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Manganese in PDB 3shd: Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1

Protein crystallography data

The structure of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1, PDB code: 3shd 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) 30.00 / 2.50
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 111.126, 111.126, 247.306, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 29.1

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 (pdb code 3shd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1, PDB code: 3shd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in 3shd

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Manganese binding site 1 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn154

b:33.0
occ:1.00
 O4 A:SO4156 2.1 35.9 1.0
O1 A:SO4157 2.1 25.0 1.0
OE1 A:GLU51 2.3 27.5 1.0
O A:HOH163 2.4 20.8 1.0
O A:HOH162 2.4 40.5 1.0
OE2 A:GLU55 2.6 21.6 1.0
O A:HOH160 2.7 34.9 1.0
S A:SO4156 3.2 34.2 1.0
O2 A:SO4156 3.3 35.1 1.0
CD A:GLU51 3.4 27.4 1.0
S A:SO4157 3.4 28.9 1.0
CD A:GLU55 3.5 25.1 1.0
MN A:MN155 3.6 40.5 1.0
O3 A:SO4157 3.6 33.2 1.0
CG A:GLU55 3.6 23.2 1.0
OE2 A:GLU51 3.7 29.3 1.0
O A:ALA35 3.7 21.3 1.0
O3 A:SO4156 4.1 35.0 1.0
O A:HOH161 4.1 18.4 1.0
O1 A:SO4156 4.2 35.5 1.0
O2 A:SO4157 4.2 27.4 1.0
O A:HOH159 4.3 24.1 1.0
OE1 A:GLU54 4.4 31.1 1.0
O A:HOH165 4.4 22.6 1.0
O4 A:SO4157 4.5 25.5 1.0
CA A:GLY36 4.5 23.4 1.0
OD2 A:ASP98 4.6 32.1 1.0
CG A:GLU51 4.7 24.6 1.0
C A:ALA35 4.7 21.2 1.0
OE1 A:GLU55 4.7 25.8 1.0
CB A:GLU51 4.9 23.3 1.0
OD1 A:ASP100 5.0 37.5 1.0

Manganese binding site 2 out of 24 in 3shd

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Manganese binding site 2 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn155

b:40.5
occ:1.00
 O A:HOH164 1.9 21.7 1.0
O A:HOH159 2.1 24.1 1.0
O A:HOH163 2.1 20.8 1.0
OE2 A:GLU51 2.2 29.3 1.0
O A:HOH166 2.4 30.3 1.0
O1 A:SO4156 2.6 35.5 1.0
O4 A:SO4156 2.8 35.9 1.0
S A:SO4156 3.0 34.2 1.0
CD A:GLU51 3.2 27.4 1.0
O2 A:SO4156 3.2 35.1 1.0
OE1 A:GLU51 3.5 27.5 1.0
MN A:MN154 3.6 33.0 1.0
OE2 A:GLU39 3.7 52.7 1.0
O A:HOH161 4.0 18.4 1.0
N A:HIS37 4.1 24.8 1.0
NH1 A:ARG50 4.3 29.0 1.0
O A:HOH160 4.3 34.9 1.0
OE1 A:GLU54 4.4 31.1 1.0
O3 A:SO4156 4.5 35.0 1.0
CG A:GLU51 4.5 24.6 1.0
O A:HIS37 4.6 25.9 1.0
O1 A:SO4157 4.7 25.0 1.0
CA A:GLY36 4.7 23.4 1.0
CB A:HIS37 4.8 24.2 1.0
CA A:HIS37 4.9 25.0 1.0
C A:GLY36 4.9 24.8 1.0
CD A:GLU39 5.0 49.9 1.0

Manganese binding site 3 out of 24 in 3shd

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Manganese binding site 3 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn154

b:37.9
occ:1.00
 O2 B:SO4156 2.2 33.8 1.0
O4 B:SO4157 2.2 22.7 1.0
OE2 B:GLU55 2.3 23.9 1.0
OE1 B:GLU51 2.3 29.9 1.0
CD B:GLU51 3.2 29.2 1.0
CD B:GLU55 3.3 25.8 1.0
OE2 B:GLU51 3.4 30.6 1.0
S B:SO4157 3.4 27.4 1.0
CG B:GLU55 3.5 26.2 1.0
S B:SO4156 3.5 34.9 1.0
O1 B:SO4157 3.6 29.3 1.0
O B:HOH177 4.0 21.9 1.0
MN B:MN155 4.0 42.2 1.0
O B:ALA35 4.0 21.2 1.0
OD2 B:ASP98 4.0 36.0 1.0
O2 B:SO4157 4.1 23.9 1.0
O4 B:SO4156 4.1 35.0 1.0
O1 B:SO4156 4.1 34.8 1.0
OE1 B:GLU54 4.2 29.9 1.0
O B:HOH223 4.2 37.1 1.0
OE1 B:GLU55 4.4 27.5 1.0
O3 B:SO4156 4.6 34.2 1.0
CG B:GLU51 4.6 26.8 1.0
O3 B:SO4157 4.6 22.8 1.0
CA B:GLY36 4.8 23.4 1.0
CG B:ASP98 4.8 32.9 1.0
OD1 B:ASP100 5.0 35.1 1.0
CB B:GLU55 5.0 24.0 1.0
C B:ALA35 5.0 21.1 1.0

Manganese binding site 4 out of 24 in 3shd

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Manganese binding site 4 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn155

b:42.2
occ:1.00
 O B:HOH177 2.0 21.9 1.0
OE2 B:GLU51 2.2 30.6 1.0
O2 B:SO4156 2.5 33.8 1.0
O3 B:SO4156 2.9 34.2 1.0
S B:SO4156 3.0 34.9 1.0
O4 B:SO4156 3.3 35.0 1.0
CD B:GLU51 3.4 29.2 1.0
N B:HIS37 4.0 25.6 1.0
MN B:MN154 4.0 37.9 1.0
OE1 B:GLU51 4.0 29.9 1.0
NH1 B:ARG50 4.1 20.7 1.0
CB B:HIS37 4.3 25.1 1.0
O1 B:SO4156 4.4 34.8 1.0
O B:HOH223 4.4 37.1 1.0
O B:HIS37 4.4 27.5 1.0
CG B:GLU51 4.5 26.8 1.0
O4 B:SO4157 4.6 22.7 1.0
CA B:HIS37 4.6 25.8 1.0
OE1 B:GLU54 4.7 29.9 1.0
O B:HOH161 4.7 31.1 1.0
OE1 B:GLU39 4.9 41.5 1.0
C B:GLY36 4.9 24.7 1.0
C B:HIS37 4.9 27.2 1.0
CA B:GLY36 4.9 23.4 1.0

Manganese binding site 5 out of 24 in 3shd

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Manganese binding site 5 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn154

b:51.5
occ:1.00
 O2 C:SO4156 2.0 55.3 1.0
OE1 C:GLU51 2.3 31.1 1.0
O3 C:SO4157 2.4 39.9 1.0
OE2 C:GLU55 2.5 40.6 1.0
CD C:GLU51 3.2 33.7 1.0
S C:SO4156 3.4 55.5 1.0
O2 C:SO4157 3.4 36.1 1.0
OE2 C:GLU51 3.5 34.6 1.0
CD C:GLU55 3.5 37.4 1.0
S C:SO4157 3.5 36.5 1.0
MN C:MN155 3.5 46.8 1.0
O4 C:SO4156 3.7 54.3 1.0
OD2 C:ASP98 3.8 61.0 1.0
CG C:GLU55 4.0 36.8 1.0
OE1 C:GLU54 4.0 43.8 1.0
O3 C:SO4156 4.2 52.9 1.0
O1 C:SO4156 4.3 54.0 1.0
OE1 C:GLU55 4.4 38.1 1.0
O C:ALA35 4.4 27.0 1.0
O4 C:SO4157 4.5 37.5 1.0
O1 C:SO4157 4.5 36.0 1.0
CG C:ASP98 4.6 60.4 1.0
CG C:GLU51 4.6 31.0 1.0
CA C:GLY36 4.8 28.3 1.0

Manganese binding site 6 out of 24 in 3shd

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Manganese binding site 6 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn155

b:46.8
occ:1.00
 O C:HOH269 2.1 45.0 1.0
OE2 C:GLU51 2.4 34.6 1.0
O3 C:SO4156 2.8 52.9 1.0
O2 C:SO4156 3.0 55.3 1.0
S C:SO4156 3.2 55.5 1.0
O4 C:SO4156 3.3 54.3 1.0
CD C:GLU51 3.5 33.7 1.0
MN C:MN154 3.5 51.5 1.0
OE1 C:GLU51 3.8 31.1 1.0
OE1 C:GLU54 3.9 43.8 1.0
O C:HOH160 4.2 27.5 1.0
OE1 C:GLU39 4.2 45.5 1.0
NH1 C:ARG50 4.3 28.5 1.0
O1 C:SO4156 4.6 54.0 1.0
N C:HIS37 4.7 29.6 1.0
CG C:GLU51 4.8 31.0 1.0
CD C:GLU54 5.0 40.1 1.0

Manganese binding site 7 out of 24 in 3shd

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Manganese binding site 7 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn154

b:54.2
occ:1.00
 OE2 D:GLU51 2.3 23.4 1.0
O4 D:SO4156 2.5 67.9 1.0
S D:SO4156 3.3 67.5 1.0
O2 D:SO4156 3.3 65.5 1.0
CD D:GLU51 3.5 26.4 1.0
O1 D:SO4156 3.5 64.8 1.0
MN D:MN155 3.7 57.9 1.0
OE1 D:GLU51 4.1 29.8 1.0
N D:HIS37 4.1 39.7 1.0
OE1 D:GLU39 4.2 51.9 1.0
OE1 D:GLU54 4.3 44.3 1.0
O D:HIS37 4.3 42.6 1.0
CB D:HIS37 4.4 41.4 1.0
O3 D:SO4156 4.6 65.8 1.0
CA D:HIS37 4.7 41.0 1.0
CG D:GLU51 4.7 29.7 1.0
OE2 D:GLU39 4.7 51.1 1.0
O D:HOH252 4.7 52.8 1.0
NH2 D:ARG50 4.8 46.6 1.0
C D:HIS37 4.8 41.6 1.0
CD D:GLU39 4.9 50.0 1.0
CA D:GLY36 5.0 38.2 1.0
C D:GLY36 5.0 39.2 1.0

Manganese binding site 8 out of 24 in 3shd

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Manganese binding site 8 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn155

b:57.9
occ:1.00
 O2 D:SO4156 1.9 65.5 1.0
OE1 D:GLU51 2.2 29.8 1.0
OE2 D:GLU55 2.5 35.6 1.0
O4 D:SO4157 2.6 43.7 1.0
CD D:GLU51 3.0 26.4 1.0
OE2 D:GLU51 3.1 23.4 1.0
S D:SO4156 3.2 67.5 1.0
CD D:GLU55 3.6 40.6 1.0
O4 D:SO4156 3.6 67.9 1.0
MN D:MN154 3.7 54.2 1.0
S D:SO4157 3.9 46.1 1.0
CG D:GLU55 3.9 42.5 1.0
O3 D:SO4156 4.0 65.8 1.0
OE1 D:GLU54 4.1 44.3 1.0
OD2 D:ASP98 4.2 67.4 1.0
O D:ALA35 4.2 36.9 1.0
O1 D:SO4156 4.2 64.8 1.0
O1 D:SO4157 4.2 47.1 1.0
CG D:GLU51 4.5 29.7 1.0
O2 D:SO4157 4.5 42.2 1.0
CA D:GLY36 4.6 38.2 1.0
OE1 D:GLU55 4.7 38.1 1.0
O3 D:SO4157 4.9 47.6 1.0
CB D:GLU51 5.0 32.9 1.0

Manganese binding site 9 out of 24 in 3shd

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Manganese binding site 9 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn154

b:43.4
occ:1.00
 OE2 E:GLU51 2.0 35.8 1.0
O E:HOH172 2.2 29.3 1.0
O2 E:SO4156 2.9 47.6 1.0
CD E:GLU51 3.2 33.3 1.0
O1 E:SO4156 3.2 46.9 1.0
O3 E:SO4156 3.3 47.5 1.0
S E:SO4156 3.3 49.9 1.0
MN E:MN155 3.6 55.9 1.0
OE1 E:GLU51 3.9 33.4 1.0
NH1 E:ARG50 4.0 39.0 1.0
OE1 E:GLU54 4.2 39.2 1.0
N E:HIS37 4.3 30.6 1.0
OE1 E:GLU39 4.3 44.8 1.0
CG E:GLU51 4.3 29.4 1.0
OE2 E:GLU39 4.4 46.9 1.0
O E:HIS37 4.5 31.0 1.0
CD E:GLU39 4.8 43.7 1.0
O4 E:SO4156 4.8 49.2 1.0
CA E:GLY36 4.9 30.2 1.0
CB E:HIS37 4.9 30.9 1.0
O2 E:SO4157 5.0 44.5 1.0

Manganese binding site 10 out of 24 in 3shd

Go back to Manganese Binding Sites List in 3shd
Manganese binding site 10 out of 24 in the Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Nudix Hydrolase ORF153, Ymfb, From Escherichia Coli K-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn155

b:55.9
occ:1.00
 O3 E:SO4156 2.1 47.5 1.0
O2 E:SO4157 2.4 44.5 1.0
OE1 E:GLU51 2.4 33.4 1.0
OE2 E:GLU55 3.0 38.5 1.0
OE2 E:GLU51 3.1 35.8 1.0
CD E:GLU51 3.1 33.3 1.0
O1 E:SO4156 3.3 46.9 1.0
S E:SO4156 3.3 49.9 1.0
MN E:MN154 3.6 43.4 1.0
S E:SO4157 3.7 45.8 1.0
O1 E:SO4157 3.7 43.9 1.0
CD E:GLU55 3.8 37.2 1.0
OD2 E:ASP98 3.9 60.4 1.0
CG E:GLU55 4.0 35.0 1.0
OE1 E:GLU54 4.2 39.2 1.0
O E:ALA35 4.2 29.4 1.0
O2 E:SO4156 4.2 47.6 1.0
CG E:ASP98 4.3 60.4 1.0
O4 E:SO4156 4.4 49.2 1.0
O4 E:SO4157 4.5 45.9 1.0
CG E:GLU51 4.6 29.4 1.0
O3 E:SO4157 4.7 41.2 1.0
O E:HOH172 4.7 29.3 1.0
OD1 E:ASP98 4.7 62.6 1.0
CB E:ASP98 4.7 59.7 1.0
OE1 E:GLU55 4.8 40.4 1.0
CA E:GLY36 5.0 30.2 1.0

Reference:

M.K.Hong, M.K.Hong, J.K.Kim, L.W.Kang. N/A N/A.
Page generated: Sat Oct 5 17:53:23 2024

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