Atomistry » Calcium » PDB 1l3w-1lkv » 1l9n
Atomistry »
  Calcium »
    PDB 1l3w-1lkv »
      1l9n »

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

Go back to Calcium Binding Sites List in 1l9n
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

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