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Bromine 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:

Chlorine (Cl) 8 atoms
Calcium (Ca) 6 atoms

Bromine Binding Sites:

The binding sites of Bromine 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 Bromine atom.
In total 9 binding sites of Bromine 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 Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 1nud

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Bromine binding site 1 out of 9 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 Bromine with other atoms in the Br 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:Br708

b:21.9
occ:0.70
 N A:ILE590 3.3 12.6 1.0
NH1 A:ARG587 3.4 12.6 1.0
NH1 A:ARG169 3.8 21.1 1.0
O A:HOH853 3.8 25.9 1.0
CA A:ILE589 3.9 13.0 1.0
CD A:ARG169 4.1 19.5 1.0
C A:ILE589 4.1 12.8 1.0
O A:ILE590 4.2 11.9 1.0
CB A:ILE590 4.2 12.2 1.0
CA A:ILE590 4.3 12.4 1.0
O A:ASP588 4.3 14.9 1.0
CD1 A:LEU492 4.3 18.0 1.0
CZ A:ARG587 4.3 13.0 1.0
NE A:ARG587 4.3 13.4 1.0
CB A:ILE589 4.4 12.8 1.0
CB A:ARG169 4.4 17.4 1.0
CG2 A:ILE589 4.6 13.3 1.0
CG1 A:ILE590 4.7 12.1 1.0
C A:ILE590 4.7 12.1 1.0
CB A:ASN168 4.7 17.7 1.0
CZ A:ARG169 4.7 20.6 1.0
NE A:ARG169 4.8 20.4 1.0
CG2 A:VAL488 4.9 20.1 1.0
CG A:ARG169 4.9 18.3 1.0
N A:ILE589 5.0 13.6 1.0

Bromine binding site 2 out of 9 in 1nud

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Bromine binding site 2 out of 9 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 Bromine with other atoms in the Br 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:Br709

b:57.7
occ:0.75
 NH2 A:ARG587 3.4 12.6 1.0
N A:VAL488 3.5 21.9 1.0
CB A:VAL488 4.1 20.8 1.0
NH1 A:ARG587 4.1 12.6 1.0
CA A:LYS487 4.1 22.6 1.0
CG A:LYS487 4.1 24.6 1.0
O A:HOH853 4.1 25.9 1.0
CG2 A:VAL488 4.2 20.1 1.0
CZ A:ARG587 4.2 13.0 1.0
NZ A:LYS485 4.2 30.2 1.0
C A:LYS487 4.3 22.4 1.0
CA A:VAL488 4.3 21.6 1.0
O A:HOH856 4.5 11.9 1.0
O A:VAL488 4.5 22.3 1.0
O A:LEU486 4.5 21.9 1.0
CB A:LYS487 4.7 23.3 1.0
C A:VAL488 4.9 22.1 1.0

Bromine binding site 3 out of 9 in 1nud

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Bromine binding site 3 out of 9 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 Bromine with other atoms in the Br 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:Br710

b:49.5
occ:0.50
 O A:HOH771 3.7 21.2 1.0
N A:PRO344 3.8 18.0 1.0
CA A:SER340 3.9 17.9 1.0
CA A:PRO344 3.9 17.6 1.0
O A:ARG339 3.9 17.4 1.0
C A:GLY343 4.0 18.4 1.0
N A:SER340 4.3 17.6 1.0
CD A:PRO344 4.3 17.9 1.0
C A:ARG339 4.3 17.2 1.0
O A:GLY343 4.4 18.8 1.0
CB A:PRO344 4.4 17.7 1.0
CB A:SER340 4.5 18.0 1.0
CA A:GLY343 4.7 18.4 1.0
C A:SER340 4.9 18.1 1.0

Bromine binding site 4 out of 9 in 1nud

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Bromine binding site 4 out of 9 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 Bromine with other atoms in the Br 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
A:Br711

b:37.4
occ:0.50
 OG B:SER98 3.2 17.5 1.0
CB B:GLN38 3.6 19.5 1.0
C B:PHE37 3.6 19.0 1.0
O B:PHE37 3.7 18.7 1.0
N B:GLN38 3.8 19.0 1.0
CB B:SER98 3.9 16.7 1.0
CA B:GLN38 4.0 19.4 1.0
ND2 B:ASN36 4.1 21.1 1.0
CA B:PHE37 4.2 19.1 1.0
CG B:ASN36 4.2 20.9 1.0
N B:PHE37 4.4 19.6 1.0
O B:ASN36 4.4 20.2 1.0
CG B:GLN38 4.4 20.0 1.0
CA B:SER98 4.4 16.3 1.0
C B:ASN36 4.4 19.9 1.0
OD1 B:ASN36 4.5 21.4 1.0
OE1 B:GLN88 4.8 21.2 1.0
CB B:ASN36 4.8 20.6 1.0
NE2 B:GLN88 4.9 21.6 1.0

Bromine binding site 5 out of 9 in 1nud

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Bromine binding site 5 out of 9 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 Bromine with other atoms in the Br 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:Br708

b:26.6
occ:0.70
 O B:HOH884 2.9 19.3 1.0
N B:ILE590 3.3 16.6 1.0
CG B:ARG169 3.4 23.9 1.0
CD B:ARG169 3.4 25.8 1.0
NH1 B:ARG587 3.7 18.1 1.0
CA B:ILE589 3.7 17.5 1.0
NE B:ARG169 4.0 26.7 1.0
C B:ILE589 4.0 17.1 1.0
O B:ASP588 4.1 19.1 1.0
CD1 B:LEU492 4.2 27.9 1.0
O B:ILE590 4.3 16.0 1.0
CB B:ILE589 4.3 17.7 1.0
CA B:ILE590 4.3 16.2 1.0
CB B:ILE590 4.3 15.8 1.0
NE B:ARG587 4.4 19.1 1.0
CG1 B:ILE590 4.5 15.8 1.0
CZ B:ARG587 4.5 18.8 1.0
CG2 B:ILE589 4.6 17.4 1.0
CB B:ARG169 4.7 21.6 1.0
CB B:ASN168 4.7 21.0 1.0
CZ B:ARG169 4.7 27.2 1.0
C B:ILE590 4.8 16.0 1.0
N B:ILE589 4.8 18.0 1.0
CG2 B:VAL488 4.9 30.2 1.0
C B:ASP588 4.9 18.6 1.0

Bromine binding site 6 out of 9 in 1nud

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Bromine binding site 6 out of 9 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 Bromine with other atoms in the Br 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:Br709

b:55.3
occ:0.50
 O B:THR129 3.2 11.9 1.0
OG1 B:THR129 3.2 12.5 1.0
C B:THR129 3.4 12.8 1.0
OE2 B:GLU28 3.6 22.6 1.0
N B:PHE130 3.6 13.3 1.0
CB B:GLU28 3.7 21.6 1.0
CA B:PHE130 3.7 14.0 1.0
CB B:THR129 3.7 12.4 1.0
NH1 B:ARG109 3.7 15.9 1.0
CG B:GLU28 3.8 22.2 1.0
CD B:GLU28 4.0 22.7 1.0
CA B:THR129 4.2 12.9 1.0
C B:PHE130 4.2 14.4 1.0
N B:LEU29 4.3 20.1 1.0
CG1 B:ILE131 4.4 14.3 1.0
N B:ILE131 4.5 14.6 1.0
CA B:GLU28 4.5 21.2 1.0
O B:LEU29 4.7 18.7 1.0
O B:PHE130 4.7 15.1 1.0
C B:GLU28 5.0 20.7 1.0
CD1 B:ILE131 5.0 13.7 1.0
N B:THR129 5.0 13.6 1.0

Bromine binding site 7 out of 9 in 1nud

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Bromine binding site 7 out of 9 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 Bromine with other atoms in the Br binding site number 7 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:Br710

b:52.9
occ:0.75
 N B:TRP236 3.1 14.7 1.0
O B:HOH908 3.5 15.3 1.0
ND2 B:ASN235 3.8 13.1 1.0
N B:SER237 3.9 14.5 1.0
CA B:ASN235 3.9 14.2 1.0
CA B:TRP236 4.0 14.3 1.0
C B:ASN235 4.0 14.6 1.0
C B:TRP236 4.1 14.4 1.0
CB B:TRP236 4.1 14.0 1.0
CE3 B:TRP236 4.1 13.4 1.0
CB B:SER237 4.6 13.6 1.0
CA B:SER237 4.7 14.6 1.0
CG B:ASN235 4.7 13.7 1.0
N B:ASN235 4.8 14.5 1.0
O B:TRP236 4.8 14.7 1.0
CD2 B:TRP236 4.9 13.8 1.0
CB B:ASN235 4.9 13.7 1.0
CG B:TRP236 4.9 14.0 1.0

Bromine binding site 8 out of 9 in 1nud

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Bromine binding site 8 out of 9 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 Bromine with other atoms in the Br binding site number 8 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:Br711

b:57.3
occ:0.75
 NH2 B:ARG587 3.2 19.1 1.0
N B:VAL488 3.5 30.6 1.0
NH1 B:ARG587 3.6 18.1 1.0
CZ B:ARG587 3.9 18.8 1.0
CA B:LYS487 4.1 30.4 1.0
CB B:VAL488 4.1 30.4 1.0
CG2 B:VAL488 4.2 30.2 1.0
C B:LYS487 4.3 30.5 1.0
CB B:LYS487 4.3 31.0 1.0
CA B:VAL488 4.4 30.7 1.0
CG B:LYS487 4.5 31.7 1.0
CD B:LYS487 4.6 32.0 1.0
O B:VAL488 4.7 31.2 1.0
O B:LEU486 4.8 28.7 1.0

Bromine binding site 9 out of 9 in 1nud

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Bromine binding site 9 out of 9 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 Bromine with other atoms in the Br binding site number 9 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:Br712

b:52.9
occ:0.50
 O A:HOH883 3.0 17.1 1.0
O A:HOH782 3.2 11.8 1.0
OD1 A:ASP588 3.2 14.2 1.0
CB A:GLU586 3.3 20.0 1.0
CD A:ARG570 3.3 13.9 1.0
NH2 A:ARG570 3.4 13.6 1.0
OH A:TYR312 3.7 21.6 1.0
N A:ARG587 3.7 17.4 1.0
CG A:ASP588 3.8 14.5 1.0
CD A:GLU586 3.9 22.1 1.0
OE1 A:GLU586 3.9 22.0 1.0
CG A:GLU586 4.1 21.0 1.0
OD2 A:ASP588 4.1 14.5 1.0
C A:GLU586 4.1 18.5 1.0
NE A:ARG570 4.2 13.9 1.0
CA A:GLU586 4.2 19.2 1.0
CZ A:ARG570 4.2 13.9 1.0
OE2 A:GLU586 4.3 22.9 1.0
N A:ASP588 4.3 15.5 1.0
CA A:ARG587 4.3 16.4 1.0
C A:ARG587 4.4 16.1 1.0
CG A:ARG570 4.4 14.3 1.0
O A:ILE571 4.6 15.8 1.0
O A:GLU586 4.8 18.8 1.0
O A:ARG587 4.9 16.2 1.0
CB A:ASP588 4.9 14.7 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: Wed Jul 10 17:01:20 2024

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