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Zinc in PDB 3ls6: Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc

Enzymatic activity of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc

All present enzymatic activity of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc:
4.1.99.12;

Protein crystallography data

The structure of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc, PDB code: 3ls6 was solved by P.Kumar, S.Karthikeyan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.86
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 66.276, 77.161, 146.827, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 19.7

Other elements in 3ls6:

The structure of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc (pdb code 3ls6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 11 binding sites of Zinc where determined in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc, PDB code: 3ls6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 11 in 3ls6

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Zinc binding site 1 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:20.2
occ:1.00
 OE1 A:GLU38 2.0 19.6 1.0
ND1 A:HIS153 2.1 13.8 1.0
O4 A:SO4300 2.1 17.0 1.0
O A:HOH402 2.1 27.9 1.0
O A:HOH400 2.4 18.8 1.0
CD A:GLU38 2.9 20.2 1.0
CE1 A:HIS153 3.0 16.3 1.0
CG A:HIS153 3.1 14.8 1.0
OE2 A:GLU38 3.2 23.8 1.0
S A:SO4300 3.3 17.6 1.0
CB A:HIS153 3.4 14.4 1.0
O3 A:SO4300 3.6 19.2 1.0
MG A:MG312 3.7 18.6 1.0
OD2 A:ASP42 3.9 15.7 1.0
O2 A:SO4300 3.9 20.2 1.0
NH1 A:ARG37 4.0 19.0 1.0
OD1 A:ASP42 4.0 13.8 1.0
NE2 A:HIS153 4.1 14.6 1.0
CD2 A:HIS153 4.2 13.6 1.0
O A:HOH612 4.2 27.5 1.0
CG A:GLU38 4.2 17.7 1.0
N A:HIS153 4.2 15.0 1.0
CG A:ASP42 4.3 15.2 1.0
OE1 A:GLU40 4.5 19.0 1.0
O A:HOH610 4.5 15.2 1.0
O1 A:SO4300 4.5 17.4 1.0
CA A:HIS153 4.5 14.9 1.0
CB A:GLU38 4.6 17.3 1.0
O A:HOH619 4.9 43.9 1.0
O B:HOH618 4.9 23.4 1.0

Zinc binding site 2 out of 11 in 3ls6

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Zinc binding site 2 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn308

b:22.9
occ:0.75
 OE2 B:GLU174 1.9 23.0 1.0
O B:HOH616 2.0 30.0 1.0
O A:HOH617 2.1 27.2 1.0
NE2 A:HIS136 2.1 26.2 1.0
O B:HOH614 2.2 20.8 1.0
O B:HOH671 2.8 22.5 1.0
CD B:GLU174 3.0 24.1 1.0
CE1 A:HIS136 3.0 27.6 1.0
O B:HOH782 3.1 43.0 1.0
CD2 A:HIS136 3.1 24.6 1.0
CG B:GLU174 3.8 21.1 1.0
OE1 B:GLU174 3.8 25.8 1.0
O B:HOH670 4.1 40.5 1.0
ND1 A:HIS136 4.2 25.2 1.0
CG A:HIS136 4.2 19.8 1.0
O B:HOH403 4.3 28.2 1.0
CB A:VAL109 4.4 18.4 1.0
CG1 A:VAL109 4.5 19.0 1.0
OE1 B:GLU40 4.5 25.7 1.0
OE2 B:GLU38 4.6 30.5 1.0
CG2 A:VAL109 4.6 18.7 1.0
O B:HOH783 4.6 23.5 1.0

Zinc binding site 3 out of 11 in 3ls6

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Zinc binding site 3 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn309

b:24.7
occ:0.80
 O A:HOH622 2.0 22.2 1.0
O A:HOH623 2.1 23.3 1.0
NE2 A:HIS195 2.1 20.9 1.0
O A:HOH621 2.1 25.5 1.0
NE2 A:HIS61 2.2 19.7 1.0
O A:HOH624 2.7 51.1 1.0
CD2 A:HIS61 3.0 20.6 1.0
CE1 A:HIS195 3.1 20.8 1.0
CD2 A:HIS195 3.1 21.7 1.0
CE1 A:HIS61 3.2 19.5 1.0
ND1 A:HIS195 4.2 19.9 1.0
CG A:HIS61 4.2 17.1 1.0
CG A:HIS195 4.2 19.6 1.0
ND1 A:HIS61 4.2 20.0 1.0
CE1 A:PHE191 4.4 20.1 1.0
CZ A:PHE191 4.8 18.9 1.0

Zinc binding site 4 out of 11 in 3ls6

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Zinc binding site 4 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn311

b:26.4
occ:0.60
 O A:HOH568 1.8 23.1 1.0
O A:HOH570 2.0 33.7 1.0
O A:HOH567 2.1 36.6 1.0
OD1 A:ASP130 2.1 19.9 1.0
O A:HOH569 2.2 29.5 1.0
CG A:ASP130 3.0 18.7 1.0
OD2 A:ASP130 3.3 20.7 1.0
O A:HOH684 4.1 35.7 1.0
CB A:ASP130 4.4 16.6 1.0
OG A:SER129 4.5 19.2 1.0
CA A:ASP130 4.7 16.4 1.0
CB A:LYS127 4.7 19.2 1.0
N A:ASP130 4.7 16.3 1.0

Zinc binding site 5 out of 11 in 3ls6

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Zinc binding site 5 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:26.6
occ:0.95
 OE1 B:GLU38 2.0 24.8 1.0
ND1 B:HIS153 2.1 19.7 1.0
O B:HOH403 2.2 28.2 1.0
O3 B:SO4301 2.3 23.5 1.0
O B:HOH783 2.5 23.5 1.0
CD B:GLU38 2.9 27.8 1.0
CE1 B:HIS153 3.0 20.3 1.0
CG B:HIS153 3.1 19.1 1.0
OE2 B:GLU38 3.2 30.5 1.0
S B:SO4301 3.4 24.2 1.0
CB B:HIS153 3.4 17.3 1.0
O4 B:SO4301 3.4 24.6 1.0
O B:HOH671 3.6 22.5 1.0
OD2 B:ASP42 3.8 20.8 1.0
NH1 B:ARG37 4.1 25.8 1.0
NE2 B:HIS153 4.1 17.9 1.0
O1 B:SO4301 4.1 24.1 1.0
OD1 B:ASP42 4.2 16.9 1.0
CD2 B:HIS153 4.2 17.4 1.0
N B:HIS153 4.2 17.1 1.0
CG B:GLU38 4.3 25.7 1.0
CG B:ASP42 4.3 18.1 1.0
O B:HOH614 4.4 20.8 1.0
CA B:HIS153 4.5 17.2 1.0
O2 B:SO4301 4.6 21.4 1.0
OE1 B:GLU40 4.6 25.7 1.0
CB B:GLU38 4.7 26.1 1.0
O A:HOH617 4.9 27.2 1.0

Zinc binding site 6 out of 11 in 3ls6

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Zinc binding site 6 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:15.5
occ:0.40
 O2 B:SO4302 1.9 19.6 1.0
OD1 B:ASP73 2.0 14.8 1.0
CG B:ASP73 2.8 15.8 1.0
OD2 B:ASP73 3.0 18.8 1.0
S B:SO4302 3.1 18.5 1.0
O4 B:SO4302 3.4 17.7 1.0
NZ B:LYS76 3.9 18.5 1.0
O1 B:SO4302 4.0 16.7 1.0
O3 B:SO4302 4.0 20.1 1.0
CB B:ASP73 4.2 14.8 1.0
O B:HOH483 4.2 16.3 0.5
N B:ASP73 4.3 13.2 1.0
CE B:LYS76 4.3 18.2 1.0
CA B:ASP73 4.5 14.3 1.0
CG B:GLU72 4.7 17.1 1.0
CB B:GLU72 4.7 15.7 1.0
C B:GLU72 4.9 14.2 1.0
O B:HOH685 5.0 36.7 1.0

Zinc binding site 7 out of 11 in 3ls6

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Zinc binding site 7 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn306

b:38.1
occ:0.80
 O B:HOH595 2.2 41.5 1.0
ND1 B:HIS195 2.3 20.2 1.0
O B:HOH596 2.4 36.7 1.0
CE1 B:HIS195 3.2 19.7 1.0
CG B:HIS195 3.3 19.4 1.0
CB B:HIS195 3.6 20.9 1.0
CA B:HIS195 3.9 21.1 1.0
O B:GLN194 4.3 20.6 1.0
NE2 B:HIS195 4.4 19.2 1.0
CD2 B:HIS195 4.4 18.2 1.0
CD2 B:LEU57 4.6 17.0 1.0
O B:HIS195 4.8 22.7 1.0
C B:HIS195 4.8 21.6 1.0
CD1 B:LEU57 4.8 15.4 1.0
N B:HIS195 4.9 20.6 1.0
C B:GLN194 4.9 20.9 1.0

Zinc binding site 8 out of 11 in 3ls6

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Zinc binding site 8 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn307

b:23.9
occ:0.80
 O B:HOH613 2.0 32.3 1.0
NE2 B:HIS61 2.1 19.0 1.0
O B:HOH772 2.2 39.0 1.0
ZN B:ZN313 2.3 36.5 0.5
CE1 B:HIS61 3.0 20.3 1.0
CD2 B:HIS61 3.1 18.8 1.0
O B:HOH669 3.8 22.9 1.0
ND1 B:HIS61 4.1 16.9 1.0
CG B:HIS61 4.2 16.9 1.0
CG B:ARG60 4.3 15.2 1.0
NE B:ARG60 4.6 20.9 1.0
CE1 B:HIS195 4.8 19.7 1.0
NE2 B:HIS195 4.9 19.2 1.0
CZ B:ARG60 4.9 21.8 1.0
NH2 B:ARG60 5.0 20.8 1.0

Zinc binding site 9 out of 11 in 3ls6

Go back to Zinc Binding Sites List in 3ls6
Zinc binding site 9 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn310

b:17.4
occ:0.50
 O A:HOH620 1.9 34.8 1.0
OE2 A:GLU174 1.9 23.5 1.0
O B:HOH618 1.9 23.4 1.0
O A:HOH610 2.1 15.2 1.0
NE2 B:HIS136 2.3 27.4 1.0
MG A:MG312 2.7 18.6 1.0
CD A:GLU174 3.0 22.6 1.0
CD2 B:HIS136 3.1 24.6 1.0
O A:HOH619 3.1 43.9 1.0
CE1 B:HIS136 3.3 26.8 1.0
O A:HOH629 3.7 34.6 1.0
O B:HOH611 3.7 33.4 1.0
CG A:GLU174 3.7 18.2 1.0
OE1 A:GLU174 3.9 21.8 1.0
O A:HOH612 4.2 27.5 1.0
CG B:HIS136 4.3 20.2 1.0
CG1 B:VAL109 4.3 15.8 1.0
O A:HOH402 4.4 27.9 1.0
CB B:VAL109 4.4 15.8 1.0
ND1 B:HIS136 4.4 24.6 1.0
OE2 A:GLU38 4.5 23.8 1.0
OE1 A:GLU40 4.5 19.0 1.0
O A:HOH400 4.7 18.8 1.0
CG2 B:VAL109 4.7 16.3 1.0

Zinc binding site 10 out of 11 in 3ls6

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Zinc binding site 10 out of 11 in the Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of 3,4-Dihydroxy-2-Butanone 4-Phosphate Synthase in Complex with Sulfate and Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn313

b:36.5
occ:0.50
 O B:HOH772 1.8 39.0 1.0
ZN B:ZN307 2.3 23.9 0.8
NE2 B:HIS61 3.4 19.0 1.0
CE1 B:HIS195 3.4 19.7 1.0
CD1 B:LEU57 3.5 15.4 1.0
CD2 B:HIS61 3.6 18.8 1.0
O B:HOH613 3.7 32.3 1.0
O B:HOH525 3.9 32.9 1.0
NE2 B:HIS195 4.0 19.2 1.0
O B:HOH669 4.3 22.9 1.0
ND1 B:HIS195 4.5 20.2 1.0
CE1 B:HIS61 4.7 20.3 1.0
CG B:ARG60 4.9 15.2 1.0
CG B:HIS61 5.0 16.9 1.0

Reference:

P.Kumar, M.Singh, R.Gautam, S.Karthikeyan. Potential Anti-Bacterial Drug Target: Structural Characterization of 3,4-Dihydroxy-2-Butanone-4-Phosphate Synthase From Salmonella Typhimurium LT2. Proteins V. 78 3292 2010.
ISSN: ISSN 0887-3585
PubMed: 20806221
DOI: 10.1002/PROT.22837
Page generated: Sat Oct 26 08:48:13 2024

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