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Manganese in PDB 4dz4: X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis

Enzymatic activity of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis

All present enzymatic activity of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis:
3.5.3.11;

Protein crystallography data

The structure of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis, PDB code: 4dz4 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 99.080, 101.250, 102.990, 90.00, 97.09, 90.00
R / Rfree (%) 15.2 / 17.5

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis (pdb code 4dz4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis, PDB code: 4dz4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 4dz4

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Manganese binding site 1 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:15.6
occ:1.00
 O A:HOH739 2.1 16.1 1.0
OD1 A:ASP159 2.1 12.4 1.0
OD2 A:ASP244 2.2 12.2 1.0
OD2 A:ASP242 2.2 13.4 1.0
ND1 A:HIS161 2.3 13.7 1.0
OD1 A:ASP244 2.4 13.1 1.0
CG A:ASP244 2.6 12.0 1.0
O A:UNK408 2.9 40.7 1.0
CG A:ASP242 3.1 12.2 1.0
CG A:ASP159 3.1 12.8 1.0
CE1 A:HIS161 3.2 13.8 1.0
MN A:MN402 3.2 21.1 0.8
CG A:HIS161 3.3 14.1 1.0
OD2 A:ASP159 3.5 12.9 1.0
OD1 A:ASP242 3.6 12.6 1.0
CB A:HIS161 3.6 13.7 1.0
N A:HIS161 4.0 13.1 1.0
CB A:ASP242 4.1 12.2 1.0
CB A:ASP244 4.1 11.3 1.0
O A:UNK407 4.2 30.9 1.0
N A:ALA160 4.2 12.3 1.0
OG1 A:THR256 4.2 14.6 1.0
NE2 A:HIS161 4.4 14.1 1.0
CD2 A:HIS161 4.4 14.3 1.0
CB A:ASP159 4.5 12.7 1.0
CA A:HIS161 4.5 14.0 1.0
O A:HOH625 4.6 17.1 1.0
CA A:ASP159 4.8 12.2 1.0
CB A:ALA160 4.8 12.2 1.0
O A:UNK409 4.8 39.6 1.0
C A:ALA160 4.9 12.8 1.0
CA A:ALA160 4.9 12.2 1.0
OD2 A:ASP163 4.9 16.3 1.0
O A:HIS161 4.9 14.1 1.0
C A:ASP159 4.9 12.5 1.0
OD1 A:ASP163 5.0 17.1 1.0

Manganese binding site 2 out of 12 in 4dz4

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Manganese binding site 2 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:21.1
occ:0.80
 O A:HOH739 2.0 16.1 1.0
OD2 A:ASP163 2.1 16.3 1.0
OD2 A:ASP159 2.1 12.9 1.0
ND1 A:HIS135 2.2 13.0 1.0
O A:UNK407 2.2 30.9 1.0
OD2 A:ASP242 2.7 13.4 1.0
CG A:ASP163 3.1 16.3 1.0
CG A:ASP159 3.1 12.8 1.0
CE1 A:HIS135 3.2 13.5 1.0
CG A:HIS135 3.2 13.5 1.0
MN A:MN401 3.2 15.6 1.0
OD1 A:ASP159 3.3 12.4 1.0
OD1 A:ASP163 3.3 17.1 1.0
CB A:HIS135 3.5 13.0 1.0
CG A:ASP242 3.7 12.2 1.0
O A:UNK408 3.7 40.7 1.0
CB A:ASP242 4.0 12.2 1.0
O A:HIS175 4.2 18.3 1.0
NE2 A:HIS157 4.2 13.5 1.0
NE2 A:HIS135 4.3 13.3 1.0
CD2 A:HIS135 4.3 12.8 1.0
CB A:ASP163 4.4 16.3 1.0
O A:HIS161 4.4 14.1 1.0
CB A:HIS161 4.4 13.7 1.0
O A:UNK409 4.4 39.6 1.0
CB A:ASP159 4.5 12.7 1.0
CE A:MET178 4.8 17.2 1.0
ND1 A:HIS161 4.8 13.7 1.0
OD1 A:ASP242 4.8 12.6 1.0
OE2 A:GLU286 5.0 15.6 1.0
CA A:HIS135 5.0 12.9 1.0

Manganese binding site 3 out of 12 in 4dz4

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Manganese binding site 3 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:14.7
occ:0.78
 O B:HOH752 1.9 13.7 1.0
OD2 B:ASP163 2.0 12.1 1.0
ND1 B:HIS135 2.2 11.1 1.0
OD2 B:ASP159 2.2 9.9 1.0
O B:UNK413 2.3 23.1 1.0
OD2 B:ASP242 2.6 11.5 1.0
CG B:ASP163 3.0 11.5 1.0
CG B:ASP159 3.1 10.2 1.0
CG B:HIS135 3.1 10.9 1.0
CE1 B:HIS135 3.2 10.9 1.0
MN B:MN402 3.2 13.0 1.0
OD1 B:ASP159 3.4 10.2 1.0
OD1 B:ASP163 3.4 11.5 1.0
CB B:HIS135 3.4 10.5 1.0
CG B:ASP242 3.6 10.8 1.0
O B:UNK414 3.6 31.8 1.0
CB B:ASP242 4.0 10.7 1.0
NE2 B:HIS135 4.3 11.1 1.0
O B:HIS175 4.3 11.4 1.0
CD2 B:HIS135 4.3 10.7 1.0
NE2 B:HIS157 4.3 10.3 1.0
CB B:ASP163 4.4 11.7 1.0
O B:HIS161 4.5 9.6 1.0
CB B:ASP159 4.5 9.5 1.0
CB B:HIS161 4.5 9.6 1.0
OD1 B:ASP242 4.7 10.8 1.0
CE B:MET178 4.8 10.9 1.0
OE2 B:GLU286 4.9 11.3 1.0
ND1 B:HIS161 4.9 10.2 1.0
CA B:HIS135 4.9 9.7 1.0
CG B:GLU286 5.0 10.1 1.0

Manganese binding site 4 out of 12 in 4dz4

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Manganese binding site 4 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:13.0
occ:1.00
 O B:HOH752 2.1 13.7 1.0
OD1 B:ASP159 2.1 10.2 1.0
OD2 B:ASP242 2.2 11.5 1.0
OD1 B:ASP244 2.2 12.3 1.0
ND1 B:HIS161 2.3 10.2 1.0
OD2 B:ASP244 2.5 12.6 1.0
CG B:ASP244 2.7 11.8 1.0
O B:UNK414 2.8 31.8 1.0
CG B:ASP159 3.1 10.2 1.0
CG B:ASP242 3.1 10.8 1.0
MN B:MN401 3.2 14.7 0.8
CE1 B:HIS161 3.2 10.2 1.0
CG B:HIS161 3.3 9.9 1.0
OD2 B:ASP159 3.4 9.9 1.0
CB B:HIS161 3.6 9.6 1.0
OD1 B:ASP242 3.6 10.8 1.0
N B:HIS161 4.0 9.3 1.0
O B:UNK413 4.1 23.1 1.0
OG1 B:THR256 4.1 10.6 1.0
CB B:ASP242 4.2 10.7 1.0
CB B:ASP244 4.2 10.6 1.0
N B:ALA160 4.3 9.5 1.0
NE2 B:HIS161 4.4 10.5 1.0
CA B:HIS161 4.4 9.6 1.0
CD2 B:HIS161 4.4 10.4 1.0
CB B:ASP159 4.5 9.5 1.0
O B:HOH556 4.6 16.8 1.0
OD2 B:ASP163 4.7 12.1 1.0
CB B:ALA160 4.8 9.4 1.0
CA B:ASP159 4.8 9.9 1.0
C B:ALA160 4.8 9.5 1.0
OD1 B:ASP163 4.9 11.5 1.0
CA B:ALA160 4.9 9.3 1.0
O B:HIS161 4.9 9.6 1.0
C B:ASP159 5.0 9.8 1.0

Manganese binding site 5 out of 12 in 4dz4

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Manganese binding site 5 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:17.5
occ:1.00
 O C:HOH711 2.1 19.8 1.0
OD2 C:ASP244 2.1 13.6 1.0
OD1 C:ASP159 2.1 14.7 1.0
OD2 C:ASP242 2.2 15.7 1.0
ND1 C:HIS161 2.3 14.4 1.0
OD1 C:ASP244 2.5 15.0 1.0
CG C:ASP244 2.6 13.4 1.0
O C:UNK411 2.8 32.9 1.0
CG C:ASP242 3.1 14.5 1.0
CG C:ASP159 3.1 15.1 1.0
CE1 C:HIS161 3.2 14.4 1.0
MN C:MN402 3.2 22.9 0.8
CG C:HIS161 3.3 14.9 1.0
OD2 C:ASP159 3.4 15.1 1.0
OD1 C:ASP242 3.6 14.0 1.0
CB C:HIS161 3.7 14.9 1.0
N C:HIS161 4.0 14.1 1.0
OG1 C:THR256 4.1 14.1 1.0
CB C:ASP242 4.1 13.8 1.0
CB C:ASP244 4.2 12.6 1.0
N C:ALA160 4.2 13.5 1.0
O C:UNK412 4.2 30.9 1.0
NE2 C:HIS161 4.4 14.3 1.0
CD2 C:HIS161 4.4 15.2 1.0
CA C:HIS161 4.5 15.1 1.0
CB C:ASP159 4.5 14.7 1.0
O C:HOH568 4.6 17.8 1.0
CB C:ALA160 4.8 12.9 1.0
CA C:ASP159 4.8 14.2 1.0
CA C:ALA160 4.8 13.5 1.0
C C:ALA160 4.8 13.8 1.0
OD2 C:ASP163 4.8 18.8 1.0
OD1 C:ASP163 4.9 18.1 1.0
O C:HIS161 4.9 15.4 1.0
C C:ASP159 5.0 13.8 1.0

Manganese binding site 6 out of 12 in 4dz4

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Manganese binding site 6 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:22.9
occ:0.85
 O C:HOH711 2.1 19.8 1.0
OD2 C:ASP163 2.1 18.8 1.0
OD2 C:ASP159 2.1 15.1 1.0
ND1 C:HIS135 2.3 15.3 1.0
O C:UNK412 2.4 30.9 1.0
OD2 C:ASP242 2.6 15.7 1.0
CG C:ASP163 3.1 18.9 1.0
CG C:ASP159 3.1 15.1 1.0
CG C:HIS135 3.2 15.4 1.0
MN C:MN401 3.2 17.5 1.0
CE1 C:HIS135 3.3 15.6 1.0
OD1 C:ASP159 3.3 14.7 1.0
OD1 C:ASP163 3.4 18.1 1.0
CB C:HIS135 3.5 15.4 1.0
CG C:ASP242 3.7 14.5 1.0
O C:UNK411 3.8 32.9 1.0
CB C:ASP242 4.0 13.8 1.0
NE2 C:HIS157 4.3 15.9 1.0
O C:HIS175 4.4 18.6 1.0
NE2 C:HIS135 4.4 15.8 1.0
CD2 C:HIS135 4.4 15.7 1.0
CB C:ASP163 4.5 18.6 1.0
O C:HIS161 4.5 15.4 1.0
CB C:ASP159 4.5 14.7 1.0
CB C:HIS161 4.5 14.9 1.0
OD1 C:ASP242 4.8 14.0 1.0
CE C:MET178 4.8 20.1 1.0
OE2 C:GLU286 4.8 14.8 1.0
ND1 C:HIS161 4.9 14.4 1.0
CA C:HIS135 5.0 15.2 1.0

Manganese binding site 7 out of 12 in 4dz4

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Manganese binding site 7 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:13.4
occ:1.00
 OD1 D:ASP159 2.1 9.6 1.0
O D:HOH793 2.1 18.4 1.0
OD2 D:ASP244 2.2 11.1 1.0
OD2 D:ASP242 2.2 10.1 1.0
ND1 D:HIS161 2.3 11.5 1.0
OD1 D:ASP244 2.5 11.7 1.0
CG D:ASP244 2.7 10.8 1.0
O D:UNK411 2.9 37.5 1.0
CG D:ASP159 3.1 9.9 1.0
CG D:ASP242 3.1 9.5 1.0
CE1 D:HIS161 3.2 11.3 1.0
MN D:MN402 3.3 16.7 0.7
CG D:HIS161 3.3 11.2 1.0
OD2 D:ASP159 3.4 9.9 1.0
CB D:HIS161 3.6 11.3 1.0
OD1 D:ASP242 3.7 9.7 1.0
N D:HIS161 4.0 10.2 1.0
CB D:ASP242 4.1 9.4 1.0
CB D:ASP244 4.2 9.9 1.0
N D:ALA160 4.2 9.2 1.0
O D:UNK412 4.2 32.2 1.0
OG1 D:THR256 4.2 12.2 1.0
NE2 D:HIS161 4.4 11.4 1.0
CB D:ASP159 4.4 9.4 1.0
CD2 D:HIS161 4.4 11.9 1.0
CA D:HIS161 4.4 11.0 1.0
O D:UNK413 4.5 35.6 1.0
O D:HOH561 4.6 15.0 1.0
CA D:ASP159 4.7 9.2 1.0
OD2 D:ASP163 4.8 15.9 1.0
CB D:ALA160 4.8 9.5 1.0
C D:ALA160 4.8 10.0 1.0
CA D:ALA160 4.8 9.7 1.0
C D:ASP159 4.9 9.4 1.0
O D:HIS161 4.9 11.8 1.0
OD1 D:ASP163 5.0 15.9 1.0

Manganese binding site 8 out of 12 in 4dz4

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Manganese binding site 8 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:16.7
occ:0.73
 OD2 D:ASP163 1.9 15.9 1.0
O D:HOH793 2.0 18.4 1.0
OD2 D:ASP159 2.2 9.9 1.0
ND1 D:HIS135 2.2 10.3 1.0
O D:UNK412 2.5 32.2 1.0
OD2 D:ASP242 2.7 10.1 1.0
CG D:ASP163 3.0 15.3 1.0
CG D:ASP159 3.1 9.9 1.0
CG D:HIS135 3.2 10.4 1.0
CE1 D:HIS135 3.2 10.7 1.0
MN D:MN401 3.3 13.4 1.0
OD1 D:ASP159 3.4 9.6 1.0
OD1 D:ASP163 3.4 15.9 1.0
CB D:HIS135 3.5 10.2 1.0
CG D:ASP242 3.8 9.5 1.0
O D:UNK411 3.9 37.5 1.0
CB D:ASP242 4.1 9.4 1.0
O D:UNK413 4.1 35.6 1.0
NE2 D:HIS157 4.2 10.2 1.0
O D:HIS175 4.3 16.8 1.0
NE2 D:HIS135 4.3 10.5 1.0
CD2 D:HIS135 4.4 10.2 1.0
CB D:ASP163 4.4 14.7 1.0
O D:HIS161 4.4 11.8 1.0
CB D:HIS161 4.4 11.3 1.0
CB D:ASP159 4.5 9.4 1.0
CE D:MET178 4.7 16.5 1.0
ND1 D:HIS161 4.8 11.5 1.0
OD1 D:ASP242 4.9 9.7 1.0
OE2 D:GLU286 4.9 10.6 1.0
CE1 D:HIS157 5.0 10.5 1.0
CA D:HIS135 5.0 9.7 1.0

Manganese binding site 9 out of 12 in 4dz4

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Manganese binding site 9 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:16.2
occ:0.75
 O E:HOH775 2.0 17.8 1.0
OD2 E:ASP163 2.1 17.5 1.0
OD2 E:ASP159 2.2 9.8 1.0
ND1 E:HIS135 2.2 10.8 1.0
O E:UNK413 2.4 33.0 1.0
OD2 E:ASP242 2.5 12.4 1.0
CG E:ASP159 3.1 9.9 1.0
CG E:ASP163 3.1 17.1 1.0
CG E:HIS135 3.2 10.5 1.0
CE1 E:HIS135 3.2 11.1 1.0
MN E:MN402 3.3 14.3 1.0
OD1 E:ASP159 3.3 9.9 1.0
OD1 E:ASP163 3.4 16.4 1.0
CB E:HIS135 3.5 10.2 1.0
CG E:ASP242 3.6 10.9 1.0
O E:UNK412 3.9 35.1 1.0
CB E:ASP242 3.9 10.7 1.0
NE2 E:HIS157 4.3 10.1 1.0
NE2 E:HIS135 4.3 10.8 1.0
CD2 E:HIS135 4.3 10.6 1.0
O E:HIS175 4.3 14.7 1.0
CB E:ASP159 4.5 9.5 1.0
CB E:ASP163 4.5 17.2 1.0
O E:HIS161 4.5 12.1 1.0
CB E:HIS161 4.6 12.3 1.0
OD1 E:ASP242 4.7 11.4 1.0
OE2 E:GLU286 4.8 11.9 1.0
CE E:MET178 4.9 13.7 1.0
ND1 E:HIS161 4.9 12.8 1.0
CA E:HIS135 4.9 9.5 1.0
CG E:GLU286 5.0 10.5 1.0

Manganese binding site 10 out of 12 in 4dz4

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Manganese binding site 10 out of 12 in the X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Crystal Structure of A Hypothetical Agmatinase From Burkholderia Thailandensis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn402

b:14.3
occ:1.00
 O E:HOH775 2.1 17.8 1.0
OD1 E:ASP159 2.1 9.9 1.0
OD1 E:ASP244 2.2 13.7 1.0
OD2 E:ASP242 2.2 12.4 1.0
ND1 E:HIS161 2.3 12.8 1.0
OD2 E:ASP244 2.4 12.5 1.0
CG E:ASP244 2.6 12.4 1.0
O E:UNK412 2.7 35.1 1.0
CG E:ASP159 3.1 9.9 1.0
CG E:ASP242 3.1 10.9 1.0
CE1 E:HIS161 3.2 12.7 1.0
MN E:MN401 3.3 16.2 0.8
CG E:HIS161 3.3 12.3 1.0
OD2 E:ASP159 3.4 9.8 1.0
OD1 E:ASP242 3.6 11.4 1.0
CB E:HIS161 3.6 12.3 1.0
N E:HIS161 4.0 10.9 1.0
CB E:ASP242 4.1 10.7 1.0
OG1 E:THR256 4.1 13.2 1.0
CB E:ASP244 4.2 11.4 1.0
O E:UNK413 4.2 33.0 1.0
N E:ALA160 4.2 9.6 1.0
NE2 E:HIS161 4.4 12.4 1.0
CB E:ASP159 4.4 9.5 1.0
CD2 E:HIS161 4.4 13.4 1.0
CA E:HIS161 4.5 11.9 1.0
O E:HOH608 4.5 17.4 1.0
CA E:ASP159 4.7 9.4 1.0
CB E:ALA160 4.8 9.8 1.0
OD2 E:ASP163 4.8 17.5 1.0
CA E:ALA160 4.8 10.1 1.0
C E:ALA160 4.9 10.7 1.0
O E:HIS161 4.9 12.1 1.0
OD1 E:ASP163 4.9 16.4 1.0
C E:ASP159 4.9 9.7 1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851
Page generated: Sat Oct 5 19:06:43 2024

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