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Calcium in PDB 5xnp: Crystal Structures of Human SALM5 in Complex with Human Ptpdelta

Enzymatic activity of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta

All present enzymatic activity of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta, PDB code: 5xnp was solved by H.Liu, Z.Lin, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.91 / 3.73
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 249.384, 249.384, 249.384, 90.00, 90.00, 90.00
R / Rfree (%) 23.2 / 26.4

Other elements in 5xnp:

The structure of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Sodium (Na) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta (pdb code 5xnp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta, PDB code: 5xnp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 1 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:95.5
occ:1.00
 NZ A:LYS206 2.8 0.6 1.0
OG1 B:THR64 3.3 0.7 1.0
CE A:LYS206 3.6 0.9 1.0
CD A:LYS206 3.7 84.8 1.0
O A:ASN205 3.7 84.2 1.0
OG1 B:THR86 4.0 0.4 1.0
O B:PHE62 4.2 92.1 1.0
CG2 B:THR86 4.3 97.6 1.0
O A:GLY239 4.3 92.7 1.0
CB B:THR86 4.4 89.8 1.0
CD A:PRO241 4.4 79.0 1.0
O A:HOH509 4.5 81.8 1.0
C A:ASN205 4.5 84.7 1.0
CB B:THR64 4.6 98.8 1.0
CG2 B:THR64 4.8 98.5 1.0
CG A:PRO241 4.9 77.0 1.0
CG A:LYS206 5.0 86.5 1.0

Calcium binding site 2 out of 12 in 5xnp

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Calcium binding site 2 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:0.3
occ:1.00
 O A:HOH518 2.5 0.0 1.0
O A:HOH526 2.6 91.9 1.0
N A:SER140 3.8 0.5 1.0
OG A:SER139 3.8 0.6 1.0
CB A:SER139 3.9 0.6 1.0
CA A:SER139 4.0 0.7 1.0
OG A:SER140 4.0 0.3 1.0
C A:SER139 4.5 1.0 1.0
CB A:SER140 4.6 0.8 1.0
CA A:SER140 4.8 0.3 1.0

Calcium binding site 3 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 3 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:0.5
occ:1.00
 O A:HOH529 2.6 0.5 1.0
NE2 A:HIS93 3.3 0.7 1.0
OD1 A:ASP117 3.3 0.6 1.0
CE1 A:HIS93 3.7 0.4 1.0
CG A:ASP117 4.2 0.2 1.0
O A:HOH528 4.3 0.6 1.0
OG A:SER120 4.5 0.3 1.0
CD2 A:HIS93 4.5 0.3 1.0
CB A:SER120 4.6 0.3 1.0
CB A:ASP117 4.8 0.9 1.0
CA A:ASP117 4.9 0.5 1.0
OD2 A:ASP117 4.9 0.4 1.0

Calcium binding site 4 out of 12 in 5xnp

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Calcium binding site 4 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:0.7
occ:1.00
 OD2 A:ASP50 2.7 0.2 1.0
OD1 A:ASP50 3.3 0.0 1.0
CG A:ASP50 3.4 0.3 1.0
CD A:ARG52 3.4 0.2 1.0
O A:PRO17 3.5 0.5 1.0
CB A:ARG52 3.9 0.2 1.0
CG A:ARG52 4.3 1.0 1.0
O A:ASP16 4.5 0.5 1.0
NE A:ARG52 4.6 0.2 1.0
C A:PRO17 4.6 0.4 1.0
CB A:ASP16 4.6 0.4 1.0
O A:PRO14 4.7 0.5 1.0
C A:ASP16 4.8 0.5 1.0
CB A:ASP50 4.8 0.7 1.0

Calcium binding site 5 out of 12 in 5xnp

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Calcium binding site 5 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:0.9
occ:1.00
 O A:HOH519 2.7 0.0 1.0
OE1 A:GLU150 2.8 0.4 1.0
ND1 A:HIS126 3.0 0.0 1.0
O A:HOH525 3.2 79.8 1.0
CD A:GLU150 3.5 0.0 1.0
OE2 A:GLU150 3.7 0.3 1.0
CG A:HIS126 3.9 0.8 1.0
CE1 A:HIS126 4.0 0.5 1.0
CB A:HIS126 4.0 0.7 1.0
NE2 A:HIS127 4.2 0.3 1.0
CG A:GLU150 4.9 0.6 1.0
CE1 A:HIS127 4.9 0.2 1.0

Calcium binding site 6 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 6 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:0.9
occ:1.00
 N A:THR367 3.6 0.6 1.0
OG1 A:THR367 3.6 0.7 1.0
CA A:ALA366 3.9 0.1 1.0
C A:ALA366 4.2 0.2 1.0
O A:GLU365 4.3 0.6 1.0
CB A:THR367 4.4 0.6 1.0
O A:THR367 4.5 0.2 1.0
CA A:THR367 4.5 0.5 1.0
CG2 A:THR367 4.6 0.5 1.0
CB A:ALA366 4.6 0.4 1.0
N A:ALA366 4.8 0.2 1.0
C A:GLU365 5.0 0.4 1.0
C A:THR367 5.0 0.8 1.0

Calcium binding site 7 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 7 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:98.2
occ:1.00
 NZ B:LYS206 2.6 99.0 1.0
CE B:LYS206 3.4 99.2 1.0
O B:ASN205 3.5 85.7 1.0
O B:GLY239 3.5 89.8 1.0
CD B:LYS206 3.8 82.7 1.0
OG1 A:THR64 3.9 0.8 1.0
O A:PHE62 4.0 94.0 1.0
OG1 A:THR86 4.1 0.5 1.0
CG2 A:THR86 4.2 98.0 1.0
CD B:PRO241 4.3 76.3 1.0
C B:ASN205 4.3 84.8 1.0
CB A:THR86 4.5 90.1 1.0
CB A:PHE62 4.6 82.7 1.0
C B:GLY239 4.7 85.8 1.0
N B:ASN205 4.9 82.6 1.0
CG B:PRO241 4.9 75.5 1.0
N B:PRO241 4.9 76.9 1.0
CA B:ASN240 5.0 89.0 1.0

Calcium binding site 8 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 8 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca406

b:0.2
occ:1.00
 O B:HOH513 2.7 0.5 1.0
O B:HOH524 2.9 88.9 1.0
O B:HOH512 3.3 0.6 1.0
N B:SER140 3.9 0.0 1.0
OG B:SER140 4.0 0.9 1.0
OG B:SER139 4.1 0.0 1.0
CB B:SER139 4.1 0.3 1.0
CA B:SER139 4.2 0.6 1.0
CB B:SER140 4.5 0.1 1.0
C B:SER139 4.6 0.2 1.0
CA B:SER140 4.8 0.8 1.0

Calcium binding site 9 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 9 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca407

b:0.3
occ:1.00
 O B:HOH529 2.8 92.6 1.0
OD1 B:ASP117 3.1 0.3 1.0
NE2 B:HIS93 3.1 0.4 1.0
CE1 B:HIS93 3.3 0.3 1.0
CG B:ASP117 3.6 0.4 1.0
OD2 B:ASP117 4.2 0.2 1.0
CB B:ASP117 4.3 0.2 1.0
CD2 B:HIS93 4.5 0.5 1.0
O B:HOH521 4.5 0.0 1.0
CA B:ASP117 4.6 0.8 1.0
ND1 B:HIS93 4.6 0.1 1.0
OG B:SER120 4.6 0.5 1.0
CB B:SER120 4.8 0.1 1.0

Calcium binding site 10 out of 12 in 5xnp

Go back to Calcium Binding Sites List in 5xnp
Calcium binding site 10 out of 12 in the Crystal Structures of Human SALM5 in Complex with Human Ptpdelta


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structures of Human SALM5 in Complex with Human Ptpdelta within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca408

b:0.8
occ:1.00
 OD2 B:ASP50 2.9 0.2 1.0
O B:PRO17 3.2 0.8 1.0
OD1 B:ASP50 3.5 0.3 1.0
CG B:ASP50 3.6 0.5 1.0
CD B:ARG52 4.1 0.7 1.0
O B:ASP16 4.2 0.8 1.0
C B:PRO17 4.3 0.3 1.0
CB B:ARG52 4.3 1.0 1.0
CB B:ASP16 4.3 1.0 1.0
C B:ASP16 4.4 0.2 1.0
O B:PRO14 4.6 0.8 1.0
NH1 B:ARG52 4.7 0.7 1.0
N B:ASP16 4.7 0.7 1.0
CA B:ASP16 4.7 0.6 1.0
CA B:GLN18 4.8 0.3 1.0
CG B:ARG52 4.8 0.4 1.0
N B:GLN18 4.9 0.3 1.0

Reference:

Z.Lin, J.Liu, H.Ding, F.Xu, H.Liu. Structural Basis of SALM5-Induced Ptp Delta Dimerization For Synaptic Differentiation Nat Commun V. 9 268 2018.
ISSN: ESSN 2041-1723
PubMed: 29348579
DOI: 10.1038/S41467-017-02414-2
Page generated: Mon Jul 15 15:02:09 2024

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