 7p73

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Calcium binding site 5 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:21.1
occ:1.00
 O A:GLY365 2.3 26.9 1.0
O A:MET361 2.3 23.3 1.0
O A:GLY363 2.4 22.9 1.0
OD1 A:ASP405 2.5 25.4 1.0
OD2 A:ASP405 2.5 23.6 1.0
CG A:ASP405 2.8 27.1 1.0
C A:MET361 3.4 19.8 1.0
C A:GLY365 3.5 29.6 1.0
C A:GLY363 3.6 27.2 1.0
N A:GLY365 3.9 22.9 1.0
CA A:MET361 4.0 22.0 1.0
N A:GLY363 4.1 25.2 1.0
CA A:GLY365 4.2 27.4 1.0
C A:LYS364 4.2 26.6 1.0
C A:LYS362 4.3 25.8 1.0
CB A:ASP405 4.3 19.6 1.0
OG1 A:THR366 4.4 29.6 1.0
CA A:GLY363 4.4 22.7 1.0
O A:HOH768 4.5 37.2 1.0
N A:LYS362 4.5 22.0 1.0
N A:THR366 4.5 24.5 1.0
N A:LYS364 4.6 25.0 1.0
O A:LYS362 4.6 29.7 1.0
CB A:MET361 4.6 22.7 1.0
O A:LYS364 4.6 23.6 1.0
CA A:LYS364 4.7 25.4 1.0
CA A:THR366 4.8 28.2 1.0
O A:HOH673 4.8 22.7 1.0
CA A:LYS362 4.9 20.7 1.0
CA A:ASP405 5.0 24.4 1.0

Calcium binding site 6 out of 7 in 7p73

Go back to Calcium Binding Sites List in 7p73
Calcium binding site 6 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca510

b:30.2
occ:1.00
 O A:THR206 2.3 29.9 1.0
O A:HOH880 2.4 36.3 1.0
O A:HOH805 2.5 40.8 1.0
OE2 A:GLU208 2.5 37.2 1.0
O A:HOH938 2.6 37.1 1.0
O A:HOH1010 2.6 33.3 1.0
O A:HOH887 2.6 34.5 1.0
OE1 A:GLU208 2.8 41.3 1.0
CD A:GLU208 3.0 40.9 1.0
C A:THR206 3.6 28.8 1.0
N A:THR206 4.1 27.8 1.0
CA A:THR206 4.4 23.7 1.0
CG A:GLU208 4.5 30.6 1.0
N A:ASP207 4.5 25.3 1.0
N A:GLU208 4.6 26.5 1.0
O A:HOH995 4.6 48.8 1.0
CA A:ASP207 4.7 25.4 1.0
O A:HOH801 4.7 35.7 1.0
O A:HOH721 4.8 54.1 1.0
CB A:THR206 4.8 33.6 1.0
O A:HOH605 5.0 49.4 1.0

Calcium binding site 7 out of 7 in 7p73

Go back to Calcium Binding Sites List in 7p73
Calcium binding site 7 out of 7 in the The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca511

b:40.2
occ:1.00
 O A:HOH803 2.3 57.5 1.0
O A:ARG328 2.3 32.3 1.0
OE1 A:GLU336 2.5 51.6 1.0
O A:HOH924 2.5 50.1 1.0
O A:HOH925 2.5 44.8 1.0
O A:VAL331 2.5 33.0 1.0
O A:HOH838 2.6 36.1 1.0
CD A:GLU336 3.4 40.0 1.0
C A:ARG328 3.4 34.3 1.0
OE2 A:GLU336 3.7 42.7 1.0
C A:VAL331 3.7 35.5 1.0
CA A:ARG328 4.0 30.0 1.0
CA A:LYS332 4.1 29.8 1.0
CB A:LYS332 4.2 34.1 1.0
N A:LYS332 4.4 29.1 1.0
N A:LYS329 4.5 30.4 1.0
O A:ILE327 4.6 27.8 1.0
CG A:GLU336 4.6 26.0 1.0
N A:VAL331 4.6 26.3 1.0
O A:HOH918 4.7 45.9 1.0
CB A:ARG328 4.8 24.8 1.0
C A:LYS329 4.8 32.2 1.0
CA A:VAL331 4.8 27.3 1.0
CA A:LYS329 4.8 29.9 1.0
O A:HOH900 5.0 50.0 1.0

Reference:

G.Gogl, A.Cousido-Siah, G.Trave. The Pdz Domain of SYNJ2BP Complexed with the Pdz-Binding Motif of HTLV1-TAX1 To Be Published.
Page generated: Thu Jul 10 00:02:35 2025

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