Calcium in PDB 8fn9: Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz

Enzymatic activity of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz

All present enzymatic activity of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz:
3.1.3.48;

Protein crystallography data

The structure of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz, PDB code: 8fn9 was solved by S.Bouyain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.96 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.325, 75.656, 88.322, 104.41, 92.4, 91.81
R / Rfree (%) 17.4 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz (pdb code 8fn9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz, PDB code: 8fn9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 8fn9

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Calcium binding site 1 out of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1401

b:24.5
occ:1.00
 OD1 A:ASP1284 2.3 22.4 1.0
O A:HOH1565 2.3 32.0 1.0
O A:ALA1286 2.4 22.6 1.0
OD2 A:ASP1282 2.4 27.1 1.0
O A:THR1288 2.5 25.9 1.0
OD1 A:ASP1282 2.7 31.1 1.0
CG A:ASP1282 2.9 33.1 1.0
CG A:ASP1284 3.1 25.7 1.0
OD2 A:ASP1284 3.2 26.9 1.0
C A:ALA1286 3.5 25.3 1.0
C A:THR1288 3.6 32.1 1.0
O A:VAL1287 4.0 30.7 1.0
N A:ALA1286 4.0 20.6 1.0
C A:VAL1287 4.1 24.2 1.0
CA A:ALA1286 4.2 25.6 1.0
O A:ASP1284 4.3 26.2 1.0
O A:HOH1506 4.3 34.7 1.0
CA A:ASN1289 4.4 30.2 1.0
N A:ASN1289 4.4 28.6 1.0
N A:THR1288 4.4 24.7 1.0
N A:VAL1287 4.4 27.8 1.0
CB A:ASP1282 4.5 24.5 1.0
C A:ASP1284 4.5 22.3 1.0
CB A:ASP1284 4.5 22.6 1.0
CB A:ALA1286 4.5 27.2 1.0
CA A:VAL1287 4.6 25.9 1.0
CA A:THR1288 4.6 30.9 1.0
N A:ASP1284 4.8 26.2 1.0
CA A:ASP1284 4.8 23.9 1.0
N A:CYS1290 5.0 21.9 1.0
N A:VAL1285 5.0 19.2 1.0
C A:VAL1285 5.0 29.7 1.0

Calcium binding site 2 out of 4 in 8fn9

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Calcium binding site 2 out of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1401

b:34.4
occ:1.00
 OD1 C:ASP1284 2.2 28.9 1.0
O C:ALA1286 2.3 34.3 1.0
OD2 C:ASP1282 2.3 32.9 1.0
O C:HOH1555 2.4 41.5 1.0
O C:THR1288 2.4 33.1 1.0
O C:HOH1539 2.4 33.0 1.0
OD1 C:ASP1282 2.8 36.3 1.0
CG C:ASP1282 2.9 35.7 1.0
CG C:ASP1284 3.1 31.7 1.0
OD2 C:ASP1284 3.3 31.4 1.0
C C:ALA1286 3.4 32.4 1.0
C C:THR1288 3.5 33.9 1.0
O C:VAL1287 4.0 38.4 1.0
C C:VAL1287 4.0 35.4 1.0
N C:ALA1286 4.0 27.7 1.0
O C:HOH1567 4.1 45.2 1.0
CA C:ALA1286 4.2 32.6 1.0
N C:THR1288 4.3 34.9 1.0
O C:HOH1582 4.3 48.0 1.0
O C:ASP1284 4.3 32.8 1.0
N C:ASN1289 4.4 31.6 1.0
CA C:ASN1289 4.4 32.5 1.0
N C:VAL1287 4.4 35.0 1.0
CB C:ALA1286 4.4 29.4 1.0
CB C:ASP1282 4.4 30.3 1.0
CA C:VAL1287 4.5 35.8 0.2
CB C:ASP1284 4.5 31.8 1.0
CA C:THR1288 4.5 38.6 1.0
CA C:VAL1287 4.5 35.8 0.8
C C:ASP1284 4.6 32.4 1.0
N C:ASP1284 4.8 31.4 1.0
CA C:ASP1284 4.9 33.7 1.0
N C:CYS1290 5.0 30.3 1.0

Calcium binding site 3 out of 4 in 8fn9

Go back to Calcium Binding Sites List in 8fn9
Calcium binding site 3 out of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1401

b:33.2
occ:1.00
 OD1 E:ASP1284 2.2 28.3 1.0
OD2 E:ASP1282 2.3 32.7 1.0
O E:HOH1583 2.4 35.5 1.0
O E:THR1288 2.4 32.5 1.0
O E:ALA1286 2.5 30.5 1.0
O E:HOH1536 2.5 38.4 1.0
OD1 E:ASP1282 2.7 40.3 1.0
CG E:ASP1282 2.9 42.3 1.0
CG E:ASP1284 3.0 36.1 1.0
OD2 E:ASP1284 3.2 34.5 1.0
C E:ALA1286 3.5 30.7 1.0
C E:THR1288 3.5 36.1 1.0
O E:VAL1287 4.0 36.4 1.0
O E:HOH1502 4.1 38.4 1.0
N E:ALA1286 4.1 29.4 1.0
C E:VAL1287 4.2 36.5 1.0
O E:ASP1284 4.2 30.0 1.0
CA E:ASN1289 4.2 30.7 1.0
CA E:ALA1286 4.3 31.6 1.0
N E:ASN1289 4.3 33.4 1.0
CB E:ASP1282 4.4 37.0 1.0
N E:THR1288 4.4 39.6 1.0
C E:ASP1284 4.4 33.0 1.0
CB E:ASP1284 4.4 34.5 1.0
CB E:ALA1286 4.5 32.0 1.0
O E:HOH1591 4.5 33.0 1.0
N E:VAL1287 4.5 33.5 1.0
CA E:THR1288 4.6 35.1 1.0
CA E:VAL1287 4.7 36.6 1.0
N E:ASP1284 4.7 27.5 1.0
CA E:ASP1284 4.8 31.7 1.0
N E:CYS1290 4.8 26.7 1.0

Calcium binding site 4 out of 4 in 8fn9

Go back to Calcium Binding Sites List in 8fn9
Calcium binding site 4 out of 4 in the Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the C-Terminal Fg Domain of Tnr with the Single Fn Domain of Ptprz within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1401

b:34.7
occ:1.00
 OD1 G:ASP1284 2.3 32.8 1.0
O G:THR1288 2.3 30.0 1.0
O G:ALA1286 2.4 33.1 1.0
O G:HOH1583 2.4 38.1 1.0
O G:HOH1562 2.5 36.2 1.0
OD2 G:ASP1282 2.5 33.6 1.0
OD1 G:ASP1282 2.8 39.4 1.0
CG G:ASP1282 3.0 37.8 1.0
CG G:ASP1284 3.2 39.4 1.0
OD2 G:ASP1284 3.4 31.9 1.0
C G:ALA1286 3.4 30.7 1.0
C G:THR1288 3.5 42.5 1.0
N G:ALA1286 4.0 31.5 1.0
C G:VAL1287 4.1 34.2 1.0
CA G:ALA1286 4.2 33.4 1.0
N G:THR1288 4.2 37.5 1.0
O G:VAL1287 4.2 39.6 1.0
N G:ASN1289 4.3 39.2 1.0
CA G:ASN1289 4.3 28.7 1.0
O G:ASP1284 4.3 35.1 1.0
CB G:ALA1286 4.4 29.2 1.0
O G:HOH1541 4.4 43.5 1.0
CA G:THR1288 4.4 37.4 1.0
N G:VAL1287 4.5 31.1 1.0
CB G:ASP1282 4.5 38.6 1.0
C G:ASP1284 4.5 33.5 1.0
O G:HOH1515 4.6 37.7 1.0
CB G:ASP1284 4.6 32.1 1.0
CA G:VAL1287 4.6 32.5 1.0
N G:ASP1284 4.9 31.3 1.0
CA G:ASP1284 4.9 33.2 1.0

Reference:

A.Sinha, J.Kawakami, K.S.Cole, A.Ladutska, M.Y.Nguyen, M.S.Zalmai, B.L.Holder, V.M.Broerman, R.T.Matthews, S.Bouyain. Protein-Protein Interactions Between Tenascin-R and Rptp Zeta /Phosphacan Are Critical to Maintain the Architecture of Perineuronal Nets. J.Biol.Chem. 04952 2023.
ISSN: ESSN 1083-351X
PubMed: 37356715
DOI: 10.1016/J.JBC.2023.104952
Page generated: Wed Jul 26 13:19:03 2023

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