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Manganese 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:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate, PDB code: 4eay:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese 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 Manganese with other atoms in the Mn 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:Mn403

b:13.9
occ:1.00
 O1B A:CS2402 2.0 37.7 1.0
ND1 A:HIS298 2.1 15.7 1.0
NE2 A:HIS233 2.3 16.2 1.0
O2 A:CS2402 2.3 35.6 1.0
OD2 A:ASP351 2.4 19.3 1.0
SG A:CYS271 2.4 15.6 1.0
C1 A:CS2402 2.9 36.1 1.0
CG A:HIS298 3.1 15.5 1.0
CE1 A:HIS298 3.1 15.2 1.0
C2 A:CS2402 3.2 36.1 1.0
CE1 A:HIS233 3.2 16.5 1.0
CD2 A:HIS233 3.3 18.1 1.0
CB A:CYS271 3.3 17.2 1.0
CG A:ASP351 3.4 18.5 1.0
CB A:HIS298 3.4 15.2 1.0
OD1 A:ASP351 3.7 19.1 1.0
OG A:SER274 4.1 17.6 1.0
O1A A:CS2402 4.1 34.2 1.0
NE2 A:HIS298 4.2 15.2 1.0
CD2 A:HIS298 4.3 16.6 1.0
NE A:ARG300 4.3 15.3 1.0
ND1 A:HIS233 4.3 18.5 1.0
NH2 A:ARG300 4.3 16.1 1.0
CG A:HIS233 4.4 17.8 1.0
CA A:CYS271 4.5 17.4 1.0
C3 A:CS2402 4.5 36.5 1.0
CB A:ASP351 4.6 17.9 1.0
C5 A:CS2402 4.7 33.4 1.0
CZ A:ARG300 4.8 15.5 1.0
C4 A:CS2402 4.9 34.5 1.0
CA A:HIS298 4.9 15.6 1.0

Manganese binding site 2 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese 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 Manganese with other atoms in the Mn 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:Mn403

b:13.2
occ:1.00
 ND1 B:HIS298 2.1 16.2 1.0
NE2 B:HIS233 2.2 17.2 1.0
O2 B:CS2402 2.3 42.2 1.0
SG B:CYS271 2.3 15.2 1.0
O1B B:CS2402 2.3 46.6 1.0
OD2 B:ASP351 2.5 21.3 1.0
CE1 B:HIS233 3.0 19.1 1.0
C1 B:CS2402 3.0 44.8 1.0
CG B:HIS298 3.1 16.1 1.0
CE1 B:HIS298 3.1 15.1 1.0
C2 B:CS2402 3.2 43.9 1.0
CD2 B:HIS233 3.3 18.5 1.0
CB B:CYS271 3.3 17.6 1.0
CB B:HIS298 3.4 16.4 1.0
CG B:ASP351 3.4 20.9 1.0
OD1 B:ASP351 3.8 22.8 1.0
ND1 B:HIS233 4.2 19.6 1.0
O1A B:CS2402 4.2 45.2 1.0
NE2 B:HIS298 4.2 16.1 1.0
CD2 B:HIS298 4.2 17.4 1.0
OG B:SER274 4.2 20.5 1.0
NE B:ARG300 4.3 14.7 1.0
CG B:HIS233 4.3 19.3 1.0
NH2 B:ARG300 4.4 17.0 1.0
CA B:CYS271 4.5 17.9 1.0
C3 B:CS2402 4.5 42.5 1.0
CB B:ASP351 4.6 18.5 1.0
CZ B:ARG300 4.8 16.8 1.0
C5 B:CS2402 4.9 39.1 1.0
CA B:HIS298 4.9 17.0 1.0
C4 B:CS2402 4.9 40.5 1.0

Manganese binding site 3 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese 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 Manganese with other atoms in the Mn 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:Mn402

b:21.6
occ:1.00
 ND1 C:HIS298 2.0 21.3 1.0
NE2 C:HIS233 2.2 24.2 1.0
SG C:CYS271 2.3 20.3 1.0
OD2 C:ASP351 2.5 26.0 1.0
CE1 C:HIS298 3.0 21.4 1.0
CG C:HIS298 3.0 20.2 1.0
CE1 C:HIS233 3.1 24.7 1.0
CD2 C:HIS233 3.3 23.9 1.0
CG C:ASP351 3.3 24.4 1.0
CB C:CYS271 3.4 22.8 1.0
CB C:HIS298 3.4 20.4 1.0
OD1 C:ASP351 3.6 25.6 1.0
NE2 C:HIS298 4.1 20.7 1.0
NH2 C:ARG300 4.1 23.2 1.0
CD2 C:HIS298 4.1 20.7 1.0
OG C:SER274 4.2 26.4 1.0
ND1 C:HIS233 4.3 26.3 1.0
NE C:ARG300 4.3 22.4 1.0
CG C:HIS233 4.4 25.0 1.0
CA C:CYS271 4.6 22.4 1.0
CB C:ASP351 4.6 22.8 1.0
CZ C:ARG300 4.7 22.7 1.0
CA C:HIS298 4.9 20.0 1.0
NH2 C:ARG349 5.0 23.4 1.0

Manganese binding site 4 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese 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 Manganese with other atoms in the Mn 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:Mn402

b:29.1
occ:1.00
 ND1 D:HIS298 2.1 28.2 1.0
NE2 D:HIS233 2.2 30.7 1.0
SG D:CYS271 2.3 25.3 1.0
OD2 D:ASP351 2.5 30.6 1.0
CE1 D:HIS298 3.0 28.8 1.0
CG D:HIS298 3.1 27.1 1.0
CE1 D:HIS233 3.2 29.7 1.0
CD2 D:HIS233 3.3 30.8 1.0
CG D:ASP351 3.3 29.2 1.0
CB D:HIS298 3.4 26.6 1.0
CB D:CYS271 3.4 28.5 1.0
OD1 D:ASP351 3.5 32.0 1.0
OG D:SER274 4.1 29.3 1.0
NH2 D:ARG300 4.1 28.0 1.0
NE2 D:HIS298 4.2 29.3 1.0
CD2 D:HIS298 4.2 28.3 1.0
ND1 D:HIS233 4.3 32.6 1.0
NE D:ARG300 4.3 25.1 1.0
CG D:HIS233 4.4 31.9 1.0
CB D:ASP351 4.6 26.9 1.0
CA D:CYS271 4.6 28.0 1.0
CZ D:ARG300 4.7 26.7 1.0
CA D:HIS298 4.9 26.8 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: Sat Oct 5 19:16:08 2024

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