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Cobalt in PDB 1gql: Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose

Enzymatic activity of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose

All present enzymatic activity of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose:
3.2.1.139;

Protein crystallography data

The structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose, PDB code: 1gql 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 / 1.67
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.256, 74.323, 87.273, 115.15, 92.94, 109.24
R / Rfree (%) 14.6 / 17.2

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 1gql

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Cobalt binding site 1 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1714

b:17.7
occ:0.50
 OG1 A:THR629 3.0 13.8 1.0
O A:HOH2624 3.1 16.8 1.0
O A:HOH2704 3.3 16.6 1.0
O A:HOH2514 3.5 16.7 1.0
O A:ALA625 3.7 12.2 1.0
CB A:MET502 3.7 12.6 1.0
CB A:THR629 3.7 12.2 1.0
CA A:MET502 3.8 12.1 1.0
CA A:MET626 3.8 11.2 1.0
CG A:MET502 3.8 13.4 1.0
C A:ALA625 3.9 11.9 1.0
N A:MET626 3.9 11.6 1.0
CG A:MET626 4.1 13.3 1.0
CG2 A:THR629 4.2 14.1 1.0
O A:HOH2625 4.3 16.6 1.0
N A:MET502 4.4 13.1 1.0
CB A:ALA625 4.5 12.7 1.0
CB A:MET626 4.5 12.1 1.0
CG1 A:VAL505 4.7 9.5 0.5
O A:HOH2631 4.8 27.8 1.0
O A:HOH2225 4.8 36.7 1.0
CA A:ALA625 4.8 12.1 1.0
C A:MET626 4.9 11.3 1.0
O A:HOH2272 5.0 20.2 1.0

Cobalt binding site 2 out of 8 in 1gql

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Cobalt binding site 2 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1715

b:13.8
occ:0.50
 O A:HOH2652 3.0 17.3 1.0
O A:HOH2489 3.0 11.7 1.0
ND2 A:ASN452 3.3 13.2 1.0
CB A:ASN452 3.6 10.0 1.0
CB A:PRO457 3.6 11.9 1.0
CA A:GLY7 3.6 12.7 1.0
CG A:PRO457 3.6 12.5 1.0
CD A:ARG641 3.7 12.9 1.0
NE2 A:GLN460 3.7 15.8 1.0
CG A:ASN452 4.0 12.3 1.0
CA A:PRO457 4.0 11.7 1.0
CG A:ARG641 4.1 11.7 1.0
N A:GLY7 4.1 13.2 1.0
O A:ASP6 4.4 14.8 1.0
CD A:GLN460 4.4 14.4 1.0
C A:ASP6 4.4 15.4 1.0
OE1 A:GLN644 4.4 18.9 1.0
OE1 A:GLN460 4.4 12.9 1.0
CD A:PRO457 4.7 11.5 1.0
C A:GLY7 4.7 12.6 1.0
N A:PRO457 4.8 10.9 1.0
O A:HOH2007 4.9 17.9 1.0
CA A:ASN452 4.9 9.9 1.0
O A:GLY7 5.0 13.3 1.0

Cobalt binding site 3 out of 8 in 1gql

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Cobalt binding site 3 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1716

b:20.8
occ:0.50
 NH1 A:ARG673 3.3 22.3 1.0
ND2 A:ASN607 3.4 19.5 1.0
CD1 A:TRP609 3.7 16.4 1.0
CD A:ARG673 3.8 22.6 1.0
OD1 A:ASN607 4.1 15.6 1.0
CG A:ASN607 4.2 16.2 1.0
CZ A:ARG673 4.3 20.2 1.0
NE2 A:GLN610 4.3 21.9 1.0
CG A:ARG673 4.3 23.2 1.0
CB A:ARG673 4.3 23.1 1.0
NE A:ARG673 4.5 21.8 1.0
CG A:TRP609 4.5 14.2 1.0
CB A:TRP609 4.6 15.8 1.0
CG A:GLN610 4.6 17.5 1.0
NE1 A:TRP609 4.6 16.0 1.0
CD A:GLN610 4.6 19.3 1.0
CD A:PRO674 4.8 26.2 1.0

Cobalt binding site 4 out of 8 in 1gql

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Cobalt binding site 4 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1717

b:16.6
occ:0.50
 O A:HOH2705 3.1 24.9 1.0
O A:HOH2696 3.2 24.1 1.0
ND2 A:ASN162 3.3 12.3 1.0
ND2 A:ASN164 3.4 16.0 1.0
CD1 A:TRP702 3.7 15.9 1.0
CB A:VAL166 3.8 11.2 1.0
CG1 A:VAL166 4.0 13.7 1.0
OD1 A:ASN164 4.0 12.5 1.0
CG A:ASN164 4.1 13.4 1.0
NE1 A:TRP702 4.2 15.3 1.0
CG A:ASN162 4.3 11.4 1.0
CG2 A:VAL166 4.4 11.2 1.0
CB A:ASN162 4.5 8.9 1.0
O A:HOH2213 4.7 18.5 1.0
O B:HOH2703 4.9 22.1 1.0
CG A:TRP702 4.9 14.1 1.0
O A:HOH2695 5.0 23.3 1.0

Cobalt binding site 5 out of 8 in 1gql

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Cobalt binding site 5 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1714

b:17.0
occ:0.50
 OG1 B:THR629 3.0 14.2 1.0
O B:HOH2621 3.1 15.1 1.0
O B:HOH2714 3.3 18.9 1.0
O B:HOH2509 3.5 17.2 1.0
O B:ALA625 3.7 13.1 1.0
CB B:THR629 3.7 13.1 1.0
CA B:MET626 3.8 11.9 1.0
CB B:MET502 3.8 12.8 1.0
CA B:MET502 3.8 12.2 1.0
N B:MET626 3.8 12.1 1.0
C B:ALA625 3.9 12.5 1.0
CG B:MET502 3.9 13.4 1.0
CG B:MET626 4.0 13.2 1.0
CG2 B:THR629 4.2 13.8 1.0
O B:HOH2625 4.3 16.3 1.0
N B:MET502 4.4 12.7 1.0
CB B:MET626 4.5 12.9 1.0
CB B:ALA625 4.5 12.5 1.0
CG1 B:VAL505 4.6 18.0 1.0
O B:HOH2631 4.8 26.3 1.0
CA B:ALA625 4.8 12.1 1.0
C B:MET626 4.9 12.2 1.0
O B:HOH2229 4.9 35.9 1.0
O B:HOH2261 5.0 20.2 1.0

Cobalt binding site 6 out of 8 in 1gql

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Cobalt binding site 6 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1715

b:14.3
occ:0.50
 O B:HOH2654 3.0 15.7 1.0
O B:HOH2481 3.1 11.8 1.0
ND2 B:ASN452 3.3 10.7 1.0
CB B:ASN452 3.5 10.2 1.0
CA B:GLY7 3.6 12.5 1.0
CB B:PRO457 3.6 11.8 1.0
CG B:PRO457 3.6 10.4 1.0
NE2 B:GLN460 3.7 14.5 1.0
CD B:ARG641 3.7 13.3 1.0
CG B:ASN452 3.9 11.0 1.0
CA B:PRO457 4.0 10.9 1.0
N B:GLY7 4.1 12.7 1.0
CG B:ARG641 4.1 11.8 1.0
O B:ASP6 4.3 14.0 1.0
C B:ASP6 4.4 14.9 1.0
CD B:GLN460 4.4 13.0 1.0
OE1 B:GLN644 4.4 19.8 1.0
OE1 B:GLN460 4.5 11.9 1.0
CD B:PRO457 4.7 11.4 1.0
C B:GLY7 4.7 12.6 1.0
N B:PRO457 4.8 10.3 1.0
O B:HOH2006 4.8 16.7 1.0
CA B:ASN452 4.9 9.9 1.0
O B:GLY7 4.9 12.4 1.0

Cobalt binding site 7 out of 8 in 1gql

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Cobalt binding site 7 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1716

b:17.1
occ:0.50
 O B:HOH2715 3.0 32.4 1.0
O B:HOH2717 3.2 27.0 1.0
O B:HOH2706 3.2 22.8 1.0
ND2 B:ASN162 3.3 12.5 1.0
ND2 B:ASN164 3.3 16.1 1.0
O B:HOH2716 3.4 34.5 1.0
CD1 B:TRP702 3.8 15.4 1.0
CB B:VAL166 3.8 11.6 1.0
CG1 B:VAL166 3.9 12.1 1.0
OD1 B:ASN164 4.0 10.4 1.0
CG B:ASN164 4.1 13.6 1.0
NE1 B:TRP702 4.2 13.6 1.0
CG B:ASN162 4.3 10.9 1.0
CG2 B:VAL166 4.3 13.2 1.0
CB B:ASN162 4.6 8.8 1.0
O B:HOH2220 4.7 16.5 1.0
O A:HOH2695 4.9 23.3 1.0
CG B:TRP702 4.9 14.1 1.0
O B:HOH2703 5.0 22.1 1.0
O B:VAL166 5.0 11.9 1.0

Cobalt binding site 8 out of 8 in 1gql

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Cobalt binding site 8 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid and Xylotriose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1717

b:21.8
occ:0.50
 NH1 B:ARG673 3.3 23.0 1.0
O B:HOH2675 3.3 31.9 1.0
ND2 B:ASN607 3.4 17.1 1.0
CD1 B:TRP609 3.7 16.8 1.0
CD B:ARG673 3.7 21.1 1.0
CG B:ARG673 4.2 22.2 1.0
OD1 B:ASN607 4.2 17.1 1.0
CB B:ARG673 4.2 22.9 1.0
CG B:ASN607 4.3 18.1 1.0
CZ B:ARG673 4.3 21.9 1.0
NE2 B:GLN610 4.3 23.2 1.0
NE B:ARG673 4.4 19.9 1.0
CG B:TRP609 4.5 14.0 1.0
CG B:GLN610 4.6 16.4 1.0
CB B:TRP609 4.6 14.1 1.0
NE1 B:TRP609 4.6 17.6 1.0
CD B:GLN610 4.7 19.3 1.0
CD B:PRO674 4.8 26.4 1.0

Reference:

D.Nurizzo, T.Nagy, H.J.Gilbert, G.J.Davies. The Structural Basis For Catalysis and Specificity of the Pseudomonas Cellulosa Alpha-Glucuronidase, GLCA67A Structure V. 10 547 2002.
ISSN: ISSN 0969-2126
PubMed: 11937059
DOI: 10.1016/S0969-2126(02)00742-6
Page generated: Tue Jul 30 14:17:15 2024

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