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Cobalt in PDB 1h41: Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid

Enzymatic activity of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid

All present enzymatic activity of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid:
3.2.1.139;

Protein crystallography data

The structure of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid, PDB code: 1h41 was solved by D.Nurizzo, T.Nagy, H.J.Gilbert, G.J.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.5
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.412, 74.393, 87.462, 115.09, 93.04, 109.44
R / Rfree (%) 11.8 / 15.3

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid (pdb code 1h41). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid, PDB code: 1h41:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 1h41

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Cobalt binding site 1 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1728

b:15.8
occ:0.50
 OG1 A:THR629 3.1 13.1 1.0
O A:HOH2693 3.2 15.6 1.0
O A:HOH2820 3.2 15.5 1.0
O A:HOH2568 3.4 17.4 1.0
O A:ALA625 3.7 12.1 1.0
CA A:MET502 3.7 10.1 1.0
CB A:MET502 3.8 11.5 1.0
CA A:MET626 3.8 10.7 1.0
CB A:THR629 3.8 10.6 1.0
N A:MET626 3.9 10.5 1.0
C A:ALA625 3.9 10.6 1.0
CG A:MET502 3.9 13.3 1.0
CG A:MET626 4.0 12.4 1.0
CG2 A:THR629 4.3 13.8 1.0
N A:MET502 4.3 11.2 1.0
O A:HOH2696 4.4 14.3 1.0
CB A:ALA625 4.5 11.2 1.0
CB A:MET626 4.5 10.7 1.0
CG1 A:VAL505 4.6 14.5 1.0
CA A:ALA625 4.8 10.5 1.0
C A:MET626 4.9 9.3 1.0
O A:HOH2262 4.9 42.9 1.0
O A:HOH2702 4.9 23.2 1.0
C A:GLN501 5.0 12.0 1.0
O A:PRO498 5.0 10.9 1.0

Cobalt binding site 2 out of 10 in 1h41

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Cobalt binding site 2 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1729

b:12.5
occ:0.50
 O A:HOH2725 3.0 17.2 1.0
O A:HOH2540 3.0 9.5 1.0
ND2 A:ASN452 3.3 10.7 1.0
CA A:GLY7 3.4 10.2 1.0
CB A:ASN452 3.5 7.7 1.0
CB A:PRO457 3.6 9.9 1.0
CG A:PRO457 3.7 10.3 1.0
NE2 A:GLN460 3.7 13.4 1.0
CD A:ARG641 3.7 11.5 1.0
N A:GLY7 3.8 11.0 1.0
CG A:ASN452 4.0 8.4 1.0
CA A:PRO457 4.1 9.6 1.0
CG A:ARG641 4.1 10.7 1.0
C A:ASP6 4.2 11.8 1.0
O A:ASP6 4.3 12.4 1.0
CD A:GLN460 4.4 10.3 1.0
OE1 A:GLN644 4.4 16.4 1.0
OE1 A:GLN460 4.4 9.4 1.0
CD A:PRO457 4.8 9.2 1.0
O A:HOH2009 4.8 15.3 1.0
C A:GLY7 4.8 9.9 1.0
N A:PRO457 4.8 8.8 1.0
CA A:ASN452 4.9 7.1 1.0

Cobalt binding site 3 out of 10 in 1h41

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Cobalt binding site 3 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1730

b:18.6
occ:0.50
 O A:HOH2821 3.1 35.5 1.0
O A:HOH2751 3.2 34.0 1.0
NH1 A:ARG673 3.3 17.7 1.0
ND2 A:ASN607 3.3 14.0 1.0
CD1 A:TRP609 3.6 14.1 1.0
CD A:ARG673 3.7 17.6 1.0
NE2 A:GLN610 4.1 20.3 1.0
OD1 A:ASN607 4.2 13.1 1.0
CG A:ASN607 4.2 12.6 1.0
CG A:ARG673 4.2 18.8 1.0
CZ A:ARG673 4.3 16.7 1.0
CB A:ARG673 4.3 19.3 1.0
CG A:TRP609 4.4 11.9 1.0
CG A:GLN610 4.4 15.4 1.0
NE A:ARG673 4.4 17.6 1.0
CD A:GLN610 4.5 17.4 1.0
CB A:TRP609 4.6 12.1 1.0
NE1 A:TRP609 4.6 14.9 1.0
CD A:PRO674 4.8 22.1 1.0

Cobalt binding site 4 out of 10 in 1h41

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Cobalt binding site 4 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1731

b:16.5
occ:0.50
 O A:HOH2823 2.8 34.1 1.0
O A:HOH2822 3.1 36.1 1.0
O B:HOH2805 3.2 27.1 1.0
O A:HOH2786 3.2 33.6 1.0
ND2 A:ASN164 3.3 11.1 1.0
ND2 A:ASN162 3.3 10.7 1.0
CD1 A:TRP702 3.7 9.6 1.0
CB A:VAL166 3.8 8.8 1.0
CG1 A:VAL166 4.0 9.2 1.0
OD1 A:ASN164 4.0 8.7 1.0
CG A:ASN164 4.0 9.4 1.0
NE1 A:TRP702 4.1 10.4 1.0
CG A:ASN162 4.3 8.6 1.0
CG2 A:VAL166 4.4 9.4 1.0
CB A:ASN162 4.5 8.7 1.0
OG B:SER707 4.8 17.9 1.0
O B:HOH2795 4.8 20.1 1.0
O A:HOH2253 4.9 15.8 1.0
CG A:TRP702 4.9 8.7 1.0

Cobalt binding site 5 out of 10 in 1h41

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Cobalt binding site 5 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1732

b:25.0
occ:0.50
 ND1 A:HIS438 1.8 18.0 1.0
NE2 A:HIS154 2.0 14.8 1.0
OE1 A:GLN153 2.3 16.1 0.5
CE1 A:HIS438 2.4 20.3 1.0
O A:HOH2824 2.5 27.9 1.0
NE2 A:GLN153 2.5 9.6 0.5
CD A:GLN153 2.5 14.2 0.5
CE1 A:HIS154 2.8 17.5 1.0
CG A:HIS438 3.0 17.1 1.0
CD2 A:HIS154 3.1 12.1 1.0
NE2 A:GLN153 3.3 16.5 0.5
NE2 A:HIS438 3.6 18.4 1.0
CB A:HIS438 3.7 14.8 1.0
O A:HOH2529 3.7 43.1 1.0
CG A:GLN153 3.9 13.9 0.5
CD2 A:HIS438 3.9 18.3 1.0
ND1 A:HIS154 4.0 18.1 1.0
CG A:HIS154 4.2 12.3 1.0
CA A:HIS438 4.3 15.1 1.0
CD A:GLN153 4.5 16.7 0.5
CG1 A:VAL321 4.5 12.4 1.0
CB A:GLN153 4.7 12.9 1.0
CD1 A:ILE356 4.9 16.9 1.0
O A:ARG437 5.0 21.3 1.0

Cobalt binding site 6 out of 10 in 1h41

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Cobalt binding site 6 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1728

b:14.2
occ:0.50
 OG1 B:THR629 3.1 11.9 1.0
O B:HOH2697 3.2 15.8 1.0
O B:HOH2840 3.3 16.6 1.0
O B:HOH2574 3.3 17.7 1.0
CA B:MET502 3.7 9.7 1.0
O B:ALA625 3.7 10.1 1.0
CB B:MET502 3.8 11.0 1.0
CA B:MET626 3.8 9.8 1.0
CB B:THR629 3.8 9.5 1.0
N B:MET626 3.9 9.3 1.0
CG B:MET502 3.9 12.1 1.0
C B:ALA625 3.9 9.9 1.0
CG B:MET626 4.1 11.9 0.5
CG B:MET626 4.1 8.2 0.5
CG2 B:THR629 4.2 11.1 1.0
N B:MET502 4.3 10.2 1.0
O B:HOH2701 4.4 14.4 1.0
CB B:MET626 4.5 9.6 1.0
CB B:ALA625 4.5 10.2 1.0
CG1 B:VAL505 4.6 14.1 1.0
CA B:ALA625 4.9 10.3 1.0
C B:MET626 4.9 9.0 1.0
O B:HOH2707 4.9 23.1 1.0
C B:GLN501 5.0 10.6 1.0
O B:PRO498 5.0 10.3 1.0
C B:MET502 5.0 10.3 1.0
O B:HOH2307 5.0 15.7 1.0

Cobalt binding site 7 out of 10 in 1h41

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Cobalt binding site 7 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1729

b:11.7
occ:0.50
 O B:HOH2731 3.0 15.6 1.0
O B:HOH2543 3.0 10.2 1.0
ND2 B:ASN452 3.3 9.5 1.0
CA B:GLY7 3.4 10.2 1.0
CB B:ASN452 3.5 8.1 1.0
CB B:PRO457 3.6 9.3 1.0
NE2 B:GLN460 3.6 13.1 1.0
CG B:PRO457 3.6 9.4 1.0
CD B:ARG641 3.7 10.1 1.0
N B:GLY7 3.9 10.8 1.0
CG B:ASN452 4.0 9.3 1.0
CA B:PRO457 4.0 8.7 1.0
CG B:ARG641 4.1 9.7 1.0
C B:ASP6 4.3 11.2 1.0
CD B:GLN460 4.4 8.2 1.0
OE1 B:GLN644 4.4 17.3 1.0
O B:ASP6 4.4 11.2 1.0
OE1 B:GLN460 4.5 9.4 1.0
CD B:PRO457 4.7 8.1 1.0
O B:HOH2009 4.8 14.7 1.0
C B:GLY7 4.8 9.1 1.0
N B:PRO457 4.8 7.7 1.0
CA B:ASN452 4.9 7.5 1.0

Cobalt binding site 8 out of 10 in 1h41

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Cobalt binding site 8 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1730

b:16.5
occ:0.50
 O B:HOH2841 2.8 17.2 0.5
O B:HOH2842 3.1 37.0 1.0
O B:HOH2798 3.1 15.3 0.5
O A:HOH2793 3.2 27.7 1.0
ND2 B:ASN162 3.3 11.1 1.0
ND2 B:ASN164 3.3 12.2 1.0
CD1 B:TRP702 3.7 9.6 1.0
CB B:VAL166 3.8 8.3 1.0
CG1 B:VAL166 3.9 9.5 1.0
OD1 B:ASN164 3.9 9.1 1.0
CG B:ASN164 4.1 9.3 1.0
NE1 B:TRP702 4.1 11.0 1.0
CG B:ASN162 4.3 9.1 1.0
CG2 B:VAL166 4.4 9.7 1.0
CB B:ASN162 4.5 7.5 1.0
O B:HOH2796 4.6 37.2 1.0
O A:HOH2784 4.8 21.9 1.0
O B:HOH2255 4.8 15.4 1.0
OG A:SER707 4.9 17.9 1.0
CG B:TRP702 4.9 9.2 1.0

Cobalt binding site 9 out of 10 in 1h41

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Cobalt binding site 9 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1731

b:19.6
occ:0.50
 O B:HOH2756 3.2 33.1 1.0
NH1 B:ARG673 3.4 18.0 1.0
ND2 B:ASN607 3.4 13.5 1.0
CD1 B:TRP609 3.6 13.2 1.0
CD B:ARG673 3.8 19.7 1.0
OD1 B:ASN607 4.2 13.6 1.0
NE2 B:GLN610 4.2 20.2 1.0
CG B:ASN607 4.2 12.8 1.0
CG B:ARG673 4.3 18.5 1.0
CB B:ARG673 4.3 20.1 1.0
CZ B:ARG673 4.3 17.4 1.0
CG B:GLN610 4.4 14.1 1.0
CG B:TRP609 4.4 12.6 1.0
NE B:ARG673 4.5 19.0 1.0
NE1 B:TRP609 4.6 14.6 1.0
CB B:TRP609 4.6 12.4 1.0
CD B:GLN610 4.6 16.5 1.0
CD B:PRO674 4.9 22.6 1.0

Cobalt binding site 10 out of 10 in 1h41

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Cobalt binding site 10 out of 10 in the Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Pseudomonas Cellulosa E292A Alpha-D-Glucuronidase Mutant Complexed with Aldotriuronic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1732

b:32.3
occ:0.50
 ND1 B:HIS438 1.8 24.5 1.0
NE2 B:HIS154 2.1 15.9 1.0
CE1 B:HIS438 2.2 24.9 1.0
OE1 B:GLN153 2.2 18.0 0.5
O B:HOH2843 2.4 33.5 1.0
CD B:GLN153 2.6 15.7 0.5
NE2 B:GLN153 2.7 15.5 0.5
CE1 B:HIS154 2.9 18.5 1.0
NE2 B:GLN153 3.1 19.0 0.5
CG B:HIS438 3.2 21.1 1.0
CD2 B:HIS154 3.2 14.0 1.0
NE2 B:HIS438 3.5 24.2 1.0
CG B:GLN153 3.8 13.0 0.5
CD2 B:HIS438 4.0 23.6 1.0
CB B:HIS438 4.0 18.3 1.0
ND1 B:HIS154 4.1 17.4 1.0
CG2 B:VAL321 4.2 11.3 0.5
CG B:HIS154 4.2 11.8 1.0
CG1 B:VAL321 4.3 11.2 0.5
CD B:GLN153 4.4 16.8 0.5
CA B:HIS438 4.5 16.8 1.0
CB B:GLN153 4.7 12.1 1.0
CD1 B:ILE356 4.9 19.3 1.0

Reference:

T.Nagy, D.Nurizzo, G.J.Davies, P.Biely, J.H.Lakey, D.N.Bolam, H.J.Gilbert. The Alpha-Glucuronidase,GLCA67A,of Cellvibrio Japonicus Utilizes the Carboxylate and Methyl Groups of Aldobiouronic Acid As Important Substrate Recognition Determinants J.Biol.Chem. V. 278 20286 2003.
ISSN: ISSN 0021-9258
PubMed: 12654910
DOI: 10.1074/JBC.M302205200
Page generated: Tue Jul 30 14:18:55 2024

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