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Calcium in PDB 1nug: Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)

Enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)

All present enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form):
2.3.2.13;

Protein crystallography data

The structure of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form), PDB code: 1nug 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 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 57.510, 66.810, 116.530, 97.24, 90.28, 98.36
R / Rfree (%) 19.4 / 24.8

Other elements in 1nug:

The structure of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) (pdb code 1nug). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form), PDB code: 1nug:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1nug

Go back to Calcium Binding Sites List in 1nug
Calcium binding site 1 out of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:20.0
occ:1.00
 OD1 A:ASN224 2.3 18.9 1.0
O A:ALA221 2.3 14.8 1.0
O A:ASN226 2.4 21.0 1.0
O A:ASN224 2.4 18.3 1.0
OD1 A:ASP228 2.5 23.4 1.0
O A:HOH957 2.5 20.2 1.0
OD2 A:ASP228 2.8 23.8 1.0
CG A:ASP228 2.9 23.6 1.0
CG A:ASN224 3.3 18.9 1.0
C A:ALA221 3.4 15.1 1.0
C A:ASN224 3.4 18.6 1.0
C A:ASN226 3.5 20.9 1.0
N A:ASN226 3.6 20.4 1.0
CA A:ASN226 4.0 20.6 1.0
ND2 A:ASN224 4.0 18.8 1.0
C A:SER225 4.1 20.1 1.0
CA A:ALA221 4.2 14.9 1.0
N A:MET222 4.2 15.3 1.0
N A:ASP228 4.2 23.2 1.0
CA A:ASN224 4.3 18.3 1.0
N A:SER225 4.3 19.1 1.0
CA A:MET222 4.3 15.8 1.0
N A:ASN224 4.3 17.5 1.0
CB A:ASN226 4.3 20.3 1.0
CB A:ASP228 4.3 23.6 1.0
CB A:ASN224 4.3 18.4 1.0
CA A:SER225 4.4 19.8 1.0
O A:PHE364 4.5 22.6 1.0
CA A:GLY230 4.5 22.7 1.0
N A:GLY230 4.6 23.6 1.0
OD2 A:ASP227 4.6 22.7 1.0
CB A:ALA221 4.6 14.6 1.0
N A:ASP227 4.6 21.6 1.0
O A:SER225 4.7 20.6 1.0
C A:MET222 4.7 16.2 1.0
CA A:ASP228 4.8 23.6 1.0
CB A:ASP227 4.8 22.5 1.0

Calcium binding site 2 out of 4 in 1nug

Go back to Calcium Binding Sites List in 1nug
Calcium binding site 2 out of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:29.5
occ:1.00
 O A:SER415 2.3 27.0 1.0
O A:HOH1027 2.5 19.8 1.0
OD1 A:ASN393 2.6 23.9 1.0
O A:HOH851 2.7 14.4 1.0
OE1 A:GLU443 2.7 34.1 1.0
OE2 A:GLU443 2.8 33.6 1.0
OE2 A:GLU448 2.8 36.1 1.0
CD A:GLU443 3.1 33.8 1.0
CG A:ASN393 3.4 23.6 1.0
C A:SER415 3.5 27.1 1.0
CD A:GLU448 3.6 36.4 1.0
NH1 A:ARG449 3.7 36.0 1.0
ND2 A:ASN393 3.8 23.9 1.0
CA A:HIS416 4.1 27.1 1.0
OE1 A:GLU448 4.2 36.4 1.0
N A:HIS416 4.3 27.0 1.0
CG A:GLU448 4.4 36.5 1.0
O A:HOH870 4.5 14.6 1.0
O A:ASN393 4.5 22.4 1.0
NZ A:LYS440 4.5 21.3 1.0
CA A:SER415 4.5 27.2 1.0
CB A:ASN393 4.6 22.8 1.0
CA A:ASN393 4.7 22.1 1.0
CG A:GLU443 4.7 33.6 1.0
OD1 A:ASP395 4.7 24.4 1.0
C A:ASN393 4.7 22.2 1.0
CB A:SER415 4.7 27.2 1.0
CG A:HIS416 4.9 30.4 1.0
CD2 A:HIS416 4.9 31.1 1.0
CZ A:ARG449 4.9 36.2 1.0
CB A:HIS416 4.9 28.6 1.0
O A:ILE418 5.0 20.4 1.0
C A:HIS416 5.0 26.1 1.0

Calcium binding site 3 out of 4 in 1nug

Go back to Calcium Binding Sites List in 1nug
Calcium binding site 3 out of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:21.1
occ:1.00
 O B:ASN226 2.3 17.8 1.0
O B:ASN224 2.4 15.8 1.0
O B:ALA221 2.5 14.6 1.0
OD1 B:ASP228 2.5 21.6 1.0
OD1 B:ASN224 2.5 14.3 1.0
O B:HOH972 2.6 16.5 1.0
OD2 B:ASP228 2.8 21.5 1.0
CG B:ASP228 2.9 21.8 1.0
C B:ASN224 3.4 15.8 1.0
C B:ASN226 3.4 18.1 1.0
C B:ALA221 3.4 14.7 1.0
CG B:ASN224 3.4 14.7 1.0
N B:ASN226 3.6 17.7 1.0
C B:SER225 3.8 17.3 1.0
CA B:ASN226 4.0 17.9 1.0
N B:SER225 4.2 16.2 1.0
ND2 B:ASN224 4.2 14.3 1.0
N B:ASP228 4.2 21.3 1.0
CA B:SER225 4.2 16.8 1.0
CA B:MET222 4.2 14.5 1.0
N B:MET222 4.2 14.5 1.0
CA B:ASN224 4.3 15.4 1.0
CB B:ASP228 4.3 21.9 1.0
N B:ASN224 4.3 15.3 1.0
O B:SER225 4.3 17.5 1.0
CA B:GLY230 4.3 21.9 1.0
CA B:ALA221 4.4 14.9 1.0
CB B:ASN224 4.4 15.0 1.0
N B:GLY230 4.5 23.2 1.0
CB B:ASN226 4.5 17.6 1.0
N B:ASP227 4.6 18.9 1.0
C B:MET222 4.6 15.0 1.0
O B:PHE364 4.7 19.6 1.0
CB B:ASP227 4.7 19.4 1.0
CA B:ASP228 4.8 21.9 1.0
CB B:ALA221 4.8 14.6 1.0
OD1 B:ASP227 4.8 19.2 1.0
O B:MET222 4.9 15.2 1.0
C B:ASP227 4.9 20.5 1.0
CA B:ASP227 5.0 19.6 1.0

Calcium binding site 4 out of 4 in 1nug

Go back to Calcium Binding Sites List in 1nug
Calcium binding site 4 out of 4 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (2 Calciums, 1 Mg, Inactive Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:36.4
occ:1.00
 O B:HOH978 2.2 34.9 1.0
OE2 B:GLU443 2.4 32.8 1.0
O B:SER415 2.4 28.6 1.0
OD1 B:ASN393 2.4 24.2 1.0
OE1 B:GLU443 2.7 33.0 1.0
O B:HOH805 2.8 29.2 1.0
OE2 B:GLU448 2.9 42.0 1.0
CD B:GLU443 2.9 32.8 1.0
CG B:ASN393 3.4 24.1 1.0
C B:SER415 3.6 28.4 1.0
CD B:GLU448 3.6 41.7 1.0
ND2 B:ASN393 4.0 24.0 1.0
CA B:HIS416 4.1 28.1 1.0
OE1 B:GLU448 4.1 42.1 1.0
NH1 B:ARG449 4.2 40.9 1.0
N B:HIS416 4.3 28.3 1.0
CG B:GLU443 4.4 32.9 1.0
NZ B:LYS440 4.4 22.5 1.0
ND1 B:HIS416 4.5 31.0 1.0
CG B:GLU448 4.5 41.0 1.0
CE B:LYS440 4.5 23.4 1.0
O B:HOH927 4.6 7.0 1.0
O B:ASN393 4.6 23.8 1.0
CB B:ASN393 4.6 23.6 1.0
CA B:ASN393 4.6 23.3 1.0
CA B:SER415 4.6 28.4 1.0
C B:ASN393 4.7 23.4 1.0
O B:ILE418 4.8 23.1 1.0
OD1 B:ASP395 4.8 25.2 1.0
C B:HIS416 4.9 27.2 1.0
CB B:SER415 5.0 28.6 1.0

Reference:

B.Ahvazi, K.M.Boeshans, W.Idler, U.Baxa, P.M.Steinert. Roles of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme J.Biol.Chem. V. 278 23834 2003.
ISSN: ISSN 0021-9258
PubMed: 12679341
DOI: 10.1074/JBC.M301162200
Page generated: Thu Jul 11 13:02:38 2024

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