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Calcium in PDB 1nud: Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form)

Enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form)

All present enzymatic activity of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active 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 (3 Calciums, Active Form), PDB code: 1nud 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.540, 115.370, 121.390, 90.00, 92.66, 90.00
R / Rfree (%) 19.9 / 26.5

Other elements in 1nud:

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

Bromine (Br) 9 atoms
Chlorine (Cl) 8 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 (3 Calciums, Active Form) (pdb code 1nud). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form), PDB code: 1nud:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1nud

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Calcium binding site 1 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active 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 (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:18.6
occ:1.00
 O A:ASN226 2.1 15.2 1.0
O A:ALA221 2.2 12.3 1.0
OD1 A:ASN224 2.3 16.3 1.0
O A:ASN224 2.5 14.8 1.0
OD1 A:ASP228 2.5 18.6 1.0
OD2 A:ASP228 2.7 18.9 1.0
CG A:ASP228 2.9 18.3 1.0
C A:ASN226 3.2 15.6 1.0
CG A:ASN224 3.3 15.8 1.0
C A:ALA221 3.4 12.7 1.0
C A:ASN224 3.5 15.2 1.0
N A:ASN226 3.7 15.7 1.0
CA A:ASN226 3.9 15.6 1.0
ND2 A:ASN224 4.0 15.6 1.0
C A:SER225 4.1 15.7 1.0
N A:ASP228 4.1 17.6 1.0
CB A:ASN226 4.2 15.7 1.0
CA A:ALA221 4.2 12.8 1.0
CB A:ASP228 4.3 18.2 1.0
N A:ASP227 4.3 15.9 1.0
N A:MET222 4.3 12.6 1.0
CA A:ASN224 4.3 15.2 1.0
CB A:ASN224 4.4 15.3 1.0
N A:SER225 4.4 15.5 1.0
CA A:MET222 4.5 12.8 1.0
N A:ASN224 4.5 15.1 1.0
O A:SER225 4.5 15.9 1.0
O A:PHE364 4.5 13.8 1.0
CB A:ASP227 4.6 16.3 1.0
CA A:SER225 4.6 15.7 1.0
CB A:ALA221 4.7 12.7 1.0
OD2 A:ASP227 4.7 17.7 1.0
CA A:GLY230 4.7 16.6 1.0
CA A:ASP228 4.7 17.9 1.0
CA A:ASP227 4.8 16.4 1.0
N A:GLY230 4.8 17.5 1.0
C A:ASP227 4.8 16.9 1.0
C A:MET222 4.8 13.4 1.0
CG A:ASP227 5.0 17.0 1.0

Calcium binding site 2 out of 6 in 1nud

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Calcium binding site 2 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active 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 (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:20.1
occ:1.00
 O A:HOH895 2.2 15.1 1.0
OD1 A:ASN393 2.2 21.3 1.0
O A:SER415 2.5 25.4 1.0
OE1 A:GLU443 2.5 25.9 1.0
OE1 A:GLU448 2.6 24.3 1.0
OE2 A:GLU443 2.8 26.2 1.0
CD A:GLU443 3.0 26.1 1.0
CG A:ASN393 3.1 20.8 1.0
C A:SER415 3.3 25.6 1.0
CD A:GLU448 3.4 24.7 1.0
ND2 A:ASN393 3.5 21.1 1.0
OE2 A:GLU448 3.6 24.6 1.0
O A:ASN393 3.9 19.1 1.0
N A:HIS416 4.1 25.5 1.0
NH2 A:ARG449 4.1 28.6 1.0
CA A:SER415 4.1 26.1 1.0
CA A:HIS416 4.2 25.2 1.0
O A:HOH855 4.3 5.3 1.0
OD1 A:ASP395 4.4 21.6 1.0
CB A:ASN393 4.4 19.6 1.0
CB A:SER415 4.4 26.6 1.0
CG A:GLU443 4.5 25.7 1.0
C A:ASN393 4.5 19.2 1.0
CA A:ASN393 4.5 19.1 1.0
ND1 A:HIS416 4.5 28.1 1.0
CG A:GLU448 4.7 25.1 1.0
NZ A:LYS440 4.7 13.3 1.0
O A:ILE418 4.9 21.4 1.0
O A:ALA394 5.0 19.5 1.0

Calcium binding site 3 out of 6 in 1nud

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Calcium binding site 3 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active 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 (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:23.7
occ:1.00
 OD1 A:ASP303 2.1 33.4 1.0
O A:SER307 2.1 25.4 1.0
O A:HOH765 2.3 10.2 1.0
OD2 A:ASP301 2.4 28.2 1.0
OD2 A:ASP324 2.6 30.0 1.0
OD1 A:ASN305 2.6 28.1 1.0
ND2 A:ASN305 3.1 27.8 1.0
CG A:ASP303 3.2 32.9 1.0
CG A:ASN305 3.2 27.9 1.0
C A:SER307 3.3 25.3 1.0
CG A:ASP324 3.4 29.4 1.0
CG A:ASP301 3.4 28.3 1.0
OD2 A:ASP303 3.6 33.5 1.0
OD1 A:ASP324 3.7 29.8 1.0
OD1 A:ASP301 4.0 28.4 1.0
CA A:SER307 4.2 25.7 1.0
N A:SER307 4.2 26.0 1.0
N A:VAL308 4.3 24.5 1.0
N A:ASP303 4.3 31.5 1.0
CA A:VAL308 4.3 24.1 1.0
N A:THR302 4.4 30.0 1.0
CB A:ASP303 4.4 32.2 1.0
CB A:SER307 4.5 25.6 1.0
CB A:ASP301 4.5 28.1 1.0
CA A:ASP301 4.5 27.9 1.0
CB A:ASN305 4.6 28.1 1.0
CB A:ASP324 4.7 29.0 1.0
OD2 A:ASP309 4.7 24.4 1.0
N A:ASN305 4.7 29.2 1.0
OG A:SER307 4.8 25.8 1.0
CA A:ASP303 4.8 31.7 1.0
C A:ASP301 4.9 29.0 1.0
C A:ASP303 5.0 31.7 1.0

Calcium binding site 4 out of 6 in 1nud

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Calcium binding site 4 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active 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 (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:13.7
occ:1.00
 O B:ASN226 2.1 19.1 1.0
O B:ALA221 2.2 18.2 1.0
OD1 B:ASN224 2.2 17.7 1.0
OD1 B:ASP228 2.5 18.9 1.0
O B:ASN224 2.6 17.1 1.0
OD2 B:ASP228 2.8 18.8 1.0
CG B:ASP228 2.9 19.2 1.0
C B:ASN226 3.2 19.3 1.0
CG B:ASN224 3.2 17.7 1.0
C B:ALA221 3.3 17.9 1.0
C B:ASN224 3.5 17.4 1.0
N B:ASN226 3.7 18.9 1.0
CA B:ASN226 3.8 19.4 1.0
ND2 B:ASN224 3.9 17.9 1.0
C B:SER225 4.0 18.4 1.0
N B:ASP228 4.0 19.5 1.0
CB B:ASN226 4.1 19.6 1.0
CA B:ALA221 4.1 18.2 1.0
N B:MET222 4.3 17.4 1.0
CA B:ASN224 4.3 17.0 1.0
CB B:ASN224 4.3 17.2 1.0
CB B:ASP228 4.3 19.5 1.0
N B:ASP227 4.3 19.2 1.0
O B:SER225 4.3 18.3 1.0
N B:ASN224 4.4 16.8 1.0
N B:SER225 4.4 18.0 1.0
CA B:MET222 4.4 17.1 1.0
CB B:ALA221 4.4 18.4 1.0
CB B:ASP227 4.5 19.3 1.0
CA B:SER225 4.6 18.3 1.0
OD2 B:ASP227 4.6 18.9 1.0
CA B:ASP228 4.7 19.8 1.0
N B:GLY230 4.7 20.9 1.0
CA B:GLY230 4.7 20.3 1.0
CA B:ASP227 4.8 19.3 1.0
C B:ASP227 4.8 19.2 1.0
O B:PHE364 4.8 17.1 1.0
C B:MET222 4.9 17.2 1.0
CG B:ASP227 5.0 19.2 1.0

Calcium binding site 5 out of 6 in 1nud

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Calcium binding site 5 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:33.3
occ:1.00
 OE1 B:GLU443 2.1 30.8 1.0
O B:HOH838 2.1 12.5 1.0
O B:SER415 2.2 30.9 1.0
OD1 B:ASN393 2.3 24.3 1.0
OE1 B:GLU448 2.4 33.2 1.0
CD B:GLU443 2.8 30.7 1.0
OE2 B:GLU443 2.9 30.9 1.0
CD B:GLU448 3.2 33.8 1.0
CG B:ASN393 3.3 24.6 1.0
C B:SER415 3.3 31.4 1.0
OE2 B:GLU448 3.7 34.5 1.0
NH1 B:ARG449 3.8 35.7 1.0
ND2 B:ASN393 3.8 24.7 1.0
CA B:HIS416 3.8 31.3 1.0
N B:HIS416 4.0 31.4 1.0
O B:HOH734 4.1 30.5 1.0
CG B:GLU443 4.2 29.9 1.0
CG B:GLU448 4.2 33.8 1.0
NZ B:LYS440 4.3 21.1 1.0
ND1 B:HIS416 4.3 34.7 1.0
O B:ASN393 4.3 24.4 1.0
CE B:LYS440 4.4 22.5 1.0
CA B:SER415 4.5 31.8 1.0
O B:ILE418 4.5 27.6 1.0
CB B:ASN393 4.5 24.4 1.0
C B:HIS416 4.6 30.4 1.0
CA B:ASN393 4.7 24.1 1.0
CB B:SER415 4.8 32.1 1.0
C B:ASN393 4.8 24.4 1.0
CB B:HIS416 4.9 32.6 1.0
OD2 B:ASP395 5.0 28.9 1.0

Calcium binding site 6 out of 6 in 1nud

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Calcium binding site 6 out of 6 in the Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Role of Calcium Ions in the Activation and Activity of the Transglutaminase 3 Enzyme (3 Calciums, Active Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:27.9
occ:1.00
 O B:SER307 2.4 28.1 1.0
OD1 B:ASP324 2.6 26.9 1.0
OD2 B:ASP301 2.6 26.8 1.0
CB B:ASP303 2.8 30.5 1.0
OD1 B:ASP303 2.9 32.0 1.0
OD1 B:ASN305 2.9 30.6 1.0
CG B:ASP303 3.0 31.4 1.0
O B:HOH879 3.1 24.9 1.0
ND2 B:ASN305 3.2 30.5 1.0
CG B:ASN305 3.3 30.3 1.0
CG B:ASP324 3.5 26.6 1.0
C B:SER307 3.6 28.2 1.0
OD2 B:ASP324 3.6 26.3 1.0
N B:ASP303 3.7 28.9 1.0
CG B:ASP301 3.7 26.5 1.0
CA B:ASP303 3.8 30.0 1.0
OD2 B:ASP303 4.0 32.4 1.0
OD1 B:ASP301 4.4 26.8 1.0
N B:SER307 4.4 28.6 1.0
N B:THR302 4.4 26.5 1.0
C B:ASP303 4.5 30.6 1.0
N B:VAL308 4.5 27.9 1.0
CA B:ASP301 4.5 25.4 1.0
CA B:SER307 4.5 28.5 1.0
CB B:ASP301 4.6 26.0 1.0
CA B:VAL308 4.6 27.6 1.0
N B:ARG304 4.6 31.0 1.0
N B:ASN305 4.7 30.2 1.0
CB B:ASN305 4.7 30.1 1.0
C B:ASP301 4.8 26.0 1.0
CB B:ASP324 4.9 26.1 1.0
CG1 B:VAL308 4.9 27.5 1.0
C B:THR302 4.9 27.7 1.0
CB B:SER307 5.0 28.7 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: Mon Jul 7 17:40:43 2025

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