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Calcium in PDB 1l9n: Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation

Enzymatic activity of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation

All present enzymatic activity of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation:
2.3.2.13;

Protein crystallography data

The structure of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation, PDB code: 1l9n was solved by B.Ahvazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.488, 116.537, 60.768, 93.23, 92.99, 89.51
R / Rfree (%) 18.9 / 23.3

Other elements in 1l9n:

The structure of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation (pdb code 1l9n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation, PDB code: 1l9n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1l9n

Go back to Calcium Binding Sites List in 1l9n
Calcium binding site 1 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca700

b:29.0
occ:1.00
 OD1 A:ASN393 2.2 27.2 1.0
O A:HOH1353 2.2 23.3 1.0
O A:SER415 2.3 29.4 1.0
O A:HOH1315 2.3 25.6 1.0
OE1 A:GLU443 2.5 34.8 1.0
OE2 A:GLU443 2.7 35.0 1.0
OE1 A:GLU448 2.9 38.0 1.0
CD A:GLU443 2.9 33.8 1.0
CG A:ASN393 3.2 26.0 1.0
C A:SER415 3.4 30.3 1.0
ND2 A:ASN393 3.7 25.8 1.0
CD A:GLU448 3.9 38.6 1.0
CA A:HIS416 4.0 31.9 1.0
NH2 A:ARG449 4.0 35.6 1.0
CD2 A:HIS416 4.1 39.0 1.0
N A:HIS416 4.1 30.7 1.0
O A:ASN393 4.2 23.6 1.0
O A:HOH1188 4.3 16.6 1.0
NZ A:LYS440 4.3 24.6 1.0
CG A:GLU443 4.3 33.4 1.0
CB A:ASN393 4.5 24.6 1.0
OE2 A:GLU448 4.5 38.7 1.0
CA A:SER415 4.5 30.6 1.0
CA A:ASN393 4.6 23.6 1.0
C A:ASN393 4.7 24.2 1.0
O A:ILE418 4.7 25.5 1.0
OD1 A:ASP395 4.7 28.6 1.0
C A:HIS416 4.8 30.7 1.0
CG A:HIS416 4.8 38.4 1.0
CB A:SER415 4.9 30.8 1.0
CB A:HIS416 4.9 34.7 1.0
CG A:GLU448 5.0 38.0 1.0

Calcium binding site 2 out of 6 in 1l9n

Go back to Calcium Binding Sites List in 1l9n
Calcium binding site 2 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:19.5
occ:1.00
 O A:ASN224 2.3 19.4 1.0
O A:ASN226 2.3 21.7 1.0
O A:ALA221 2.3 18.6 1.0
OD1 A:ASN224 2.4 18.7 1.0
OD1 A:ASP228 2.4 21.6 1.0
O A:HOH1290 2.4 14.6 1.0
OD2 A:ASP228 2.7 22.9 1.0
CG A:ASP228 2.8 23.3 1.0
C A:ASN224 3.3 19.4 1.0
CG A:ASN224 3.3 18.0 1.0
C A:ALA221 3.4 17.9 1.0
C A:ASN226 3.4 22.5 1.0
N A:ASN226 3.6 22.0 1.0
C A:SER225 4.0 21.9 1.0
CA A:ASN226 4.0 21.9 1.0
ND2 A:ASN224 4.1 18.2 1.0
CA A:ASN224 4.2 18.2 1.0
N A:ASP228 4.2 23.8 1.0
N A:MET222 4.2 16.9 1.0
CA A:ALA221 4.2 18.2 1.0
CB A:ASP228 4.2 23.7 1.0
N A:ASN224 4.3 18.1 1.0
N A:SER225 4.3 20.6 1.0
CA A:MET222 4.3 17.8 1.0
CB A:ASN224 4.3 18.2 1.0
CB A:ASN226 4.4 21.6 1.0
OD2 A:ASP227 4.4 21.3 1.0
CA A:SER225 4.4 21.7 1.0
O A:SER225 4.4 21.9 1.0
O A:PHE364 4.5 22.6 1.0
N A:ASP227 4.5 22.3 1.0
C A:MET222 4.6 17.6 1.0
CB A:ALA221 4.7 19.0 1.0
CA A:GLY230 4.7 24.5 1.0
N A:GLY230 4.7 24.6 1.0
CA A:ASP228 4.8 24.1 1.0
CB A:ASP227 4.8 21.8 1.0
C A:ASP227 4.9 23.4 1.0
CG A:ASP227 4.9 22.8 1.0
O A:MET222 4.9 17.4 1.0
CA A:ASP227 4.9 22.9 1.0

Calcium binding site 3 out of 6 in 1l9n

Go back to Calcium Binding Sites List in 1l9n
Calcium binding site 3 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:34.1
occ:1.00
 O A:SER307 2.1 26.9 1.0
O A:HOH1502 2.2 29.5 1.0
OD2 A:ASP301 2.3 34.8 1.0
OD1 A:ASN305 2.5 35.0 1.0
OD2 A:ASP324 2.5 40.2 1.0
CB A:ASP303 2.8 42.3 1.0
CG A:ASN305 3.3 35.6 1.0
C A:SER307 3.3 26.6 1.0
CG A:ASP301 3.4 35.2 1.0
ND2 A:ASN305 3.5 36.5 1.0
OD1 A:ASP303 3.6 45.4 1.0
CG A:ASP303 3.6 43.9 1.0
CG A:ASP324 3.6 40.6 1.0
N A:ASP303 3.8 40.6 1.0
CA A:ASP303 3.8 41.2 1.0
N A:SER307 4.1 28.3 1.0
OD1 A:ASP301 4.1 34.8 1.0
OD1 A:ASP324 4.1 41.5 1.0
CA A:SER307 4.2 27.3 1.0
CB A:ASP301 4.3 35.2 1.0
N A:VAL308 4.3 25.8 1.0
CA A:ASP301 4.3 35.4 1.0
CA A:VAL308 4.4 25.2 1.0
C A:ASP303 4.5 40.9 1.0
N A:THR302 4.5 37.7 1.0
N A:ASN305 4.5 36.5 1.0
N A:ARG304 4.6 40.6 1.0
CB A:SER307 4.6 27.6 1.0
C A:ASP301 4.6 36.8 1.0
CG1 A:VAL308 4.7 24.6 1.0
OD2 A:ASP303 4.7 45.5 1.0
CB A:ASN305 4.7 35.1 1.0
CB A:ASP324 4.8 40.7 1.0
N A:LEU306 5.0 31.6 1.0
C A:THR302 5.0 39.8 1.0
CA A:ASN305 5.0 34.8 1.0

Calcium binding site 4 out of 6 in 1l9n

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Calcium binding site 4 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:30.1
occ:1.00
 O B:HOH1486 2.2 24.2 1.0
O B:SER415 2.3 27.2 1.0
O B:HOH1447 2.4 25.4 1.0
OE2 B:GLU443 2.5 33.3 1.0
OE1 B:GLU443 2.5 33.3 1.0
OD1 B:ASN393 2.5 29.6 1.0
CD B:GLU443 2.8 34.1 1.0
OE1 B:GLU448 3.3 42.7 1.0
CG B:ASN393 3.4 29.4 1.0
C B:SER415 3.4 28.1 1.0
OE2 B:GLU448 3.5 43.1 1.0
O B:HOH1128 3.6 66.0 1.0
CD B:GLU448 3.7 42.1 1.0
ND2 B:ASN393 3.7 30.6 1.0
NH1 B:ARG449 4.1 39.3 1.0
CA B:HIS416 4.2 29.0 1.0
N B:HIS416 4.2 28.5 1.0
O B:ASN393 4.3 26.7 1.0
CG B:GLU443 4.3 35.1 1.0
CA B:SER415 4.4 29.0 1.0
O B:HOH1256 4.4 26.0 1.0
NZ B:LYS440 4.5 22.5 1.0
CB B:ASN393 4.6 27.3 1.0
CB B:SER415 4.6 29.2 1.0
CA B:ASN393 4.7 26.4 1.0
C B:ASN393 4.8 26.6 1.0
O B:ILE418 4.8 23.8 1.0
OD1 B:ASP395 4.8 30.3 1.0
C B:HIS416 5.0 27.8 1.0

Calcium binding site 5 out of 6 in 1l9n

Go back to Calcium Binding Sites List in 1l9n
Calcium binding site 5 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca706

b:18.7
occ:1.00
 O B:ALA221 2.2 15.7 1.0
OD1 B:ASN224 2.2 16.6 1.0
O B:ASN226 2.3 18.4 1.0
O B:ASN224 2.4 16.4 1.0
O B:HOH1303 2.5 19.6 1.0
OD1 B:ASP228 2.6 22.5 1.0
OD2 B:ASP228 2.7 23.7 1.0
CG B:ASP228 2.9 23.7 1.0
C B:ALA221 3.2 16.3 1.0
CG B:ASN224 3.3 16.4 1.0
C B:ASN226 3.4 19.3 1.0
C B:ASN224 3.4 17.7 1.0
N B:ASN226 3.7 18.8 1.0
CA B:ASN226 4.0 18.9 1.0
C B:SER225 4.0 19.2 1.0
ND2 B:ASN224 4.1 15.7 1.0
CA B:ALA221 4.1 16.8 1.0
N B:MET222 4.1 15.7 1.0
CA B:MET222 4.2 17.0 1.0
CA B:ASN224 4.2 17.0 1.0
N B:ASP228 4.2 23.1 1.0
CB B:ASN224 4.3 16.8 1.0
CB B:ASN226 4.3 18.5 1.0
N B:ASN224 4.3 17.5 1.0
N B:SER225 4.3 18.8 1.0
CB B:ASP228 4.4 23.0 1.0
O B:SER225 4.4 19.6 1.0
CA B:SER225 4.5 19.1 1.0
CB B:ALA221 4.5 16.7 1.0
O B:PHE364 4.5 20.3 1.0
OD2 B:ASP227 4.5 24.1 1.0
N B:ASP227 4.6 21.1 1.0
C B:MET222 4.6 17.1 1.0
CA B:GLY230 4.7 21.6 1.0
CB B:ASP227 4.8 22.1 1.0
N B:GLY230 4.8 23.2 1.0
CA B:ASP228 4.8 23.3 1.0
CA B:ASP227 5.0 22.1 1.0
C B:ASP227 5.0 22.6 1.0

Calcium binding site 6 out of 6 in 1l9n

Go back to Calcium Binding Sites List in 1l9n
Calcium binding site 6 out of 6 in the Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Change Structure For Activation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca707

b:44.4
occ:1.00
 OD2 B:ASP301 2.4 31.5 1.0
O B:SER307 2.4 26.5 1.0
O B:HOH1450 2.5 38.1 1.0
OD1 B:ASP324 2.6 42.5 1.0
OD1 B:ASN305 2.6 35.2 1.0
CB B:ASP303 3.2 42.0 1.0
ND2 B:ASN305 3.2 36.5 1.0
CG B:ASN305 3.2 35.0 1.0
CG B:ASP303 3.3 44.2 1.0
CG B:ASP301 3.4 32.5 1.0
CG B:ASP324 3.5 41.3 1.0
C B:SER307 3.6 26.8 1.0
OD1 B:ASP303 3.6 45.6 1.0
N B:ASP303 3.6 38.8 1.0
OD2 B:ASP303 3.8 46.3 1.0
OD2 B:ASP324 3.8 42.0 1.0
CA B:ASP303 3.9 39.8 1.0
OD1 B:ASP301 4.2 32.9 1.0
CA B:ASP301 4.2 33.0 1.0
CB B:ASP301 4.3 32.7 1.0
N B:THR302 4.3 35.3 1.0
N B:SER307 4.3 27.6 1.0
CA B:SER307 4.5 27.1 1.0
C B:ASP301 4.5 34.3 1.0
C B:ASP303 4.5 39.1 1.0
N B:VAL308 4.5 26.4 1.0
N B:ASN305 4.5 34.8 1.0
N B:ARG304 4.5 38.9 1.0
CA B:VAL308 4.6 25.9 1.0
CB B:ASN305 4.6 34.4 1.0
C B:THR302 4.8 37.8 1.0
CB B:SER307 4.9 27.3 1.0
CG1 B:VAL308 4.9 25.4 1.0
CB B:ASP324 4.9 40.4 1.0

Reference:

B.Ahvazi, H.C.Kim, S.H.Kee, Z.Nemes, P.M.Steinert. Three-Dimensional Structure of the Human Transglutaminase 3 Enzyme: Binding of Calcium Ions Changes Structure For Activation. Embo J. V. 21 2055 2002.
ISSN: ISSN 0261-4189
PubMed: 11980702
DOI: 10.1093/EMBOJ/21.9.2055
Page generated: Thu Jul 11 11:49:11 2024

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