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Bromine in PDB 3tuu: Structure of Dihydrodipicolinate Synthase From the Common Grapevine

Enzymatic activity of Structure of Dihydrodipicolinate Synthase From the Common Grapevine

All present enzymatic activity of Structure of Dihydrodipicolinate Synthase From the Common Grapevine:
4.2.1.52;

Protein crystallography data

The structure of Structure of Dihydrodipicolinate Synthase From the Common Grapevine, PDB code: 3tuu was solved by M.A.Perugini, R.C.Dobson, S.C.Atkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.17 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.550, 78.900, 135.350, 93.19, 95.02, 100.61
R / Rfree (%) 18 / 22.7

Other elements in 3tuu:

The structure of Structure of Dihydrodipicolinate Synthase From the Common Grapevine also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms

Bromine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Bromine atom in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine (pdb code 3tuu). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 15 binding sites of Bromine where determined in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine, PDB code: 3tuu:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 15 in 3tuu

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Bromine binding site 1 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br328

b:36.7
occ:0.80
 NE A:ARG277 3.7 32.7 1.0
CG A:ARG277 3.7 22.0 1.0
CB A:ARG277 3.8 20.1 1.0
CG A:PRO40 3.8 20.5 1.0
CD A:ARG277 3.9 25.9 1.0
CD A:PRO278 4.2 19.3 1.0
CD A:PRO40 4.4 20.4 1.0
CG2 A:VAL279 4.5 17.6 1.0
CG A:PRO278 4.6 18.6 1.0
CD1 A:ILE322 4.6 24.6 1.0
CA A:ARG277 4.7 19.9 1.0
CZ A:ARG277 4.8 35.6 1.0
CB A:PRO40 4.8 20.8 1.0
N A:PRO278 4.9 19.2 1.0

Bromine binding site 2 out of 15 in 3tuu

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Bromine binding site 2 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br329

b:59.8
occ:1.00
 O A:HOH368 3.2 23.6 1.0
N A:VAL313 3.3 28.8 1.0
CD A:ARG304 3.5 29.6 1.0
CA A:ASP312 3.6 30.0 1.0
CG A:ARG304 3.6 30.1 1.0
CG1 A:VAL313 3.7 28.3 1.0
CB A:ARG304 3.9 30.1 1.0
C A:ASP312 4.0 29.3 1.0
CB A:ASP312 4.0 30.2 1.0
OD2 A:ASP312 4.0 32.2 1.0
O A:HOH660 4.0 33.7 1.0
NE A:ARG304 4.1 30.1 1.0
CG A:ASP312 4.3 31.9 1.0
CB A:VAL313 4.3 28.4 1.0
CA A:VAL313 4.3 28.3 1.0
N A:ASP312 4.7 29.9 1.0
O A:LYS311 4.7 30.2 1.0
O A:VAL313 4.9 27.7 1.0
CG1 A:VAL299 5.0 29.5 1.0

Bromine binding site 3 out of 15 in 3tuu

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Bromine binding site 3 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br328

b:43.3
occ:0.80
 NE B:ARG277 3.6 33.2 1.0
CG B:ARG277 3.7 22.3 1.0
CB B:ARG277 3.8 21.1 1.0
CG B:PRO40 4.0 21.5 1.0
CD B:ARG277 4.0 26.5 1.0
CD B:PRO278 4.2 19.9 1.0
O B:HOH547 4.3 33.7 1.0
CD B:PRO40 4.5 20.7 1.0
CD1 B:ILE322 4.6 24.1 1.0
CG2 B:VAL279 4.6 18.6 1.0
CZ B:ARG277 4.6 35.0 1.0
NH2 B:ARG277 4.7 37.5 1.0
CA B:ARG277 4.8 20.5 1.0
CB B:PRO40 4.8 21.2 1.0
CG B:PRO278 4.9 20.0 1.0

Bromine binding site 4 out of 15 in 3tuu

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Bromine binding site 4 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br328

b:51.5
occ:1.00
 CG C:ARG277 3.5 22.1 1.0
NE C:ARG277 3.7 32.2 1.0
CB C:ARG277 3.7 20.5 1.0
CD C:ARG277 3.9 26.7 1.0
CG C:PRO40 3.9 21.4 1.0
CD C:PRO278 4.2 19.3 1.0
O C:HOH381 4.3 33.1 1.0
CD C:PRO40 4.5 20.6 1.0
CG2 C:VAL279 4.5 16.4 1.0
CA C:ARG277 4.7 19.8 1.0
CD1 C:ILE322 4.7 24.4 1.0
CZ C:ARG277 4.8 34.4 1.0
N C:PRO278 4.9 19.1 1.0
CG C:PRO278 4.9 19.2 1.0
CB C:PRO40 5.0 21.4 1.0

Bromine binding site 5 out of 15 in 3tuu

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Bromine binding site 5 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br329

b:58.8
occ:1.00
 O C:HOH379 3.2 23.3 1.0
N C:VAL313 3.4 28.2 1.0
CD C:ARG304 3.5 28.9 1.0
CG C:ARG304 3.7 28.9 1.0
CA C:ASP312 3.7 29.8 1.0
CB C:ARG304 3.8 29.5 1.0
CG1 C:VAL313 3.8 27.8 1.0
O C:HOH520 4.0 33.8 1.0
C C:ASP312 4.0 29.1 1.0
CB C:ASP312 4.1 30.4 1.0
OD2 C:ASP312 4.1 32.5 1.0
NE C:ARG304 4.3 28.4 1.0
CB C:VAL313 4.4 27.9 1.0
CA C:VAL313 4.4 27.9 1.0
CG C:ASP312 4.5 32.0 1.0
N C:ASP312 4.8 29.8 1.0
O C:LYS311 4.9 30.0 1.0
CG1 C:VAL299 5.0 28.8 1.0

Bromine binding site 6 out of 15 in 3tuu

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Bromine binding site 6 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br328

b:58.7
occ:1.00
 CG D:ARG277 3.6 22.7 1.0
NE D:ARG277 3.6 32.9 1.0
O D:HOH1105 3.6 33.9 1.0
CD D:ARG277 3.7 26.7 1.0
CB D:ARG277 3.8 21.3 1.0
CG D:PRO40 3.8 22.2 1.0
CD D:PRO278 4.3 19.9 1.0
CD D:PRO40 4.4 22.2 1.0
O D:HOH960 4.5 38.5 1.0
CG2 D:VAL279 4.6 17.4 1.0
CZ D:ARG277 4.7 34.5 1.0
CA D:ARG277 4.7 20.8 1.0
CD1 D:ILE322 4.9 25.2 1.0
CB D:PRO40 4.9 22.3 1.0
CG D:PRO278 5.0 20.1 1.0

Bromine binding site 7 out of 15 in 3tuu

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Bromine binding site 7 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br329

b:59.8
occ:1.00
 NZ H:LYS300 3.4 43.1 1.0
N D:VAL313 3.5 29.9 1.0
CE H:LYS300 3.6 42.8 1.0
CG D:ARG304 3.7 30.8 1.0
CA D:ASP312 3.7 31.3 1.0
CD D:ARG304 3.7 30.6 1.0
CG1 D:VAL313 3.8 28.8 1.0
CB D:ARG304 3.8 30.6 1.0
CB D:ASP312 4.0 31.7 1.0
C D:ASP312 4.1 30.8 1.0
OD2 D:ASP312 4.1 33.6 1.0
CG D:ASP312 4.4 33.3 1.0
NE D:ARG304 4.5 30.6 1.0
CB D:VAL313 4.5 29.3 1.0
CA D:VAL313 4.6 29.4 1.0
O D:HOH702 4.8 32.5 1.0
O D:VAL313 4.9 29.1 1.0
CD H:LYS300 4.9 40.4 1.0
N D:ASP312 4.9 31.1 1.0

Bromine binding site 8 out of 15 in 3tuu

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Bromine binding site 8 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br328

b:50.2
occ:1.00
 CG E:ARG277 3.7 22.1 1.0
NE E:ARG277 3.8 32.4 1.0
CB E:ARG277 3.8 19.6 1.0
CG E:PRO40 3.9 20.5 1.0
CD E:ARG277 4.0 26.1 1.0
CD E:PRO278 4.2 18.4 1.0
O E:HOH827 4.3 28.8 1.0
CD E:PRO40 4.4 20.0 1.0
CD1 E:ILE322 4.6 24.1 1.0
CG2 E:VAL279 4.7 16.2 1.0
CA E:ARG277 4.7 19.4 1.0
CG E:PRO278 4.8 18.2 1.0
CZ E:ARG277 4.8 34.7 1.0
N E:PRO278 4.9 19.0 1.0

Bromine binding site 9 out of 15 in 3tuu

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Bromine binding site 9 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Br329

b:90.1
occ:1.00
 NH2 E:ARG161 3.5 22.0 1.0
NE E:ARG161 3.6 22.5 1.0
OD1 E:ASN262 3.6 18.6 1.0
CZ E:ARG161 4.0 22.2 1.0
OH E:TYR156 4.2 24.6 1.0
C1 E:KPI184 4.3 28.5 1.0
CG E:ASN262 4.4 18.0 1.0
CB E:ASN262 4.4 17.0 1.0
CE1 E:PHE258 4.6 26.4 1.0
CG2 E:VAL225 4.7 18.5 1.0
CD E:ARG161 4.7 20.6 1.0
CB E:THR69 4.8 17.5 1.0
CG2 E:THR69 4.8 17.6 1.0
O2 E:KPI184 4.8 22.6 1.0
CX1 E:KPI184 4.9 27.1 1.0
O E:HOH376 4.9 19.1 1.0
OG1 E:THR70 4.9 18.1 1.0

Bromine binding site 10 out of 15 in 3tuu

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Bromine binding site 10 out of 15 in the Structure of Dihydrodipicolinate Synthase From the Common Grapevine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Structure of Dihydrodipicolinate Synthase From the Common Grapevine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Br328

b:49.0
occ:1.00
 NE F:ARG277 3.5 32.3 1.0
CG F:ARG277 3.7 22.4 1.0
CB F:ARG277 3.8 19.9 1.0
CG F:PRO40 3.8 21.0 1.0
CD F:ARG277 3.9 25.7 1.0
O F:HOH430 4.2 28.6 1.0
CD F:PRO278 4.3 19.6 1.0
CD F:PRO40 4.5 20.6 1.0
CZ F:ARG277 4.6 34.5 1.0
CD1 F:ILE322 4.6 24.5 1.0
CG2 F:VAL279 4.7 17.7 1.0
CA F:ARG277 4.7 19.9 1.0
NH2 F:ARG277 4.8 36.0 1.0
CB F:PRO40 4.8 21.2 1.0
CG F:PRO278 4.9 19.3 1.0
N F:PRO278 5.0 19.4 1.0

Reference:

S.C.Atkinson, C.Dogovski, M.T.Downton, F.G.Pearce, C.F.Reboul, A.M.Buckle, J.A.Gerrard, R.C.Dobson, J.Wagner, M.A.Perugini. Crystal, Solution and in Silico Structural Studies of Dihydrodipicolinate Synthase From the Common Grapevine. Plos One V. 7 38318 2012.
ISSN: ESSN 1932-6203
PubMed: 22761676
DOI: 10.1371/JOURNAL.PONE.0038318
Page generated: Sat Dec 12 02:15:55 2020

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