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Chlorine in PDB 4eay: Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate

Enzymatic activity of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate

All present enzymatic activity of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate, PDB code: 4eay was solved by X.Qiu, Y.Zhu, Y.Yuan, Y.Zhang, H.Liu, Y.Gao, M.Teng, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.470, 238.580, 54.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.6

Other elements in 4eay:

The structure of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate also contains other interesting chemical elements:

Manganese (Mn) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate (pdb code 4eay). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate, PDB code: 4eay:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4eay

Go back to Chlorine Binding Sites List in 4eay
Chlorine binding site 1 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:11.5
occ:1.00
 NH1 A:ARG373 3.2 10.2 1.0
NH1 A:ARG349 3.2 16.3 1.0
N A:ARG6 3.3 15.1 1.0
N A:ASP351 3.5 17.3 1.0
CD A:ARG349 3.7 17.8 1.0
CG A:PRO350 3.7 16.1 1.0
CD A:PRO350 3.7 16.8 1.0
CB A:ARG349 3.7 17.6 1.0
CD A:ARG373 3.8 9.8 1.0
CA A:ASP351 4.0 17.8 1.0
CA A:TRP5 4.0 16.2 1.0
CG A:ARG349 4.0 17.1 1.0
O A:ASP351 4.0 19.1 1.0
CB A:ARG6 4.0 15.0 1.0
N A:PRO350 4.1 16.9 1.0
C A:TRP5 4.1 16.1 1.0
CA A:ARG6 4.2 15.4 1.0
CZ A:ARG349 4.3 18.7 1.0
CZ A:ARG373 4.3 10.6 1.0
C A:ASP351 4.3 18.5 1.0
NE A:ARG349 4.4 18.1 1.0
C A:PRO350 4.4 16.6 1.0
NE A:ARG373 4.5 10.6 1.0
C A:ARG349 4.5 17.1 1.0
CA A:ARG349 4.6 17.5 1.0
O A:THR4 4.6 17.6 1.0
CA A:PRO350 4.7 16.5 1.0
CG A:TRP5 4.7 15.0 1.0
CB A:PRO350 4.7 16.2 1.0
CD2 A:TRP5 4.8 13.4 1.0
CE1 A:TYR368 4.8 18.5 1.0
O A:ARG6 4.8 14.6 1.0
CG A:ARG373 4.8 11.5 1.0
CB A:TRP5 4.8 15.8 1.0
N A:TRP5 4.9 17.2 1.0
CE3 A:TRP5 5.0 13.2 1.0

Chlorine binding site 2 out of 4 in 4eay

Go back to Chlorine Binding Sites List in 4eay
Chlorine binding site 2 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:11.1
occ:1.00
 NH1 B:ARG373 3.1 8.7 1.0
NH1 B:ARG349 3.2 16.3 1.0
N B:ARG6 3.3 13.6 1.0
CD B:PRO350 3.6 15.0 1.0
N B:ASP351 3.6 16.7 1.0
CG B:PRO350 3.7 15.3 1.0
CB B:ARG349 3.7 14.6 1.0
CD B:ARG349 3.7 15.6 1.0
CD B:ARG373 3.8 9.4 1.0
CA B:TRP5 3.9 14.1 1.0
CG B:ARG349 3.9 14.9 1.0
CB B:ARG6 4.0 12.9 1.0
N B:PRO350 4.0 15.5 1.0
C B:TRP5 4.1 14.0 1.0
CA B:ASP351 4.1 17.9 1.0
O B:ASP351 4.2 19.5 1.0
CA B:ARG6 4.2 13.5 1.0
CZ B:ARG373 4.2 9.1 1.0
CZ B:ARG349 4.3 17.2 1.0
CG B:TRP5 4.4 14.1 1.0
NE B:ARG349 4.5 16.4 1.0
C B:ASP351 4.5 18.5 1.0
NE B:ARG373 4.5 8.6 1.0
C B:ARG349 4.5 15.1 1.0
C B:PRO350 4.6 16.1 1.0
CD2 B:TRP5 4.6 12.7 1.0
O B:THR4 4.6 14.3 1.0
CA B:ARG349 4.6 15.4 1.0
CB B:TRP5 4.6 13.6 1.0
CA B:PRO350 4.7 15.8 1.0
CB B:PRO350 4.8 15.6 1.0
CD1 B:TRP5 4.8 11.9 1.0
O B:ARG6 4.8 13.7 1.0
CG B:ARG373 4.9 10.7 1.0
N B:TRP5 4.9 14.8 1.0
CE3 B:TRP5 4.9 13.1 1.0
CE2 B:TRP5 5.0 12.9 1.0

Chlorine binding site 3 out of 4 in 4eay

Go back to Chlorine Binding Sites List in 4eay
Chlorine binding site 3 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:19.0
occ:1.00
 NH1 C:ARG349 3.2 21.9 1.0
N C:ARG6 3.3 17.8 1.0
NH1 C:ARG373 3.3 14.1 1.0
N C:ASP351 3.5 20.9 1.0
CB C:ARG349 3.6 18.7 1.0
CG C:PRO350 3.6 17.9 1.0
CD C:PRO350 3.6 18.0 1.0
CD C:ARG349 3.7 20.8 1.0
CG C:ARG349 3.8 19.6 1.0
CD C:ARG373 3.9 14.0 1.0
CA C:TRP5 3.9 17.6 1.0
O C:ASP351 3.9 24.7 1.0
CA C:ASP351 4.0 22.6 1.0
N C:PRO350 4.1 18.2 1.0
CB C:ARG6 4.1 18.8 1.0
C C:TRP5 4.1 18.2 1.0
CA C:ARG6 4.2 18.5 1.0
CZ C:ARG349 4.2 23.0 1.0
C C:ASP351 4.3 23.5 1.0
CZ C:ARG373 4.4 14.7 1.0
NE C:ARG349 4.4 22.2 1.0
C C:PRO350 4.5 19.6 1.0
C C:ARG349 4.5 18.3 1.0
CA C:ARG349 4.5 18.2 1.0
CG C:TRP5 4.6 17.0 1.0
NE C:ARG373 4.6 14.4 1.0
CA C:PRO350 4.7 18.6 1.0
CD2 C:TRP5 4.7 15.2 1.0
O C:THR4 4.7 18.7 1.0
CB C:PRO350 4.7 17.8 1.0
CB C:TRP5 4.8 17.2 1.0
O C:ARG6 4.9 17.9 1.0
CE1 C:TYR368 4.9 24.0 1.0
N C:TRP5 5.0 18.1 1.0
CE3 C:TRP5 5.0 13.6 1.0
CG C:ARG373 5.0 14.3 1.0

Chlorine binding site 4 out of 4 in 4eay

Go back to Chlorine Binding Sites List in 4eay
Chlorine binding site 4 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:23.9
occ:1.00
 NH1 D:ARG373 3.1 20.0 1.0
NH1 D:ARG349 3.1 28.9 1.0
N D:ARG6 3.1 25.8 1.0
CD D:PRO350 3.6 23.3 1.0
N D:ASP351 3.6 25.6 1.0
CD D:ARG349 3.6 28.6 1.0
CD D:ARG373 3.7 17.6 1.0
CA D:TRP5 3.8 25.1 1.0
CB D:ARG349 3.8 26.0 1.0
CG D:ARG349 3.8 26.5 1.0
CG D:PRO350 3.9 22.9 1.0
CB D:ARG6 3.9 26.6 1.0
C D:TRP5 4.0 26.0 1.0
O D:ASP351 4.1 28.6 1.0
N D:PRO350 4.1 23.6 1.0
CA D:ARG6 4.1 26.7 1.0
CA D:ASP351 4.1 27.0 1.0
CZ D:ARG349 4.1 29.6 1.0
CZ D:ARG373 4.2 19.8 1.0
NE D:ARG349 4.3 29.6 1.0
NE D:ARG373 4.4 18.6 1.0
CG D:TRP5 4.4 23.8 1.0
C D:ASP351 4.5 27.1 1.0
CD2 D:TRP5 4.6 20.7 1.0
C D:ARG349 4.6 24.2 1.0
CB D:TRP5 4.6 24.6 1.0
C D:PRO350 4.6 23.9 1.0
O D:THR4 4.7 25.3 1.0
CA D:ARG349 4.7 25.4 1.0
CA D:PRO350 4.8 23.2 1.0
O D:ARG6 4.8 26.4 1.0
CE3 D:TRP5 4.9 18.0 1.0
CD1 D:TRP5 4.9 22.8 1.0
CE1 D:TYR368 4.9 28.7 1.0
N D:TRP5 4.9 26.1 1.0
CB D:PRO350 4.9 21.6 1.0
CG D:ARG373 4.9 17.9 1.0
C D:ARG6 5.0 27.1 1.0

Reference:

X.Qiu, Y.Tao, Y.Zhu, Y.Yuan, Y.Zhang, H.Liu, Y.Gao, M.Teng, L.Niu. Structural Insights Into Decreased Enzymatic Activity Induced By An Insert Sequence in Mannonate Dehydratase From Gram Negative Bacterium. J.Struct.Biol. V. 180 327 2012.
ISSN: ISSN 1047-8477
PubMed: 22796868
DOI: 10.1016/J.JSB.2012.06.013
Page generated: Sun Jul 21 12:42:52 2024

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