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Manganese in PDB 3cev: Arginase From Bacillus Caldevelox, Complexed with L-Arginine

Enzymatic activity of Arginase From Bacillus Caldevelox, Complexed with L-Arginine

All present enzymatic activity of Arginase From Bacillus Caldevelox, Complexed with L-Arginine:
3.5.3.1;

Protein crystallography data

The structure of Arginase From Bacillus Caldevelox, Complexed with L-Arginine, PDB code: 3cev 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) 8.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 106.800, 277.700, 140.000, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.3

Manganese Binding Sites:

The binding sites of Manganese atom in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine (pdb code 3cev). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine, PDB code: 3cev:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3cev

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Manganese binding site 1 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn300

b:24.6
occ:1.00
 OD2 A:ASP122 2.1 22.4 1.0
OD2 A:ASP226 2.2 17.2 1.0
ND1 A:HIS99 2.2 19.9 1.0
O A:HOH408 2.2 29.4 1.0
OD2 A:ASP126 2.3 28.9 1.0
NH2 A:ARG407 2.5 26.2 1.0
CG A:ASP122 3.0 21.1 1.0
CE1 A:HIS99 3.1 20.3 1.0
CG A:ASP226 3.2 17.3 1.0
OD1 A:ASP122 3.2 17.5 1.0
CZ A:ARG407 3.2 28.2 1.0
CG A:ASP126 3.3 24.3 1.0
CG A:HIS99 3.3 19.6 1.0
CB A:ASP226 3.5 15.7 1.0
OD1 A:ASP126 3.6 23.9 1.0
CB A:HIS99 3.6 16.2 1.0
NH1 A:ARG407 3.9 26.2 1.0
NE A:ARG407 3.9 25.6 1.0
NE1 A:TRP120 4.2 19.1 1.0
NE2 A:HIS99 4.3 18.0 1.0
OD1 A:ASP226 4.3 18.2 1.0
CD2 A:HIS99 4.4 15.1 1.0
CB A:ASP122 4.4 19.7 1.0
OD2 A:ASP228 4.5 20.4 1.0
O A:HIS139 4.6 23.3 1.0
CB A:ASP126 4.6 20.8 1.0
OE2 A:GLU271 4.7 22.9 1.0
OD1 A:ASP228 4.7 24.6 1.0
O A:HOH455 4.9 31.6 1.0
CE2 A:TRP120 4.9 20.5 1.0
CG A:GLU271 4.9 21.2 1.0
CG A:ASP228 4.9 22.1 1.0
CA A:ASP226 5.0 15.5 1.0
CZ2 A:TRP120 5.0 19.1 1.0

Manganese binding site 2 out of 6 in 3cev

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Manganese binding site 2 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn300

b:26.4
occ:1.00
 OD2 B:ASP122 2.1 23.8 1.0
OD2 B:ASP226 2.2 23.4 1.0
ND1 B:HIS99 2.2 20.0 1.0
O B:HOH409 2.3 21.5 1.0
OD2 B:ASP126 2.3 22.7 1.0
NH2 B:ARG408 2.5 26.0 1.0
CG B:ASP122 3.0 21.9 1.0
CE1 B:HIS99 3.1 19.6 1.0
CG B:ASP226 3.2 20.7 1.0
OD1 B:ASP122 3.2 23.8 1.0
CZ B:ARG408 3.2 27.2 1.0
CG B:ASP126 3.3 20.4 1.0
CG B:HIS99 3.3 18.2 1.0
CB B:ASP226 3.5 18.7 1.0
OD1 B:ASP126 3.5 15.4 1.0
CB B:HIS99 3.6 16.7 1.0
NH1 B:ARG408 3.9 25.3 1.0
NE B:ARG408 3.9 24.9 1.0
NE1 B:TRP120 4.2 24.5 1.0
NE2 B:HIS99 4.3 21.5 1.0
OD1 B:ASP226 4.3 19.4 1.0
OD2 B:ASP228 4.3 22.1 1.0
CD2 B:HIS99 4.4 20.1 1.0
CB B:ASP122 4.4 20.4 1.0
O B:HIS139 4.6 21.6 1.0
CB B:ASP126 4.6 19.8 1.0
OD1 B:ASP228 4.7 26.8 1.0
CE2 B:TRP120 4.9 19.6 1.0
CZ2 B:TRP120 4.9 18.2 1.0
CG B:ASP228 4.9 22.8 1.0
OE2 B:GLU271 4.9 18.2 1.0
CG B:GLU271 5.0 17.3 1.0
CA B:ASP226 5.0 17.6 1.0

Manganese binding site 3 out of 6 in 3cev

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Manganese binding site 3 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn300

b:23.2
occ:1.00
 OD2 C:ASP122 2.1 22.7 1.0
OD2 C:ASP226 2.2 22.5 1.0
ND1 C:HIS99 2.2 24.0 1.0
O C:HOH410 2.2 23.9 1.0
OD2 C:ASP126 2.3 23.7 1.0
NH2 C:ARG409 2.6 26.0 1.0
CG C:ASP122 3.0 20.5 1.0
CE1 C:HIS99 3.1 23.5 1.0
CG C:ASP226 3.2 20.2 1.0
CG C:HIS99 3.2 21.4 1.0
OD1 C:ASP122 3.3 20.6 1.0
CG C:ASP126 3.3 25.8 1.0
CZ C:ARG409 3.3 25.5 1.0
CB C:ASP226 3.6 19.5 1.0
OD1 C:ASP126 3.6 26.1 1.0
CB C:HIS99 3.6 17.9 1.0
NE C:ARG409 3.9 23.3 1.0
NH1 C:ARG409 3.9 26.6 1.0
NE1 C:TRP120 4.2 23.7 1.0
NE2 C:HIS99 4.3 21.9 1.0
OD1 C:ASP226 4.3 20.0 1.0
CD2 C:HIS99 4.4 22.6 1.0
CB C:ASP122 4.4 20.4 1.0
OD2 C:ASP228 4.5 21.5 1.0
O C:HIS139 4.6 24.4 1.0
CB C:ASP126 4.6 25.3 1.0
OD1 C:ASP228 4.7 23.2 1.0
OE2 C:GLU271 4.8 18.6 1.0
CE2 C:TRP120 4.9 22.2 1.0
CZ2 C:TRP120 4.9 20.7 1.0
CG C:GLU271 4.9 18.2 1.0
CA C:ASP226 5.0 19.2 1.0
CG C:ASP228 5.0 25.4 1.0
O C:HOH456 5.0 31.5 1.0

Manganese binding site 4 out of 6 in 3cev

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Manganese binding site 4 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn300

b:23.7
occ:1.00
 OD2 D:ASP122 2.1 21.7 1.0
OD2 D:ASP226 2.2 17.5 1.0
ND1 D:HIS99 2.2 15.6 1.0
OD2 D:ASP126 2.3 23.2 1.0
O D:HOH411 2.3 14.8 1.0
NH2 D:ARG410 2.5 18.5 1.0
CG D:ASP122 3.0 20.7 1.0
CE1 D:HIS99 3.1 14.1 1.0
CG D:ASP226 3.2 18.2 1.0
CZ D:ARG410 3.2 22.1 1.0
CG D:ASP126 3.2 21.3 1.0
CG D:HIS99 3.3 17.1 1.0
OD1 D:ASP122 3.3 21.9 1.0
OD1 D:ASP126 3.5 18.3 1.0
CB D:ASP226 3.6 17.7 1.0
CB D:HIS99 3.6 16.5 1.0
NH1 D:ARG410 3.9 19.8 1.0
NE D:ARG410 3.9 20.4 1.0
NE1 D:TRP120 4.2 17.2 1.0
NE2 D:HIS99 4.3 15.8 1.0
OD1 D:ASP226 4.3 14.5 1.0
CD2 D:HIS99 4.4 14.6 1.0
CB D:ASP122 4.4 20.9 1.0
OD2 D:ASP228 4.5 18.5 1.0
O D:HIS139 4.6 15.7 1.0
CB D:ASP126 4.6 17.4 1.0
OD1 D:ASP228 4.7 18.6 1.0
CE2 D:TRP120 4.8 14.5 1.0
CZ2 D:TRP120 4.9 13.4 1.0
OE2 D:GLU271 4.9 16.1 1.0
O D:HOH457 4.9 26.0 1.0
CG D:ASP228 4.9 21.2 1.0
CA D:ASP226 5.0 17.7 1.0
CG D:GLU271 5.0 15.2 1.0

Manganese binding site 5 out of 6 in 3cev

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Manganese binding site 5 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn300

b:25.3
occ:1.00
 OD2 E:ASP122 2.1 25.9 1.0
OD2 E:ASP226 2.2 25.2 1.0
ND1 E:HIS99 2.2 23.9 1.0
O E:HOH412 2.3 18.2 1.0
OD2 E:ASP126 2.3 26.5 1.0
NH2 E:ARG411 2.4 21.6 1.0
CG E:ASP122 3.0 24.9 1.0
CE1 E:HIS99 3.1 23.1 1.0
CG E:ASP226 3.2 25.9 1.0
OD1 E:ASP122 3.2 27.2 1.0
CZ E:ARG411 3.2 21.6 1.0
CG E:HIS99 3.3 21.6 1.0
CG E:ASP126 3.3 21.8 1.0
CB E:ASP226 3.5 24.0 1.0
OD1 E:ASP126 3.6 26.4 1.0
CB E:HIS99 3.6 22.4 1.0
NE E:ARG411 3.9 19.9 1.0
NH1 E:ARG411 3.9 22.9 1.0
NE1 E:TRP120 4.2 18.9 1.0
OD1 E:ASP226 4.3 26.7 1.0
NE2 E:HIS99 4.3 19.5 1.0
CD2 E:HIS99 4.4 22.7 1.0
CB E:ASP122 4.4 22.3 1.0
OD2 E:ASP228 4.4 28.9 1.0
CB E:ASP126 4.6 22.2 1.0
OD1 E:ASP228 4.6 26.5 1.0
O E:HIS139 4.6 24.7 1.0
OE2 E:GLU271 4.8 26.1 1.0
CG E:ASP228 4.9 26.9 1.0
CG E:GLU271 4.9 24.4 1.0
CE2 E:TRP120 4.9 19.2 1.0
CZ2 E:TRP120 5.0 18.1 1.0
CA E:ASP226 5.0 20.4 1.0

Manganese binding site 6 out of 6 in 3cev

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Manganese binding site 6 out of 6 in the Arginase From Bacillus Caldevelox, Complexed with L-Arginine


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 Caldevelox, Complexed with L-Arginine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn300

b:26.2
occ:1.00
 OD2 F:ASP122 2.2 19.4 1.0
OD2 F:ASP226 2.2 19.5 1.0
ND1 F:HIS99 2.2 18.3 1.0
O F:HOH413 2.2 21.1 1.0
OD2 F:ASP126 2.3 21.4 1.0
NH2 F:ARG412 2.5 22.9 1.0
CG F:ASP122 3.1 20.0 1.0
CE1 F:HIS99 3.1 18.0 1.0
CG F:ASP226 3.2 21.0 1.0
CZ F:ARG412 3.2 23.9 1.0
CG F:HIS99 3.2 20.0 1.0
CG F:ASP126 3.3 23.3 1.0
OD1 F:ASP122 3.3 22.1 1.0
OD1 F:ASP126 3.6 21.8 1.0
CB F:ASP226 3.6 17.6 1.0
CB F:HIS99 3.6 18.6 1.0
NE F:ARG412 3.8 23.1 1.0
NH1 F:ARG412 3.9 28.1 1.0
NE1 F:TRP120 4.2 20.4 1.0
NE2 F:HIS99 4.3 17.6 1.0
OD1 F:ASP226 4.3 25.3 1.0
CD2 F:HIS99 4.3 17.1 1.0
OD2 F:ASP228 4.4 23.6 1.0
CB F:ASP122 4.5 20.2 1.0
O F:HIS139 4.5 22.5 1.0
CB F:ASP126 4.6 20.2 1.0
OD1 F:ASP228 4.7 23.9 1.0
OE2 F:GLU271 4.7 20.3 1.0
CE2 F:TRP120 4.9 16.9 1.0
CZ2 F:TRP120 4.9 16.5 1.0
CG F:GLU271 5.0 19.0 1.0
CG F:ASP228 5.0 24.3 1.0
CA F:ASP226 5.0 20.2 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 16:02:30 2024

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