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Cobalt in PDB 3d03: 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes

Enzymatic activity of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes

All present enzymatic activity of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes:
3.1.4.46;

Protein crystallography data

The structure of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes, PDB code: 3d03 was solved by K.S.Hadler, E.Tanifum, S.H.-C.Yip, N.Miti, L.W.Guddat, C.J.Jackson, L.R.Gahan, P.D.Carr, K.Nguyen, D.L.Ollis, A.C.Hengge, J.A.Larrabee, G.Schenk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.27 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 94.967, 133.842, 168.941, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.3

Cobalt Binding Sites:

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes (pdb code 3d03). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 12 binding sites of Cobalt where determined in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes, PDB code: 3d03:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 12 in 3d03

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Cobalt binding site 1 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1001

b:3.5
occ:0.75
 OD2 A:ASP8 2.2 8.3 1.0
NE2 A:HIS197 2.2 3.2 1.0
OD2 A:ASP50 2.2 4.5 1.0
NE2 A:HIS10 2.3 2.0 1.0
O A:HOH2001 2.3 13.9 1.0
O A:HOH2003 2.6 12.2 1.0
CE1 A:HIS10 3.1 2.0 1.0
CE1 A:HIS197 3.2 4.2 1.0
CG A:ASP8 3.2 5.2 1.0
CG A:ASP50 3.2 3.4 1.0
CD2 A:HIS197 3.3 5.6 1.0
CD2 A:HIS10 3.4 2.0 1.0
CB A:ASP50 3.4 4.9 1.0
CB A:ASP8 3.6 2.4 1.0
CO A:CO1002 3.7 4.0 0.5
OD1 A:ASP8 4.3 9.7 1.0
ND1 A:HIS197 4.3 2.0 1.0
ND1 A:HIS10 4.3 2.5 1.0
OD1 A:ASP50 4.4 3.2 1.0
CG A:HIS197 4.4 3.5 1.0
O A:HIS195 4.4 5.4 1.0
CG A:HIS10 4.5 2.0 1.0
CA A:ASP8 4.5 2.0 1.0
CE1 A:HIS156 4.5 2.8 1.0
CD2 A:HIS81 4.6 6.8 1.0
NE2 A:HIS81 4.7 8.3 1.0
CA A:HIS195 4.7 4.5 1.0
NE2 A:HIS156 4.7 4.4 1.0
C A:HIS195 4.9 4.3 1.0
CA A:ASP50 4.9 4.3 1.0
O A:HOH2002 5.0 24.4 1.0

Cobalt binding site 2 out of 12 in 3d03

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Cobalt binding site 2 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1002

b:4.0
occ:0.45
 OD1 A:ASN80 2.3 7.3 1.0
NE2 A:HIS156 2.3 4.4 1.0
OD2 A:ASP50 2.3 4.5 1.0
ND1 A:HIS195 2.5 6.0 1.0
O A:HOH2001 2.7 13.9 1.0
CG A:ASP50 3.1 3.4 1.0
CE1 A:HIS156 3.2 2.8 1.0
OD1 A:ASP50 3.3 3.2 1.0
CD2 A:HIS156 3.3 3.7 1.0
CE1 A:HIS195 3.3 9.4 1.0
CG A:ASN80 3.3 3.1 1.0
O A:HOH2002 3.6 24.4 1.0
CG A:HIS195 3.6 6.8 1.0
CO A:CO1001 3.7 3.5 0.8
CA A:HIS195 3.7 4.5 1.0
ND2 A:ASN80 3.8 6.4 1.0
CD2 A:HIS81 4.0 6.8 1.0
CB A:HIS195 4.0 3.0 1.0
OD2 A:ASP8 4.1 8.3 1.0
O A:HOH2003 4.3 12.2 1.0
O A:HIS195 4.3 5.4 1.0
N A:ASN80 4.3 2.3 1.0
ND1 A:HIS156 4.4 2.7 1.0
CB A:ASP50 4.4 4.9 1.0
CG A:HIS156 4.4 2.8 1.0
NE2 A:HIS195 4.5 7.7 1.0
C A:HIS195 4.5 4.3 1.0
NE2 A:HIS81 4.6 8.3 1.0
N A:HIS195 4.6 3.9 1.0
CB A:ASN80 4.6 3.3 1.0
CD2 A:HIS195 4.7 6.5 1.0

Cobalt binding site 3 out of 12 in 3d03

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Cobalt binding site 3 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1001

b:4.6
occ:0.75
 OD2 B:ASP8 2.0 7.1 1.0
NE2 B:HIS197 2.2 8.5 1.0
NE2 B:HIS10 2.3 3.5 1.0
OD2 B:ASP50 2.4 5.0 1.0
O B:HOH2001 2.4 16.5 1.0
O B:HOH2002 3.0 17.9 1.0
CG B:ASP8 3.1 5.3 1.0
CE1 B:HIS10 3.1 4.8 1.0
CE1 B:HIS197 3.2 8.3 1.0
CD2 B:HIS197 3.2 7.2 1.0
CG B:ASP50 3.3 5.2 1.0
CD2 B:HIS10 3.4 2.8 1.0
CB B:ASP50 3.4 4.7 1.0
CB B:ASP8 3.6 2.0 1.0
CO B:CO1002 3.7 5.2 0.5
OD1 B:ASP8 4.2 8.4 1.0
ND1 B:HIS10 4.3 4.9 1.0
ND1 B:HIS197 4.3 6.2 1.0
O B:HOH2003 4.3 17.8 1.0
CG B:HIS197 4.4 7.3 1.0
O B:HIS195 4.4 7.2 1.0
CA B:ASP8 4.4 2.6 1.0
CG B:HIS10 4.4 3.0 1.0
OD1 B:ASP50 4.5 4.3 1.0
CD2 B:HIS81 4.6 9.1 1.0
CE1 B:HIS156 4.6 4.8 1.0
NE2 B:HIS81 4.8 11.2 1.0
NE2 B:HIS156 4.8 5.6 1.0
CA B:HIS195 4.8 7.0 1.0
C B:HIS195 4.9 6.7 1.0
CA B:ASP50 4.9 5.3 1.0

Cobalt binding site 4 out of 12 in 3d03

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Cobalt binding site 4 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1002

b:5.2
occ:0.45
 OD1 B:ASN80 2.2 7.1 1.0
OD2 B:ASP50 2.3 5.0 1.0
ND1 B:HIS195 2.4 10.2 1.0
NE2 B:HIS156 2.5 5.6 1.0
O B:HOH2001 2.5 16.5 1.0
CE1 B:HIS195 3.1 12.9 1.0
CG B:ASP50 3.1 5.2 1.0
CG B:ASN80 3.3 7.8 1.0
CE1 B:HIS156 3.4 4.8 1.0
OD1 B:ASP50 3.4 4.3 1.0
CD2 B:HIS156 3.5 3.5 1.0
CG B:HIS195 3.6 9.0 1.0
O B:HOH2006 3.7 26.3 1.0
CO B:CO1001 3.7 4.6 0.8
ND2 B:ASN80 3.8 7.0 1.0
CA B:HIS195 3.8 7.0 1.0
CD2 B:HIS81 4.0 9.1 1.0
CB B:HIS195 4.1 7.2 1.0
OD2 B:ASP8 4.1 7.1 1.0
O B:HIS195 4.3 7.2 1.0
NE2 B:HIS195 4.4 12.7 1.0
N B:ASN80 4.4 4.9 1.0
CB B:ASP50 4.5 4.7 1.0
O B:HOH2002 4.5 17.9 1.0
ND1 B:HIS156 4.5 5.5 1.0
C B:HIS195 4.6 6.7 1.0
CB B:ASN80 4.6 6.0 1.0
CG B:HIS156 4.6 3.6 1.0
CD2 B:HIS195 4.6 10.7 1.0
NE2 B:HIS81 4.6 11.2 1.0
N B:HIS195 4.7 7.1 1.0
CA B:ASN80 5.0 5.6 1.0

Cobalt binding site 5 out of 12 in 3d03

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Cobalt binding site 5 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1001

b:4.5
occ:0.75
 OD2 C:ASP8 2.1 10.9 1.0
NE2 C:HIS10 2.3 5.2 1.0
OD2 C:ASP50 2.3 6.1 1.0
NE2 C:HIS197 2.3 7.2 1.0
O C:HOH2001 2.4 15.5 1.0
O C:HOH2002 2.7 17.2 1.0
CG C:ASP8 3.1 6.2 1.0
CE1 C:HIS197 3.2 6.8 1.0
CE1 C:HIS10 3.2 4.2 1.0
CG C:ASP50 3.3 7.0 1.0
CD2 C:HIS10 3.3 4.5 1.0
CD2 C:HIS197 3.4 8.5 1.0
CB C:ASP50 3.5 6.1 1.0
CB C:ASP8 3.5 2.8 1.0
CO C:CO1002 3.7 7.6 0.5
OD1 C:ASP8 4.2 8.9 1.0
ND1 C:HIS197 4.3 3.3 1.0
CA C:ASP8 4.4 2.7 1.0
ND1 C:HIS10 4.4 2.0 1.0
O C:HIS195 4.4 6.8 1.0
OD1 C:ASP50 4.4 5.8 1.0
CG C:HIS10 4.4 3.6 1.0
CG C:HIS197 4.5 6.2 1.0
CE1 C:HIS156 4.6 2.0 1.0
CD2 C:HIS81 4.6 6.5 1.0
O C:HOH2005 4.8 25.7 1.0
NE2 C:HIS156 4.8 2.6 1.0
CA C:HIS195 4.8 7.2 1.0
NE2 C:HIS81 4.8 7.9 1.0
C C:HIS195 4.9 6.7 1.0

Cobalt binding site 6 out of 12 in 3d03

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Cobalt binding site 6 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co1002

b:7.6
occ:0.45
 NE2 C:HIS156 2.2 2.6 1.0
OD1 C:ASN80 2.3 9.6 1.0
OD2 C:ASP50 2.4 6.1 1.0
ND1 C:HIS195 2.4 12.1 1.0
O C:HOH2001 2.5 15.5 1.0
CE1 C:HIS156 3.1 2.0 1.0
CG C:ASP50 3.1 7.0 1.0
O C:HOH2005 3.1 25.7 1.0
CE1 C:HIS195 3.2 10.5 1.0
CD2 C:HIS156 3.3 4.8 1.0
OD1 C:ASP50 3.3 5.8 1.0
CG C:ASN80 3.4 6.7 1.0
CG C:HIS195 3.6 9.0 1.0
CO C:CO1001 3.7 4.5 0.8
CA C:HIS195 3.7 7.2 1.0
ND2 C:ASN80 3.9 12.0 1.0
CB C:HIS195 4.0 7.6 1.0
OD2 C:ASP8 4.0 10.9 1.0
CD2 C:HIS81 4.2 6.5 1.0
O C:HOH2002 4.2 17.2 1.0
ND1 C:HIS156 4.3 3.3 1.0
N C:ASN80 4.3 4.7 1.0
O C:HIS195 4.3 6.8 1.0
CG C:HIS156 4.4 2.7 1.0
NE2 C:HIS195 4.4 9.1 1.0
CB C:ASP50 4.4 6.1 1.0
N C:HIS195 4.5 6.1 1.0
C C:HIS195 4.5 6.7 1.0
CD2 C:HIS195 4.6 9.1 1.0
CB C:ASN80 4.7 6.0 1.0
NE2 C:HIS81 4.8 7.9 1.0

Cobalt binding site 7 out of 12 in 3d03

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Cobalt binding site 7 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1001

b:4.9
occ:0.75
 OD2 D:ASP8 2.2 8.3 1.0
NE2 D:HIS197 2.2 5.7 1.0
OD2 D:ASP50 2.3 6.4 1.0
NE2 D:HIS10 2.3 2.0 1.0
O D:HOH2001 2.5 31.2 1.0
O D:HOH2002 2.8 16.8 1.0
CE1 D:HIS10 3.2 3.9 1.0
CG D:ASP8 3.2 4.0 1.0
CE1 D:HIS197 3.2 5.2 1.0
CG D:ASP50 3.2 5.5 1.0
CD2 D:HIS197 3.2 5.3 1.0
CD2 D:HIS10 3.3 3.4 1.0
CB D:ASP50 3.4 4.4 1.0
CB D:ASP8 3.5 2.0 1.0
CO D:CO1002 3.7 6.3 0.5
OD1 D:ASP8 4.3 8.9 1.0
ND1 D:HIS197 4.3 3.2 1.0
ND1 D:HIS10 4.3 2.0 1.0
CA D:ASP8 4.3 2.0 1.0
CG D:HIS197 4.3 3.8 1.0
O D:HOH2003 4.4 13.6 1.0
OD1 D:ASP50 4.4 2.0 1.0
O D:HIS195 4.4 7.3 1.0
CG D:HIS10 4.4 3.2 1.0
CE1 D:HIS156 4.6 3.3 1.0
CD2 D:HIS81 4.6 8.0 1.0
O D:HOH2006 4.7 20.4 1.0
CA D:HIS195 4.7 6.2 1.0
NE2 D:HIS81 4.8 8.1 1.0
NE2 D:HIS156 4.8 2.6 1.0
C D:HIS195 4.9 5.9 1.0
CA D:ASP50 4.9 4.3 1.0
N D:HIS195 5.0 6.5 1.0

Cobalt binding site 8 out of 12 in 3d03

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Cobalt binding site 8 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co1002

b:6.3
occ:0.45
 OD1 D:ASN80 2.2 9.4 1.0
NE2 D:HIS156 2.3 2.6 1.0
OD2 D:ASP50 2.4 6.4 1.0
ND1 D:HIS195 2.5 11.1 1.0
O D:HOH2001 2.7 31.2 1.0
CG D:ASP50 3.1 5.5 1.0
O D:HOH2006 3.2 20.4 1.0
CE1 D:HIS156 3.2 3.3 1.0
OD1 D:ASP50 3.3 2.0 1.0
CE1 D:HIS195 3.3 11.7 1.0
CG D:ASN80 3.3 7.4 1.0
CD2 D:HIS156 3.4 3.0 1.0
CG D:HIS195 3.6 7.9 1.0
CO D:CO1001 3.7 4.9 0.8
CA D:HIS195 3.8 6.2 1.0
ND2 D:ASN80 3.8 7.4 1.0
CD2 D:HIS81 4.0 8.0 1.0
CB D:HIS195 4.0 5.8 1.0
OD2 D:ASP8 4.1 8.3 1.0
N D:ASN80 4.3 3.9 1.0
O D:HOH2002 4.3 16.8 1.0
ND1 D:HIS156 4.4 4.6 1.0
CB D:ASP50 4.4 4.4 1.0
O D:HIS195 4.4 7.3 1.0
CG D:HIS156 4.5 2.9 1.0
NE2 D:HIS195 4.5 8.1 1.0
N D:HIS195 4.6 6.5 1.0
C D:HIS195 4.6 5.9 1.0
CB D:ASN80 4.6 5.1 1.0
NE2 D:HIS81 4.6 8.1 1.0
CD2 D:HIS195 4.7 10.4 1.0
N D:HIS81 5.0 4.0 1.0

Cobalt binding site 9 out of 12 in 3d03

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Cobalt binding site 9 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1001

b:7.1
occ:0.75
 OD2 E:ASP8 2.0 8.0 1.0
NE2 E:HIS197 2.2 7.5 1.0
NE2 E:HIS10 2.3 5.5 1.0
OD2 E:ASP50 2.3 7.4 1.0
O E:HOH2001 2.6 14.5 1.0
CG E:ASP8 3.0 6.0 1.0
CE1 E:HIS197 3.1 7.8 1.0
CD2 E:HIS197 3.1 8.0 1.0
CE1 E:HIS10 3.2 3.2 1.0
CG E:ASP50 3.3 7.9 1.0
O E:HOH2002 3.3 21.8 1.0
CD2 E:HIS10 3.4 4.7 1.0
CB E:ASP50 3.4 7.7 1.0
CB E:ASP8 3.5 4.9 1.0
CO E:CO1002 3.6 8.3 0.5
OD1 E:ASP8 4.1 11.7 1.0
ND1 E:HIS197 4.3 9.6 1.0
CG E:HIS197 4.3 8.5 1.0
ND1 E:HIS10 4.3 4.0 1.0
O E:HOH2003 4.4 15.0 1.0
O E:HIS195 4.4 7.5 1.0
OD1 E:ASP50 4.4 10.1 1.0
CA E:ASP8 4.4 4.5 1.0
CG E:HIS10 4.5 2.8 1.0
CD2 E:HIS81 4.5 12.5 1.0
CE1 E:HIS156 4.6 4.8 1.0
CA E:HIS195 4.7 7.2 1.0
NE2 E:HIS156 4.7 6.2 1.0
NE2 E:HIS81 4.8 14.8 1.0
C E:HIS195 4.9 7.6 1.0
CA E:ASP50 5.0 7.1 1.0

Cobalt binding site 10 out of 12 in 3d03

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Cobalt binding site 10 out of 12 in the 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of 1.9A Structure of Glycerophoshphodiesterase (Gpdq) From Enterobacter Aerogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co1002

b:8.3
occ:0.45
 OD2 E:ASP50 2.3 7.4 1.0
OD1 E:ASN80 2.3 8.9 1.0
NE2 E:HIS156 2.4 6.2 1.0
ND1 E:HIS195 2.5 10.6 1.0
O E:HOH2001 2.6 14.5 1.0
CG E:ASP50 3.1 7.9 1.0
CE1 E:HIS195 3.2 11.7 1.0
OD1 E:ASP50 3.3 10.1 1.0
CG E:ASN80 3.3 8.0 1.0
CE1 E:HIS156 3.4 4.8 1.0
CD2 E:HIS156 3.4 7.3 1.0
O E:HOH2006 3.4 26.2 1.0
CG E:HIS195 3.6 8.5 1.0
CO E:CO1001 3.6 7.1 0.8
ND2 E:ASN80 3.7 7.2 1.0
CA E:HIS195 3.7 7.2 1.0
OD2 E:ASP8 3.9 8.0 1.0
CB E:HIS195 4.0 7.2 1.0
CD2 E:HIS81 4.0 12.5 1.0
O E:HIS195 4.3 7.5 1.0
CB E:ASP50 4.4 7.7 1.0
NE2 E:HIS195 4.4 11.9 1.0
N E:ASN80 4.4 7.8 1.0
ND1 E:HIS156 4.5 5.5 1.0
CG E:HIS156 4.5 7.4 1.0
C E:HIS195 4.6 7.6 1.0
N E:HIS195 4.6 7.6 1.0
CD2 E:HIS195 4.6 7.7 1.0
CB E:ASN80 4.7 7.5 1.0
O E:HOH2002 4.7 21.8 1.0
NE2 E:HIS81 4.7 14.8 1.0

Reference:

K.S.Hadler, E.A.Tanifum, S.H.Yip, N.Mitic, L.W.Guddat, C.J.Jackson, L.R.Gahan, K.Nguyen, P.D.Carr, D.L.Ollis, A.C.Hengge, J.A.Larrabee, G.Schenk. Substrate-Promoted Formation of A Catalytically Competent Binuclear Center and Regulation of Reactivity in A Glycerophosphodiesterase From Enterobacter Aerogenes. J.Am.Chem.Soc. V. 130 14129 2008.
ISSN: ISSN 0002-7863
PubMed: 18831553
DOI: 10.1021/JA803346W
Page generated: Tue Jul 30 15:53:03 2024

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