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Manganese in PDB 8hmo: Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii

Enzymatic activity of Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii

All present enzymatic activity of Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii:
3.5.1.9;

Protein crystallography data

The structure of Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii, PDB code: 8hmo was solved by K.Yoneda, H.Sakuraba, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.45 / 2.53
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.21, 70.198, 104.839, 90, 105.77, 90
R / Rfree (%) 25 / 29.9

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii (pdb code 8hmo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii, PDB code: 8hmo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 8hmo

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Manganese binding site 1 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:42.8
occ:1.00
 NE2 A:HIS49 2.2 36.6 1.0
OE1 A:GLU167 2.3 45.6 1.0
OD1 A:ASP51 2.4 53.0 1.0
ND1 A:HIS45 2.6 37.0 1.0
CE1 A:HIS49 3.0 36.9 1.0
MN A:MN302 3.0 44.6 1.0
O A:HOH460 3.2 27.3 1.0
CG A:ASP51 3.3 50.6 1.0
CD2 A:HIS49 3.3 36.8 1.0
CG A:HIS45 3.5 37.2 1.0
CD A:GLU167 3.5 44.0 1.0
OD2 A:ASP51 3.5 50.5 1.0
CE1 A:HIS45 3.6 35.7 1.0
CB A:HIS45 3.6 37.9 1.0
O A:LEU143 4.1 39.1 1.0
OE2 A:GLU167 4.1 44.5 1.0
CE1 A:HIS55 4.2 59.1 1.0
ND1 A:HIS49 4.2 35.7 1.0
CG A:HIS49 4.4 35.7 1.0
CA A:HIS45 4.4 40.1 1.0
ND1 A:HIS55 4.5 59.0 1.0
CG A:GLU167 4.6 41.2 1.0
CD2 A:HIS45 4.6 37.3 1.0
CB A:GLU167 4.7 40.2 1.0
NE2 A:HIS45 4.7 35.3 1.0
CB A:ASP51 4.7 48.6 1.0
O A:HOH454 4.8 59.3 1.0

Manganese binding site 2 out of 12 in 8hmo

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Manganese binding site 2 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:44.6
occ:1.00
 OD2 A:ASP51 2.1 50.5 1.0
OE2 A:GLU167 2.2 44.5 1.0
NE2 A:HIS155 2.3 49.6 1.0
OE1 A:GLU167 2.5 45.6 1.0
O A:HOH460 2.6 27.3 1.0
CD A:GLU167 2.7 44.0 1.0
CE1 A:HIS155 2.8 51.9 1.0
MN A:MN301 3.0 42.8 1.0
CG A:ASP51 3.1 50.6 1.0
OD1 A:ASP51 3.4 53.0 1.0
CD2 A:HIS155 3.6 51.5 1.0
CE1 A:HIS55 3.7 59.1 1.0
ND1 A:HIS55 3.9 59.0 1.0
ND1 A:HIS155 4.1 51.1 1.0
CG A:GLU167 4.2 41.2 1.0
CG A:HIS155 4.4 51.4 1.0
CB A:ASP51 4.5 48.6 1.0
N A:ILE145 4.6 40.8 1.0
CG1 A:VAL165 4.7 37.3 1.0
CA A:GLY144 4.8 41.7 1.0
NE2 A:HIS49 4.8 36.6 1.0
O A:LEU143 4.9 39.1 1.0
ND1 A:HIS45 4.9 37.0 1.0
CG2 A:ILE145 4.9 41.4 1.0
NE2 A:HIS55 5.0 57.0 1.0

Manganese binding site 3 out of 12 in 8hmo

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Manganese binding site 3 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:53.2
occ:1.00
 ND1 B:HIS45 2.3 43.4 1.0
MN B:MN302 2.4 61.9 1.0
OE1 B:GLU167 2.5 43.7 1.0
O B:HOH454 2.6 23.6 1.0
OD1 B:ASP51 2.9 57.5 1.0
CE1 B:HIS45 3.0 44.1 1.0
NE2 B:HIS49 3.1 46.5 1.0
CG B:HIS45 3.3 39.5 1.0
CD B:GLU167 3.4 41.9 1.0
CE1 B:HIS55 3.4 52.1 1.0
OE2 B:GLU167 3.5 35.6 1.0
OD2 B:ASP51 3.5 53.3 1.0
CG B:ASP51 3.6 53.4 1.0
CB B:HIS45 3.7 39.9 1.0
CE1 B:HIS49 3.8 49.4 1.0
O B:LEU143 3.9 40.9 1.0
ND1 B:HIS55 4.0 52.6 1.0
NE2 B:HIS45 4.1 41.8 1.0
CD2 B:HIS45 4.3 40.1 1.0
CD2 B:HIS49 4.3 45.4 1.0
NE2 B:HIS55 4.4 56.4 1.0
NE2 B:HIS155 4.6 55.8 1.0
CA B:HIS45 4.8 40.2 1.0
CG B:GLU167 4.8 40.0 1.0

Manganese binding site 4 out of 12 in 8hmo

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Manganese binding site 4 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:61.9
occ:1.00
 OD2 B:ASP51 2.2 53.3 1.0
NE2 B:HIS155 2.3 55.8 1.0
MN B:MN301 2.4 53.2 1.0
OE2 B:GLU167 2.5 35.6 1.0
O B:HOH454 2.5 23.6 1.0
CE1 B:HIS155 2.8 55.7 1.0
CE1 B:HIS55 2.8 52.1 1.0
ND1 B:HIS55 3.0 52.6 1.0
CG B:ASP51 3.1 53.4 1.0
OE1 B:GLU167 3.2 43.7 1.0
CD B:GLU167 3.2 41.9 1.0
OD1 B:ASP51 3.3 57.5 1.0
CD2 B:HIS155 3.4 59.1 1.0
ND1 B:HIS155 3.9 56.0 1.0
NE2 B:HIS55 4.1 56.4 1.0
ND1 B:HIS45 4.1 43.4 1.0
CE1 B:HIS45 4.1 44.1 1.0
CG B:HIS155 4.2 60.4 1.0
CG B:HIS55 4.4 55.0 1.0
CB B:ASP51 4.5 48.5 1.0
CG B:GLU167 4.7 40.0 1.0
CD2 B:HIS55 4.9 52.2 1.0
NE2 B:HIS49 4.9 46.5 1.0

Manganese binding site 5 out of 12 in 8hmo

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Manganese binding site 5 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:49.0
occ:1.00
 OE1 C:GLU167 2.1 44.3 1.0
NE2 C:HIS49 2.2 31.6 1.0
OD1 C:ASP51 2.4 56.1 1.0
ND1 C:HIS45 2.6 45.0 1.0
MN C:MN302 2.9 53.0 1.0
CE1 C:HIS49 2.9 30.4 1.0
O C:HOH454 3.2 28.4 1.0
CD C:GLU167 3.4 41.9 1.0
CG C:ASP51 3.4 54.3 1.0
CD2 C:HIS49 3.4 32.1 1.0
CG C:HIS45 3.5 43.9 1.0
OD2 C:ASP51 3.6 54.1 1.0
CB C:HIS45 3.6 43.0 1.0
CE1 C:HIS45 3.6 42.4 1.0
OE2 C:GLU167 4.0 39.6 1.0
O C:LEU143 4.0 41.6 1.0
CE1 C:HIS55 4.1 61.8 1.0
ND1 C:HIS49 4.1 29.8 1.0
ND1 C:HIS55 4.4 60.6 1.0
CG C:HIS49 4.4 32.0 1.0
CG C:GLU167 4.5 40.7 1.0
CA C:HIS45 4.5 44.5 1.0
CB C:GLU167 4.5 40.1 1.0
CD2 C:HIS45 4.6 46.6 1.0
NE2 C:HIS45 4.7 43.6 1.0
CB C:ASP51 4.8 51.9 1.0
O C:HIS45 5.0 48.1 1.0
NE2 C:HIS155 5.0 49.9 1.0

Manganese binding site 6 out of 12 in 8hmo

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Manganese binding site 6 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:53.0
occ:1.00
 NE2 C:HIS155 2.2 49.9 1.0
OD2 C:ASP51 2.2 54.1 1.0
OE2 C:GLU167 2.3 39.6 1.0
OE1 C:GLU167 2.5 44.3 1.0
O C:HOH454 2.5 28.4 1.0
CD C:GLU167 2.7 41.9 1.0
CE1 C:HIS155 2.8 51.8 1.0
MN C:MN301 2.9 49.0 1.0
CG C:ASP51 3.1 54.3 1.0
OD1 C:ASP51 3.3 56.1 1.0
CD2 C:HIS155 3.4 50.1 1.0
ND1 C:HIS55 3.7 60.6 1.0
CE1 C:HIS55 3.7 61.8 1.0
ND1 C:HIS155 4.0 52.5 1.0
CG C:GLU167 4.2 40.7 1.0
CG C:HIS155 4.4 51.0 1.0
O C:HOH418 4.4 58.9 1.0
CB C:ASP51 4.5 51.9 1.0
CA C:GLY144 4.7 40.9 1.0
N C:ILE145 4.7 40.6 1.0
NE2 C:HIS49 4.7 31.6 1.0
ND1 C:HIS45 4.8 45.0 1.0
O C:LEU143 4.9 41.6 1.0

Manganese binding site 7 out of 12 in 8hmo

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Manganese binding site 7 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:53.1
occ:1.00
 OE1 D:GLU167 2.2 46.9 1.0
O D:HOH461 2.4 12.8 1.0
ND1 D:HIS45 2.5 45.4 1.0
MN D:MN302 2.8 50.8 1.0
NE2 D:HIS49 3.1 54.1 1.0
CG D:HIS45 3.3 44.9 1.0
CD D:GLU167 3.3 46.0 1.0
CE1 D:HIS45 3.3 48.4 1.0
O D:LEU143 3.5 39.2 1.0
CB D:HIS45 3.5 43.9 1.0
OD1 D:ASP51 3.6 62.1 1.0
OD2 D:ASP51 3.7 53.9 1.0
CE1 D:HIS55 3.8 66.6 1.0
OE2 D:GLU167 3.8 41.9 1.0
CE1 D:HIS49 3.9 50.3 1.0
CG D:ASP51 4.1 57.0 1.0
CD2 D:HIS49 4.2 50.3 1.0
CD2 D:HIS45 4.3 45.3 1.0
NE2 D:HIS45 4.4 46.7 1.0
ND1 D:HIS55 4.5 71.0 1.0
NE2 D:HIS55 4.5 72.3 1.0
CG D:GLU167 4.6 44.6 1.0
CA D:HIS45 4.6 44.0 1.0
C D:LEU143 4.7 38.7 1.0
O D:HIS45 4.7 45.3 1.0
NE2 D:HIS155 5.0 56.5 1.0
CA D:GLY144 5.0 41.5 1.0

Manganese binding site 8 out of 12 in 8hmo

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Manganese binding site 8 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:50.8
occ:1.00
 NE2 D:HIS155 2.3 56.5 1.0
OD2 D:ASP51 2.3 53.9 1.0
O D:HOH461 2.4 12.8 1.0
OE2 D:GLU167 2.5 41.9 1.0
CE1 D:HIS155 2.5 54.1 1.0
MN D:MN301 2.8 53.1 1.0
CE1 D:HIS55 2.8 66.6 1.0
OE1 D:GLU167 2.8 46.9 1.0
CD D:GLU167 3.0 46.0 1.0
ND1 D:HIS55 3.2 71.0 1.0
CG D:ASP51 3.4 57.0 1.0
CD2 D:HIS155 3.5 57.5 1.0
ND1 D:HIS155 3.7 53.8 1.0
OD1 D:ASP51 3.9 62.1 1.0
NE2 D:HIS55 4.1 72.3 1.0
ND1 D:HIS45 4.2 45.4 1.0
CE1 D:HIS45 4.2 48.4 1.0
CG D:HIS155 4.2 57.0 1.0
CG D:HIS55 4.5 72.2 1.0
CG D:GLU167 4.6 44.6 1.0
CB D:ASP51 4.7 49.7 1.0
CD2 D:HIS55 5.0 69.4 1.0

Manganese binding site 9 out of 12 in 8hmo

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Manganese binding site 9 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:61.3
occ:1.00
 ND1 E:HIS45 2.3 40.8 1.0
OE1 E:GLU167 2.3 51.2 1.0
NE2 E:HIS49 2.4 40.6 1.0
OD1 E:ASP51 2.6 55.6 1.0
MN E:MN302 2.8 70.3 1.0
CE1 E:HIS49 3.1 40.7 1.0
CG E:HIS45 3.1 39.3 1.0
CE1 E:HIS45 3.2 41.0 1.0
O E:HOH445 3.4 44.9 1.0
CD E:GLU167 3.4 49.2 1.0
CB E:HIS45 3.4 39.9 1.0
CG E:ASP51 3.5 57.7 1.0
CD2 E:HIS49 3.5 40.3 1.0
OD2 E:ASP51 3.5 61.0 1.0
OE2 E:GLU167 3.8 45.7 1.0
O E:LEU143 3.9 54.9 1.0
CA E:HIS45 4.1 42.0 1.0
CD2 E:HIS45 4.2 40.8 1.0
NE2 E:HIS45 4.2 41.5 1.0
CE1 E:HIS55 4.2 60.5 1.0
ND1 E:HIS49 4.3 40.9 1.0
CG E:HIS49 4.5 42.1 1.0
ND1 E:HIS55 4.6 60.8 1.0
CG E:GLU167 4.7 46.2 1.0
O E:HIS45 4.7 41.0 1.0
CB E:GLU167 4.9 46.0 1.0
CB E:ASP51 4.9 53.4 1.0
C E:HIS45 4.9 42.3 1.0
NE2 E:HIS155 5.0 64.8 1.0

Manganese binding site 10 out of 12 in 8hmo

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Manganese binding site 10 out of 12 in the Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii


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 Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn302

b:70.3
occ:1.00
 OE2 E:GLU167 2.2 45.7 1.0
NE2 E:HIS155 2.5 64.8 1.0
O E:HOH445 2.5 44.9 1.0
OD2 E:ASP51 2.6 61.0 1.0
CE1 E:HIS155 2.8 67.6 1.0
OE1 E:GLU167 2.8 51.2 1.0
MN E:MN301 2.8 61.3 1.0
CD E:GLU167 2.8 49.2 1.0
CE1 E:HIS55 3.5 60.5 1.0
CG E:ASP51 3.5 57.7 1.0
OD1 E:ASP51 3.7 55.6 1.0
CD2 E:HIS155 3.8 66.5 1.0
ND1 E:HIS55 3.9 60.8 1.0
ND1 E:HIS155 4.0 66.9 1.0
CG E:GLU167 4.4 46.2 1.0
ND1 E:HIS45 4.4 40.8 1.0
CA E:GLY144 4.4 54.9 1.0
CG E:HIS155 4.5 67.3 1.0
O E:LEU143 4.6 54.9 1.0
N E:ILE145 4.6 56.5 1.0
CE1 E:HIS45 4.7 41.0 1.0
NE2 E:HIS49 4.7 40.6 1.0
NE2 E:HIS55 4.8 61.7 1.0
CB E:ASP51 5.0 53.4 1.0

Reference:

K.Yoneda, H.Sakuraba, T.Ohshima. Crystal Structure of Metal-Dependent Hydrolase Complexed with Manganese From Bacillus Smithii To Be Published.
Page generated: Thu Dec 28 11:05:23 2023

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