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Manganese in PDB 1cev: Arginase From Bacillus Caldovelox, Native Structure at pH 5.6

Enzymatic activity of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6

All present enzymatic activity of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6:
3.5.3.1;

Protein crystallography data

The structure of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6, PDB code: 1cev was solved by M.C.Bewley, P.D.Jeffrey, M.L.Patchett, Z.F.Kanyo, E.N.Baker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.600, 145.600, 155.400, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26.5

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 (pdb code 1cev). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6, PDB code: 1cev:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 1cev

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Manganese binding site 1 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:29.9
occ:0.62
 OD2 A:ASP122 2.0 23.1 1.0
ND1 A:HIS99 2.1 17.1 1.0
OD2 A:ASP126 2.4 27.9 1.0
OD2 A:ASP226 2.4 15.3 1.0
CG A:HIS99 2.9 17.6 1.0
CG A:ASP122 3.0 25.3 1.0
CB A:HIS99 3.1 13.2 1.0
CE1 A:HIS99 3.2 18.1 1.0
CG A:ASP126 3.3 20.8 1.0
OD1 A:ASP122 3.3 26.7 1.0
MN A:MN301 3.4 28.2 0.7
CG A:ASP226 3.5 16.6 1.0
OD1 A:ASP126 3.5 22.3 1.0
CB A:ASP226 3.8 19.0 1.0
CD2 A:HIS99 4.0 18.9 1.0
NE2 A:HIS99 4.2 20.5 1.0
NE1 A:TRP120 4.2 22.9 1.0
CB A:ASP122 4.3 21.4 1.0
CZ2 A:TRP120 4.5 18.5 1.0
O A:HIS139 4.6 25.9 1.0
OD1 A:ASP226 4.6 13.7 1.0
CB A:ASP126 4.6 21.4 1.0
CA A:HIS99 4.6 18.6 1.0
CE2 A:TRP120 4.7 19.4 1.0
CG A:GLU271 4.8 20.2 1.0
OE2 A:GLU271 4.9 24.0 1.0

Manganese binding site 2 out of 12 in 1cev

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Manganese binding site 2 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:28.2
occ:0.73
 OD2 A:ASP228 2.0 28.5 1.0
OD1 A:ASP122 2.3 26.7 1.0
OD2 A:ASP226 2.3 15.3 1.0
ND1 A:HIS124 2.6 21.2 1.0
OD1 A:ASP228 2.7 33.3 1.0
CG A:ASP228 2.7 27.6 1.0
CG A:ASP226 3.2 16.6 1.0
CG A:ASP122 3.3 25.3 1.0
CE1 A:HIS124 3.3 22.1 1.0
MN A:MN300 3.4 29.9 0.6
OD2 A:ASP122 3.6 23.1 1.0
CG A:HIS124 3.6 21.6 1.0
OD1 A:ASP226 3.7 13.7 1.0
CB A:HIS124 4.0 19.7 1.0
CB A:ASP228 4.2 26.3 1.0
N A:HIS124 4.2 20.7 1.0
CB A:ASP226 4.3 19.0 1.0
N A:ALA123 4.3 20.9 1.0
NE2 A:HIS124 4.4 20.5 1.0
CD2 A:HIS124 4.6 22.0 1.0
CB A:ASP122 4.7 21.4 1.0
CB A:ALA123 4.7 16.6 1.0
CA A:HIS124 4.7 20.4 1.0
OD1 A:ASP126 4.8 22.3 1.0
CA A:ALA123 4.9 19.5 1.0
C A:ALA123 5.0 21.2 1.0

Manganese binding site 3 out of 12 in 1cev

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Manganese binding site 3 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:37.5
occ:0.51
 OD2 B:ASP126 1.8 31.0 1.0
ND1 B:HIS99 2.5 24.4 1.0
OD2 B:ASP122 2.5 22.3 1.0
CG B:ASP126 2.7 28.3 1.0
CB B:HIS99 2.9 18.0 1.0
OD1 B:ASP126 2.9 22.1 1.0
CG B:HIS99 3.0 22.1 1.0
OD2 B:ASP226 3.1 26.4 1.0
CG B:ASP122 3.6 18.5 1.0
CE1 B:HIS99 3.6 28.1 1.0
O B:HIS139 3.8 24.3 1.0
MN B:MN301 3.8 27.8 0.6
OD1 B:ASP122 3.9 21.3 1.0
CB B:ASP126 4.1 27.8 1.0
CD2 B:HIS99 4.2 21.1 1.0
CG B:ASP226 4.2 24.8 1.0
NE1 B:TRP120 4.4 23.2 1.0
CA B:HIS99 4.4 21.1 1.0
CZ2 B:TRP120 4.4 21.0 1.0
NE2 B:HIS99 4.4 25.5 1.0
CB B:ASP226 4.6 20.0 1.0
CG B:PRO142 4.7 26.7 1.0
CE2 B:TRP120 4.7 19.8 1.0
OE2 B:GLU271 4.8 22.1 1.0
CB B:ASP122 4.9 14.7 1.0
C B:HIS139 5.0 22.2 1.0

Manganese binding site 4 out of 12 in 1cev

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Manganese binding site 4 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:27.8
occ:0.63
 OD2 B:ASP228 2.1 38.5 1.0
OD1 B:ASP122 2.2 21.3 1.0
OD2 B:ASP226 2.2 26.4 1.0
OD1 B:ASP228 2.6 34.8 1.0
ND1 B:HIS124 2.6 23.4 1.0
CG B:ASP228 2.6 29.1 1.0
CG B:ASP226 3.1 24.8 1.0
CG B:ASP122 3.2 18.5 1.0
CE1 B:HIS124 3.4 26.3 1.0
OD2 B:ASP122 3.5 22.3 1.0
CG B:HIS124 3.6 19.0 1.0
OD1 B:ASP226 3.6 21.7 1.0
MN B:MN300 3.8 37.5 0.5
CB B:HIS124 4.0 19.6 1.0
N B:HIS124 4.1 18.1 1.0
CB B:ASP228 4.1 24.7 1.0
N B:ALA123 4.1 16.9 1.0
CB B:ASP226 4.2 20.0 1.0
NE2 B:HIS124 4.5 24.9 1.0
CB B:ASP122 4.5 14.7 1.0
CB B:ALA123 4.6 12.9 1.0
CD2 B:HIS124 4.6 20.6 1.0
CA B:HIS124 4.7 21.4 1.0
CA B:ALA123 4.8 15.7 1.0
C B:ALA123 4.8 18.0 1.0
OD1 B:ASP126 4.9 22.1 1.0
CA B:ASP122 4.9 18.6 1.0
C B:ASP122 5.0 19.6 1.0

Manganese binding site 5 out of 12 in 1cev

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Manganese binding site 5 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:32.0
occ:0.56
 OD2 C:ASP126 2.2 34.0 1.0
OD2 C:ASP122 2.3 25.8 1.0
ND1 C:HIS99 2.4 16.4 1.0
OD2 C:ASP226 2.8 23.2 1.0
CG C:HIS99 3.0 19.0 1.0
CB C:HIS99 3.0 17.1 1.0
CG C:ASP126 3.0 25.2 1.0
OD1 C:ASP126 3.2 18.1 1.0
CG C:ASP122 3.4 24.2 1.0
CE1 C:HIS99 3.5 15.8 1.0
MN C:MN301 3.6 26.0 0.7
OD1 C:ASP122 3.6 19.7 1.0
CG C:ASP226 3.8 19.2 1.0
O C:HIS139 4.1 24.3 1.0
CD2 C:HIS99 4.2 18.0 1.0
CB C:ASP226 4.3 17.3 1.0
NE2 C:HIS99 4.4 20.2 1.0
NE1 C:TRP120 4.4 17.4 1.0
CB C:ASP126 4.4 22.6 1.0
CA C:HIS99 4.5 15.1 1.0
CZ2 C:TRP120 4.5 19.4 1.0
CB C:ASP122 4.7 19.7 1.0
OE2 C:GLU271 4.7 29.4 1.0
CE2 C:TRP120 4.8 18.7 1.0
CG C:GLU271 4.9 27.8 1.0
OD1 C:ASP226 4.9 20.4 1.0
CD C:GLU271 5.0 32.2 1.0

Manganese binding site 6 out of 12 in 1cev

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Manganese binding site 6 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:26.0
occ:0.70
 OD2 C:ASP228 1.9 40.4 1.0
OD2 C:ASP226 2.3 23.2 1.0
OD1 C:ASP122 2.4 19.7 1.0
ND1 C:HIS124 2.6 21.3 1.0
CG C:ASP228 2.6 31.4 1.0
OD1 C:ASP228 2.7 26.7 1.0
CG C:ASP226 3.2 19.2 1.0
CE1 C:HIS124 3.3 16.8 1.0
CG C:ASP122 3.3 24.2 1.0
MN C:MN300 3.6 32.0 0.6
OD2 C:ASP122 3.6 25.8 1.0
CG C:HIS124 3.6 21.9 1.0
OD1 C:ASP226 3.6 20.4 1.0
CB C:HIS124 4.1 21.6 1.0
CB C:ASP228 4.1 26.0 1.0
N C:HIS124 4.2 21.8 1.0
N C:ALA123 4.4 20.4 1.0
CB C:ASP226 4.4 17.3 1.0
NE2 C:HIS124 4.4 18.9 1.0
CD2 C:HIS124 4.6 21.0 1.0
CB C:ALA123 4.7 15.5 1.0
CB C:ASP122 4.7 19.7 1.0
CA C:HIS124 4.8 19.6 1.0
OD1 C:ASP126 4.9 18.1 1.0
O C:THR240 5.0 20.3 1.0
CA C:ALA123 5.0 20.6 1.0

Manganese binding site 7 out of 12 in 1cev

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Manganese binding site 7 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:32.8
occ:0.58
 OD2 D:ASP122 2.0 28.0 1.0
OD2 D:ASP126 2.2 43.0 1.0
ND1 D:HIS99 2.6 31.8 1.0
OD2 D:ASP226 2.6 35.0 1.0
CG D:ASP126 2.9 39.3 1.0
CG D:ASP122 3.0 27.1 1.0
OD1 D:ASP126 3.0 37.2 1.0
OD1 D:ASP122 3.2 31.3 1.0
CG D:HIS99 3.3 32.8 1.0
CB D:HIS99 3.4 30.4 1.0
MN D:MN301 3.5 29.7 0.6
CE1 D:HIS99 3.6 29.7 1.0
CG D:ASP226 3.7 31.9 1.0
CB D:ASP226 4.2 28.7 1.0
NE1 D:TRP120 4.2 22.9 1.0
CB D:ASP122 4.3 25.2 1.0
CB D:ASP126 4.3 33.1 1.0
O D:HIS139 4.3 32.4 1.0
CD2 D:HIS99 4.5 30.8 1.0
NE2 D:HIS99 4.6 28.2 1.0
CZ2 D:TRP120 4.6 26.4 1.0
CE2 D:TRP120 4.7 24.7 1.0
OD1 D:ASP226 4.8 31.6 1.0
CB D:HIS124 4.8 29.1 1.0
O D:HIS124 4.8 32.1 1.0
CA D:HIS99 4.9 29.5 1.0
OE2 D:GLU271 5.0 25.3 1.0

Manganese binding site 8 out of 12 in 1cev

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Manganese binding site 8 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:29.7
occ:0.64
 OD2 D:ASP228 1.8 34.2 1.0
OD2 D:ASP226 2.3 35.0 1.0
CG D:ASP228 2.5 29.8 1.0
OD1 D:ASP122 2.5 31.3 1.0
OD1 D:ASP228 2.7 34.2 1.0
ND1 D:HIS124 2.7 24.9 1.0
CG D:ASP226 3.2 31.9 1.0
CE1 D:HIS124 3.3 30.1 1.0
MN D:MN300 3.5 32.8 0.6
CG D:ASP122 3.5 27.1 1.0
OD1 D:ASP226 3.6 31.6 1.0
CG D:HIS124 3.7 28.4 1.0
OD2 D:ASP122 3.8 28.0 1.0
CB D:ASP228 4.0 29.3 1.0
CB D:HIS124 4.2 29.1 1.0
CB D:ASP226 4.4 28.7 1.0
N D:HIS124 4.4 26.6 1.0
NE2 D:HIS124 4.4 28.9 1.0
N D:ALA123 4.5 24.6 1.0
CD2 D:HIS124 4.7 29.4 1.0
CB D:ALA123 4.7 24.3 1.0
O D:THR240 4.7 18.2 1.0
OE1 D:GLU271 4.9 21.6 1.0
CB D:ASP122 4.9 25.2 1.0
CD D:GLU271 4.9 19.4 1.0
CG D:GLU271 4.9 13.7 1.0
CA D:HIS124 5.0 27.1 1.0

Manganese binding site 9 out of 12 in 1cev

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Manganese binding site 9 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:37.0
occ:0.53
 OD2 E:ASP126 1.9 45.8 1.0
OD2 E:ASP122 2.1 26.1 1.0
ND1 E:HIS99 2.3 24.6 1.0
CG E:ASP126 2.8 41.2 1.0
OD2 E:ASP226 2.9 32.4 1.0
CG E:HIS99 3.0 26.8 1.0
OD1 E:ASP126 3.1 40.6 1.0
CB E:HIS99 3.1 27.1 1.0
CG E:ASP122 3.2 25.1 1.0
CE1 E:HIS99 3.3 25.7 1.0
OD1 E:ASP122 3.6 21.3 1.0
MN E:MN301 3.7 28.8 0.7
CG E:ASP226 3.9 23.9 1.0
NE1 E:TRP120 4.1 33.9 1.0
CD2 E:HIS99 4.1 28.3 1.0
CB E:ASP126 4.2 39.7 1.0
O E:HIS139 4.2 30.2 1.0
CB E:ASP226 4.3 23.0 1.0
NE2 E:HIS99 4.3 24.9 1.0
CZ2 E:TRP120 4.3 34.6 1.0
CB E:ASP122 4.5 21.8 1.0
CE2 E:TRP120 4.5 34.4 1.0
CA E:HIS99 4.6 27.6 1.0
CG E:PRO142 5.0 29.1 1.0

Manganese binding site 10 out of 12 in 1cev

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Manganese binding site 10 out of 12 in the Arginase From Bacillus Caldovelox, Native Structure at pH 5.6


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Arginase From Bacillus Caldovelox, Native Structure at pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:28.8
occ:0.66
 OD2 E:ASP228 1.9 29.8 1.0
OD2 E:ASP226 2.3 32.4 1.0
OD1 E:ASP122 2.5 21.3 1.0
CG E:ASP228 2.6 25.9 1.0
OD1 E:ASP228 2.7 31.5 1.0
ND1 E:HIS124 2.8 29.2 1.0
CG E:ASP226 3.2 23.9 1.0
CE1 E:HIS124 3.4 29.8 1.0
CG E:ASP122 3.5 25.1 1.0
OD1 E:ASP226 3.6 24.0 1.0
MN E:MN300 3.7 37.0 0.5
OD2 E:ASP122 3.7 26.1 1.0
CG E:HIS124 3.8 21.5 1.0
CB E:ASP228 4.1 27.9 1.0
CB E:HIS124 4.2 22.4 1.0
CB E:ASP226 4.4 23.0 1.0
N E:HIS124 4.4 21.2 1.0
N E:ALA123 4.5 22.5 1.0
NE2 E:HIS124 4.5 25.9 1.0
CD2 E:HIS124 4.7 24.1 1.0
CB E:ALA123 4.8 19.7 1.0
CB E:ASP122 4.9 21.8 1.0
O E:THR240 4.9 25.6 1.0
OE1 E:GLU271 4.9 28.3 1.0
OD1 E:ASP126 4.9 40.6 1.0
CG E:GLU271 4.9 25.1 1.0
CA E:HIS124 4.9 19.2 1.0
CD E:GLU271 5.0 27.6 1.0

Reference:

M.C.Bewley, P.D.Jeffrey, M.L.Patchett, Z.F.Kanyo, E.N.Baker. Crystal Structures of Bacillus Caldovelox Arginase in Complex with Substrate and Inhibitors Reveal New Insights Into Activation, Inhibition and Catalysis in the Arginase Superfamily. Structure Fold.Des. V. 7 435 1999.
ISSN: ISSN 0969-2126
PubMed: 10196128
DOI: 10.1016/S0969-2126(99)80056-2
Page generated: Sat Oct 5 09:54:23 2024

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