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Manganese in PDB 6nbk: Crystal Structure of Arginase From Bacillus Cereus

Enzymatic activity of Crystal Structure of Arginase From Bacillus Cereus

All present enzymatic activity of Crystal Structure of Arginase From Bacillus Cereus:
3.5.3.1;

Protein crystallography data

The structure of Crystal Structure of Arginase From Bacillus Cereus, PDB code: 6nbk was solved by C.Chang, E.Evdokimova, M.Mcchesney, A.Joachimiak, A.Savchenko, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.44 / 1.91
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 148.022, 153.803, 83.137, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.3

Other elements in 6nbk:

The structure of Crystal Structure of Arginase From Bacillus Cereus also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Arginase From Bacillus Cereus (pdb code 6nbk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 14 binding sites of Manganese where determined in the Crystal Structure of Arginase From Bacillus Cereus, PDB code: 6nbk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 14 in 6nbk

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Manganese binding site 1 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:17.3
occ:1.00
 OD1 A:ASP121 2.2 12.2 1.0
OD2 A:ASP226 2.3 20.6 1.0
OD2 A:ASP224 2.4 20.5 1.0
O A:HOH447 2.4 14.3 1.0
ND1 A:HIS123 2.5 14.4 1.0
OD1 A:ASP226 2.6 17.9 1.0
O A:HOH556 2.6 25.6 1.0
CG A:ASP226 2.8 16.9 1.0
CG A:ASP121 3.2 16.1 1.0
MN A:MN302 3.2 12.2 1.0
CG A:ASP224 3.2 15.9 1.0
CE1 A:HIS123 3.4 18.0 1.0
OD2 A:ASP121 3.5 15.6 1.0
CG A:HIS123 3.6 10.7 1.0
OD1 A:ASP224 3.7 20.7 1.0
CB A:HIS123 3.9 11.9 1.0
N A:HIS123 4.1 12.7 1.0
CB A:ASP224 4.2 10.2 1.0
O A:HOH428 4.3 25.2 1.0
CB A:ASP226 4.3 12.6 1.0
N A:ALA122 4.3 7.2 1.0
O A:HOH442 4.4 14.9 1.0
NE2 A:HIS123 4.5 17.2 1.0
CB A:ASP121 4.6 13.0 1.0
CA A:HIS123 4.6 11.4 1.0
OD1 A:ASP125 4.6 12.7 1.0
CD2 A:HIS123 4.6 15.5 1.0
OD2 A:ASP125 4.8 16.4 1.0
CA A:ASP121 4.9 12.9 1.0
C A:ALA122 5.0 13.0 1.0
CB A:ALA122 5.0 8.6 1.0
CA A:ALA122 5.0 8.8 1.0

Manganese binding site 2 out of 14 in 6nbk

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Manganese binding site 2 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:12.2
occ:1.00
 O A:HOH447 1.8 14.3 1.0
OD2 A:ASP121 1.9 15.6 1.0
ND1 A:HIS98 2.1 10.2 1.0
OD2 A:ASP125 2.1 16.4 1.0
OD2 A:ASP224 2.5 20.5 1.0
CG A:ASP121 2.9 16.1 1.0
CG A:HIS98 3.0 9.9 1.0
CE1 A:HIS98 3.1 9.5 1.0
CG A:ASP125 3.1 19.7 1.0
MN A:MN301 3.2 17.3 1.0
OD1 A:ASP121 3.2 12.2 1.0
CB A:HIS98 3.3 5.8 1.0
OD1 A:ASP125 3.4 12.7 1.0
CG A:ASP224 3.6 15.9 1.0
CB A:ASP224 3.8 10.2 1.0
NE1 A:TRP119 4.1 11.6 1.0
O A:HOH428 4.1 25.2 1.0
NE2 A:HIS98 4.2 9.6 1.0
CD2 A:HIS98 4.2 7.9 1.0
CB A:ASP121 4.2 13.0 1.0
O A:HOH556 4.4 25.6 1.0
CB A:ASP125 4.5 13.8 1.0
CZ2 A:TRP119 4.6 13.4 1.0
CE2 A:TRP119 4.6 13.0 1.0
O A:HIS138 4.6 23.5 1.0
OD1 A:ASP224 4.7 20.7 1.0
CA A:HIS98 4.9 5.8 1.0
CG A:GLU269 5.0 12.9 1.0
CB A:HIS123 5.0 11.9 1.0

Manganese binding site 3 out of 14 in 6nbk

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Manganese binding site 3 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:27.4
occ:1.00
 OE2 A:GLU86 2.2 26.5 1.0
OD2 A:ASP82 2.4 15.5 1.0
OD1 A:ASP82 2.7 11.7 1.0
CG A:ASP82 2.9 10.4 1.0
O A:HOH483 3.0 35.9 1.0
CD A:GLU86 3.4 26.9 1.0
CG A:GLU86 4.3 19.9 1.0
OE1 A:GLU86 4.3 29.5 1.0
OH A:TYR157 4.3 17.1 1.0
CB A:ASP82 4.4 10.7 1.0
NE2 A:HIS111 4.7 20.5 1.0
O A:HOH497 4.8 38.5 1.0
NE2 A:HIS83 5.0 28.2 0.5

Manganese binding site 4 out of 14 in 6nbk

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Manganese binding site 4 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:15.2
occ:1.00
 OD2 B:ASP121 2.0 21.4 1.0
ND1 B:HIS98 2.0 14.5 1.0
OD2 B:ASP125 2.1 18.2 1.0
OD2 B:ASP224 2.6 19.7 1.0
CG B:ASP121 3.0 17.2 1.0
CG B:HIS98 3.0 14.4 1.0
CE1 B:HIS98 3.0 13.3 1.0
CG B:ASP125 3.1 15.3 1.0
MN B:MN302 3.3 20.7 1.0
OD1 B:ASP121 3.3 14.5 1.0
CB B:HIS98 3.3 14.1 1.0
OD1 B:ASP125 3.4 14.5 1.0
CG B:ASP224 3.6 17.8 1.0
CB B:ASP224 3.9 9.9 1.0
NE1 B:TRP119 4.0 14.2 1.0
NE2 B:HIS98 4.1 15.8 1.0
CD2 B:HIS98 4.1 14.1 1.0
O B:HOH469 4.2 25.7 1.0
CB B:ASP121 4.3 10.3 1.0
CB B:ASP125 4.4 11.2 1.0
O B:HOH517 4.5 22.7 1.0
CZ2 B:TRP119 4.5 16.3 1.0
CE2 B:TRP119 4.6 12.4 1.0
O B:HIS138 4.7 23.9 1.0
OD1 B:ASP224 4.7 17.3 1.0
CA B:HIS98 4.9 12.6 1.0
CB B:HIS123 4.9 14.3 1.0

Manganese binding site 5 out of 14 in 6nbk

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Manganese binding site 5 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:20.7
occ:1.00
 OD1 B:ASP121 2.2 14.5 1.0
OD2 B:ASP224 2.3 19.7 1.0
OD2 B:ASP226 2.3 18.5 1.0
ND1 B:HIS123 2.4 16.7 1.0
OD1 B:ASP226 2.6 15.0 1.0
O B:HOH517 2.6 22.7 1.0
CG B:ASP226 2.8 15.7 1.0
CG B:ASP224 3.2 17.8 1.0
CG B:ASP121 3.2 17.2 1.0
MN B:MN301 3.3 15.2 1.0
CE1 B:HIS123 3.3 19.8 1.0
CG B:HIS123 3.5 15.8 1.0
OD2 B:ASP121 3.5 21.4 1.0
OD1 B:ASP224 3.7 17.3 1.0
CB B:HIS123 3.8 14.3 1.0
N B:HIS123 4.1 13.7 1.0
CB B:ASP224 4.2 9.9 1.0
O B:HOH423 4.2 18.0 1.0
CB B:ASP226 4.3 11.8 1.0
N B:ALA122 4.3 9.2 1.0
O B:HOH469 4.4 25.7 1.0
NE2 B:HIS123 4.5 18.9 1.0
CA B:HIS123 4.6 17.5 1.0
CD2 B:HIS123 4.6 17.2 1.0
CB B:ASP121 4.6 10.3 1.0
OD1 B:ASP125 4.8 14.5 1.0
OD2 B:ASP125 4.8 18.2 1.0
CB B:ALA122 4.9 9.2 1.0
C B:ALA122 4.9 12.0 1.0
CA B:ASP121 4.9 11.4 1.0
CA B:ALA122 4.9 13.2 1.0

Manganese binding site 6 out of 14 in 6nbk

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Manganese binding site 6 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:35.8
occ:1.00
 OE1 B:GLU86 2.1 32.9 1.0
OD2 B:ASP82 2.4 23.0 1.0
OD1 B:ASP82 2.7 17.5 1.0
CG B:ASP82 2.9 18.6 1.0
CD B:GLU86 3.3 31.9 1.0
CG B:GLU86 4.1 24.4 1.0
OE2 B:GLU86 4.2 33.0 1.0
CB B:ASP82 4.4 16.2 1.0
OH B:TYR157 4.4 19.5 1.0
NE2 B:HIS111 4.8 32.2 1.0

Manganese binding site 7 out of 14 in 6nbk

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Manganese binding site 7 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:17.6
occ:1.00
 O C:HOH444 1.8 20.4 1.0
OD2 C:ASP121 2.0 22.4 1.0
ND1 C:HIS98 2.0 13.4 1.0
OD2 C:ASP125 2.2 24.0 1.0
OD2 C:ASP224 2.5 21.0 1.0
CG C:ASP121 2.9 18.3 1.0
CE1 C:HIS98 3.0 14.4 1.0
CG C:HIS98 3.0 16.5 1.0
CG C:ASP125 3.1 21.4 1.0
MN C:MN302 3.2 21.6 1.0
OD1 C:ASP121 3.3 17.4 1.0
OD1 C:ASP125 3.3 21.1 1.0
CB C:HIS98 3.4 19.0 1.0
CG C:ASP224 3.5 22.8 1.0
CB C:ASP224 3.8 12.7 1.0
NE1 C:TRP119 4.1 14.4 1.0
NE2 C:HIS98 4.1 13.0 1.0
CD2 C:HIS98 4.1 16.9 1.0
O C:HOH427 4.1 31.8 1.0
CB C:ASP121 4.3 16.7 1.0
O C:HOH525 4.5 29.2 1.0
CZ2 C:TRP119 4.5 16.6 1.0
CB C:ASP125 4.5 14.3 1.0
CE2 C:TRP119 4.6 15.9 1.0
OD1 C:ASP224 4.6 20.0 1.0
O C:HIS138 4.7 28.1 1.0
CB C:HIS123 4.9 15.8 1.0
CA C:HIS98 4.9 17.6 1.0
O C:HIS123 4.9 17.6 1.0
CG C:GLU269 5.0 18.1 1.0

Manganese binding site 8 out of 14 in 6nbk

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Manganese binding site 8 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:21.6
occ:1.00
 OD1 C:ASP121 2.2 17.4 1.0
OD2 C:ASP226 2.4 19.9 1.0
OD2 C:ASP224 2.4 21.0 1.0
ND1 C:HIS123 2.4 18.2 1.0
OD1 C:ASP226 2.6 14.0 1.0
O C:HOH444 2.6 20.4 1.0
O C:HOH525 2.7 29.2 1.0
CG C:ASP226 2.9 15.5 1.0
CG C:ASP224 3.2 22.8 1.0
CG C:ASP121 3.2 18.3 1.0
MN C:MN301 3.2 17.6 1.0
CE1 C:HIS123 3.3 18.9 1.0
CG C:HIS123 3.5 17.1 1.0
OD2 C:ASP121 3.5 22.4 1.0
OD1 C:ASP224 3.6 20.0 1.0
CB C:HIS123 3.7 15.8 1.0
N C:HIS123 4.1 12.6 1.0
CB C:ASP224 4.2 12.7 1.0
O C:HOH427 4.3 31.8 1.0
N C:ALA122 4.4 10.0 1.0
O C:HOH409 4.4 14.9 1.0
CB C:ASP226 4.4 8.0 1.0
NE2 C:HIS123 4.5 19.8 1.0
CA C:HIS123 4.5 17.0 1.0
CD2 C:HIS123 4.6 17.9 1.0
CB C:ASP121 4.6 16.7 1.0
OD1 C:ASP125 4.7 21.1 1.0
OD2 C:ASP125 4.9 24.0 1.0
CA C:ASP121 4.9 10.9 1.0
ND1 C:HIS98 4.9 13.4 1.0
C C:ALA122 4.9 13.2 1.0
CB C:ALA122 5.0 9.9 1.0
CA C:ALA122 5.0 9.9 1.0
CG C:GLU269 5.0 18.1 1.0

Manganese binding site 9 out of 14 in 6nbk

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Manganese binding site 9 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:14.7
occ:1.00
 OD2 D:ASP121 2.0 15.4 1.0
ND1 D:HIS98 2.0 14.8 1.0
OD2 D:ASP125 2.2 17.3 1.0
OD2 D:ASP224 2.5 20.9 1.0
CG D:ASP121 2.9 16.7 1.0
CG D:HIS98 3.0 14.5 1.0
CE1 D:HIS98 3.0 11.6 1.0
CG D:ASP125 3.1 22.8 1.0
MN D:MN302 3.2 20.3 1.0
OD1 D:ASP121 3.2 15.5 1.0
CB D:HIS98 3.3 11.6 1.0
OD1 D:ASP125 3.5 18.4 1.0
CG D:ASP224 3.5 22.5 1.0
CB D:ASP224 3.8 15.8 1.0
O D:HOH426 4.0 24.2 1.0
NE1 D:TRP119 4.1 15.3 1.0
NE2 D:HIS98 4.1 13.7 1.0
CD2 D:HIS98 4.1 11.7 1.0
CB D:ASP121 4.3 10.0 1.0
O D:HOH533 4.5 24.1 1.0
CB D:ASP125 4.5 16.2 1.0
CZ2 D:TRP119 4.5 14.2 1.0
CE2 D:TRP119 4.6 13.2 1.0
OD1 D:ASP224 4.7 22.3 1.0
O D:HIS138 4.7 25.2 1.0
CA D:HIS98 4.9 10.3 1.0
CB D:HIS123 4.9 21.6 1.0
CG D:GLU269 4.9 11.0 1.0
O D:HIS123 5.0 21.3 1.0

Manganese binding site 10 out of 14 in 6nbk

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Manganese binding site 10 out of 14 in the Crystal Structure of Arginase From Bacillus Cereus


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 Arginase From Bacillus Cereus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:20.3
occ:1.00
 OD1 D:ASP121 2.3 15.5 1.0
OD2 D:ASP226 2.3 18.6 1.0
OD2 D:ASP224 2.4 20.9 1.0
ND1 D:HIS123 2.4 18.4 1.0
O D:HOH533 2.6 24.1 1.0
OD1 D:ASP226 2.7 15.2 1.0
CG D:ASP226 2.8 16.6 1.0
CG D:ASP224 3.2 22.5 1.0
CG D:ASP121 3.2 16.7 1.0
MN D:MN301 3.2 14.7 1.0
CE1 D:HIS123 3.3 17.6 1.0
CG D:HIS123 3.5 21.6 1.0
OD2 D:ASP121 3.5 15.4 1.0
OD1 D:ASP224 3.6 22.3 1.0
CB D:HIS123 3.8 21.6 1.0
N D:HIS123 4.1 14.6 1.0
CB D:ASP224 4.2 15.8 1.0
O D:HOH437 4.3 10.6 1.0
O D:HOH426 4.3 24.2 1.0
CB D:ASP226 4.3 12.8 1.0
N D:ALA122 4.4 9.8 1.0
NE2 D:HIS123 4.5 18.8 1.0
CA D:HIS123 4.6 15.6 1.0
CD2 D:HIS123 4.6 17.0 1.0
CB D:ASP121 4.6 10.0 1.0
OD2 D:ASP125 4.9 17.3 1.0
OD1 D:ASP125 4.9 18.4 1.0
CB D:ALA122 4.9 9.8 1.0
CA D:ASP121 4.9 10.6 1.0
C D:ALA122 5.0 15.4 1.0
CA D:ALA122 5.0 9.8 1.0

Reference:

C.Chang, E.Evdokimova, M.Mcchesney, A.Joachimiak. Crystal Structure of Arginase From Bacillus Cereus To Be Published.
Page generated: Tue Dec 15 04:57:52 2020

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