Manganese in PDB 4nfw: Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli

The structure of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli, PDB code: 4nfw was solved by M.K.Hong, J.K.Kim, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.42 / 2.30
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	111.387, 111.387, 247.489, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Manganese atom in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli (pdb code 4nfw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 22 binding sites of Manganese where determined in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli, PDB code: 4nfw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn201 b:78.5 occ:1.00 O3 A:SO4203 2.1 45.9 1.0 O1 A:SO4204 2.5 62.8 1.0 OE1 A:GLU51 2.7 24.3 1.0 OE2 A:GLU55 2.8 34.7 1.0 O A:HOH329 3.0 48.9 1.0 O A:HOH332 3.1 27.0 1.0 S A:SO4203 3.5 50.5 1.0 MN A:MN202 3.5 65.5 1.0 O A:HOH330 3.5 41.9 1.0 O A:ALA35 3.6 17.2 1.0 CD A:GLU55 3.6 34.0 1.0 S A:SO4204 3.7 71.7 1.0 O3 A:SO4204 3.7 75.2 1.0 CD A:GLU51 3.7 24.9 1.0 O1 A:SO4203 3.8 45.5 1.0 CG A:GLU55 3.8 30.6 1.0 OD2 A:ASP98 4.0 33.8 1.0 OE2 A:GLU51 4.1 25.6 1.0 O2 A:SO4203 4.3 48.3 1.0 CA A:GLY36 4.3 18.9 1.0 O4 A:SO4203 4.4 48.0 1.0 O4 A:SO4204 4.4 60.4 1.0 C A:ALA35 4.6 16.7 1.0 OE1 A:GLU54 4.7 30.5 1.0 OE1 A:GLU55 4.7 39.8 1.0 O2 A:SO4204 4.8 61.5 1.0 N A:GLY36 5.0 17.9 1.0 O A:HOH336 5.0 41.4 1.0

Manganese binding site 2 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:65.5 occ:1.00 O A:HOH333 2.5 32.9 1.0 OE2 A:GLU51 2.5 25.6 1.0 O A:HOH334 2.6 50.7 1.0 O1 A:SO4203 2.7 45.5 1.0 O A:HOH328 2.8 25.9 1.0 O A:HOH332 2.9 27.0 1.0 CD A:GLU51 3.3 24.9 1.0 O3 A:SO4203 3.4 45.9 1.0 OE1 A:GLU51 3.4 24.3 1.0 MN A:MN201 3.5 78.5 1.0 O A:HOH329 3.5 48.9 1.0 S A:SO4203 3.5 50.5 1.0 O2 A:SO4203 3.8 48.3 1.0 OE1 A:GLU54 4.0 30.5 1.0 OE2 A:GLU39 4.0 46.5 1.0 NH1 A:ARG50 4.1 21.6 1.0 N A:HIS37 4.3 21.8 1.0 CA A:GLY36 4.7 18.9 1.0 CG A:GLU51 4.8 24.3 1.0 O A:HIS37 4.8 22.4 1.0 O4 A:SO4203 4.9 48.0 1.0

Manganese binding site 3 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:75.9 occ:1.00 O4 B:SO4203 2.7 46.0 1.0 OE1 B:GLU51 2.8 27.4 1.0 O4 B:SO4204 2.8 63.6 1.0 OE2 B:GLU55 3.1 37.0 1.0 OD2 B:ASP98 3.3 41.0 1.0 MN B:MN202 3.6 60.9 1.0 OE1 B:GLU54 3.6 33.8 1.0 CD B:GLU51 3.7 25.2 1.0 CG B:GLU55 3.8 31.9 1.0 CD B:GLU55 3.9 33.7 1.0 OE2 B:GLU51 4.0 24.1 1.0 S B:SO4203 4.1 51.6 1.0 O B:ALA35 4.1 18.5 1.0 O B:HOH308 4.2 36.5 1.0 S B:SO4204 4.3 71.4 1.0 CG B:ASP98 4.4 37.8 1.0 O2 B:SO4203 4.5 46.9 1.0 O B:HOH321 4.6 40.0 1.0 O3 B:SO4203 4.7 48.5 1.0 O1 B:SO4204 4.8 79.8 1.0 CA B:GLY36 4.8 19.1 1.0 CD B:GLU54 4.8 32.4 1.0 CB B:GLU54 4.9 29.8 1.0 O2 B:SO4204 4.9 61.9 1.0

Manganese binding site 4 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:60.9 occ:1.00 O B:HOH308 1.9 36.5 1.0 OE2 B:GLU51 2.6 24.1 1.0 O3 B:SO4203 2.6 48.5 1.0 O4 B:SO4203 2.9 46.0 1.0 S B:SO4203 3.1 51.6 1.0 O2 B:SO4203 3.4 46.9 1.0 CD B:GLU51 3.6 25.2 1.0 MN B:MN201 3.6 75.9 1.0 OE1 B:GLU51 3.8 27.4 1.0 N B:HIS37 4.0 21.8 1.0 OE1 B:GLU54 4.2 33.8 1.0 NH1 B:ARG50 4.5 25.7 1.0 O1 B:SO4203 4.6 49.8 1.0 CA B:GLY36 4.6 19.1 1.0 O B:HIS37 4.7 19.7 1.0 CB B:HIS37 4.7 21.6 1.0 O4 B:SO4204 4.8 63.6 1.0 C B:GLY36 4.8 20.5 1.0 CA B:HIS37 4.8 21.1 1.0 CG B:GLU51 4.9 24.6 1.0 O B:HOH321 5.0 40.0 1.0

Manganese binding site 5 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn201 b:95.4 occ:1.00 O2 C:SO4203 2.8 70.4 1.0 OE1 C:GLU51 2.9 38.3 1.0 OE2 C:GLU55 3.0 38.7 1.0 OE1 C:GLU54 3.3 43.2 1.0 O3 C:SO4204 3.4 0.4 1.0 OD2 C:ASP98 3.4 64.7 1.0 MN C:MN202 3.7 92.8 1.0 CD C:GLU51 3.7 37.0 1.0 OE2 C:GLU51 3.8 40.8 1.0 CG C:ASP98 4.0 62.0 1.0 CD C:GLU55 4.1 30.2 1.0 S C:SO4203 4.2 74.8 1.0 CB C:GLU54 4.3 36.2 1.0 CG C:GLU55 4.3 30.3 1.0 CD C:GLU54 4.4 40.8 1.0 CB C:ASP98 4.5 58.8 1.0 O4 C:SO4203 4.6 77.7 1.0 OD1 C:ASP98 4.7 57.8 1.0 S C:SO4204 4.7 97.4 1.0 O2 C:SO4204 4.7 91.2 1.0 O C:ALA35 4.9 29.6 1.0 CG C:GLU54 5.0 38.8 1.0 O3 C:SO4203 5.0 68.3 1.0

Manganese binding site 6 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn202 b:92.8 occ:1.00 O C:HOH327 2.0 47.2 1.0 OE2 C:GLU51 2.9 40.8 1.0 O2 C:SO4203 3.3 70.4 1.0 O4 C:SO4203 3.5 77.7 1.0 NH1 C:ARG50 3.6 26.1 1.0 OE1 C:GLU39 3.6 35.4 1.0 MN C:MN201 3.7 95.4 1.0 O3 C:SO4203 3.7 68.3 1.0 S C:SO4203 3.8 74.8 1.0 CD C:GLU51 3.9 37.0 1.0 OE1 C:GLU54 3.9 43.2 1.0 OE1 C:GLU51 4.3 38.3 1.0 OE2 C:GLU39 4.4 42.1 1.0 CD C:GLU39 4.4 38.5 1.0 O C:HOH303 4.4 48.9 1.0 O C:HIS37 4.7 25.7 1.0 CZ C:ARG50 4.7 25.8 1.0 CD C:GLU54 4.7 40.8 1.0 OE2 C:GLU54 4.8 42.3 1.0 NH2 C:ARG50 4.9 24.8 1.0 N C:HIS37 4.9 25.5 1.0

Manganese binding site 7 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn201 b:1.0 occ:1.00 OE2 D:GLU51 2.8 29.2 1.0 O4 D:SO4203 2.9 53.2 1.0 OE1 D:GLU39 3.5 56.6 1.0 MN D:MN202 3.8 87.3 1.0 CD D:GLU51 3.8 27.0 1.0 S D:SO4203 3.9 62.4 1.0 O2 D:SO4203 3.9 54.2 1.0 OE2 D:GLU39 3.9 60.5 1.0 OE1 D:GLU54 3.9 36.0 1.0 NH2 D:ARG50 4.1 39.4 1.0 O D:HIS37 4.1 37.5 1.0 CD D:GLU39 4.1 60.2 1.0 OE1 D:GLU51 4.2 29.7 1.0 O3 D:SO4203 4.2 58.2 1.0 NH1 D:ARG50 4.5 42.0 1.0 N D:HIS37 4.5 31.0 1.0 CZ D:ARG50 4.5 37.2 1.0 CB D:HIS37 4.6 34.2 1.0 CD D:GLU54 4.8 36.1 1.0 C D:HIS37 4.9 34.1 1.0 OE2 D:GLU54 4.9 31.6 1.0 CA D:HIS37 4.9 32.3 1.0

Manganese binding site 8 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn202 b:87.3 occ:1.00 OE1 D:GLU51 2.4 29.7 1.0 O2 D:SO4203 2.8 54.2 1.0 O4 D:SO4204 3.3 93.4 1.0 OE2 D:GLU55 3.3 35.1 1.0 CD D:GLU51 3.3 27.0 1.0 OE1 D:GLU54 3.5 36.0 1.0 OE2 D:GLU51 3.5 29.2 1.0 O4 D:SO4203 3.7 53.2 1.0 MN D:MN201 3.8 1.0 1.0 S D:SO4203 3.9 62.4 1.0 CD D:GLU55 4.2 35.1 1.0 CG D:GLU55 4.3 32.5 1.0 O D:ALA35 4.3 24.0 1.0 OD2 D:ASP98 4.4 62.9 1.0 O1 D:SO4203 4.7 64.0 1.0 CD D:GLU54 4.7 36.1 1.0 CG D:GLU51 4.7 28.3 1.0 S D:SO4204 4.7 0.3 1.0 CB D:GLU54 4.7 33.2 1.0 CA D:GLY36 4.8 25.8 1.0

Manganese binding site 9 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn201 b:82.9 occ:1.00 O E:HOH304 2.2 62.7 1.0 OE2 E:GLU51 2.5 42.9 1.0 O2 E:SO4203 3.0 55.4 1.0 O1 E:SO4203 3.4 62.5 1.0 MN E:MN202 3.5 96.3 1.0 OE2 E:GLU39 3.5 39.9 1.0 CD E:GLU51 3.5 38.7 1.0 S E:SO4203 3.5 66.0 1.0 O3 E:SO4203 3.7 60.6 1.0 NH1 E:ARG50 3.8 26.8 1.0 OE1 E:GLU51 3.8 37.0 1.0 OE1 E:GLU54 4.2 31.6 1.0 O E:HIS37 4.2 26.4 1.0 N E:HIS37 4.3 24.7 1.0 CD E:GLU39 4.4 39.7 1.0 NH2 E:ARG50 4.5 27.7 1.0 CZ E:ARG50 4.6 26.3 1.0 OE1 E:GLU39 4.8 39.5 1.0 CA E:GLY36 4.8 22.7 1.0 CG E:GLU51 4.9 36.0 1.0 C E:GLY36 4.9 23.3 1.0 O4 E:SO4203 5.0 58.8 1.0

Manganese binding site 10 out of 22 in the Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure and Atypical Hydrolysis Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn202 b:96.3 occ:1.00 O2 E:SO4204 2.8 87.3 1.0 O3 E:SO4203 3.0 60.6 1.0 OE1 E:GLU51 3.1 37.0 1.0 OD2 E:ASP98 3.4 62.1 1.0 O1 E:SO4203 3.4 62.5 1.0 MN E:MN201 3.5 82.9 1.0 OE2 E:GLU55 3.5 40.0 1.0 S E:SO4203 3.8 66.0 1.0 CD E:GLU51 3.9 38.7 1.0 OE2 E:GLU51 4.0 42.9 1.0 CD E:GLU55 4.0 33.9 1.0 O E:ALA35 4.1 24.7 1.0 OE1 E:GLU54 4.1 31.6 1.0 CG E:GLU55 4.1 31.5 1.0 CG E:ASP98 4.2 60.0 1.0 S E:SO4204 4.3 0.5 1.0 O2 E:SO4203 4.5 55.4 1.0 CB E:ASP98 4.7 58.0 1.0 O4 E:SO4204 4.9 0.8 1.0 O1 E:SO4204 4.9 99.0 1.0 OE1 E:GLU55 4.9 31.2 1.0 O E:HOH304 5.0 62.7 1.0 OD1 E:ASP98 5.0 57.1 1.0 CA E:GLY36 5.0 22.7 1.0

M.K.Hong, A.J.M.Ribeiro, J.K.Kim, H.P.T.Ngo, J.Kim, C.H.Lee, Y.J.Ahn, P.A.Fernandes, Q.Li, M.J.Ramos, L.W.Kang. Divalent Metal Ion-Based Catalytic Mechanism of the Nudix Hydrolase ORF153 (Ymfb) From Escherichia Coli Acta Crystallogr.,Sect.D V. 70 1297 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004714002570