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

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

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

Protein crystallography data

The structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid, PDB code: 1gqk 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) 19.73 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.707, 74.879, 87.481, 115.34, 93.06, 109.20
R / Rfree (%) 15.1 / 18.6

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Glucuronic Acid (pdb code 1gqk). 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, PDB code: 1gqk:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1720

b:22.2
occ:0.50
 OG1 A:THR629 3.0 14.0 1.0
O A:HOH2546 3.1 20.6 1.0
O A:HOH2439 3.4 23.2 1.0
O A:HOH2649 3.5 17.6 1.0
O A:ALA625 3.6 13.9 1.0
CB A:THR629 3.7 15.1 1.0
CA A:MET626 3.8 14.6 1.0
CA A:MET502 3.8 16.0 1.0
CB A:MET502 3.8 15.6 1.0
C A:ALA625 3.8 13.2 1.0
N A:MET626 3.9 13.9 1.0
CG A:MET502 3.9 15.8 1.0
CG A:MET626 4.1 17.4 1.0
CG2 A:THR629 4.2 14.8 1.0
N A:MET502 4.4 16.2 1.0
CB A:ALA625 4.5 12.2 1.0
O A:HOH2547 4.5 19.4 1.0
CB A:MET626 4.5 14.4 1.0
CG1 A:VAL505 4.5 18.2 1.0
CA A:ALA625 4.8 13.4 1.0
O A:HOH2170 4.8 39.1 1.0
O A:HOH2554 4.8 24.1 1.0
C A:MET626 4.9 14.1 1.0

Cobalt binding site 2 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1721

b:17.6
occ:0.50
 O A:HOH2572 2.9 20.5 1.0
O A:HOH2412 3.0 13.9 1.0
ND2 A:ASN452 3.3 16.3 1.0
CB A:ASN452 3.5 13.5 1.0
CB A:PRO457 3.6 13.4 1.0
CG A:PRO457 3.6 12.4 1.0
CA A:GLY7 3.7 16.3 1.0
NE2 A:GLN460 3.7 20.4 1.0
CD A:ARG641 3.8 13.1 1.0
CG A:ASN452 3.9 15.1 1.0
CA A:PRO457 4.0 13.4 1.0
N A:GLY7 4.2 17.6 1.0
CG A:ARG641 4.2 12.0 1.0
OE1 A:GLN644 4.3 17.5 1.0
CD A:GLN460 4.4 15.1 1.0
OE1 A:GLN460 4.5 13.9 1.0
O A:ASP6 4.5 18.4 1.0
C A:ASP6 4.5 18.6 1.0
CD A:PRO457 4.6 11.8 1.0
N A:PRO457 4.7 13.6 1.0
O A:HOH2010 4.7 24.8 1.0
C A:GLY7 4.8 15.8 1.0
CA A:ASN452 4.9 13.5 1.0
O A:GLY7 5.0 15.7 1.0

Cobalt binding site 3 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1722

b:19.4
occ:0.50
 NH1 A:ARG673 3.4 22.9 1.0
ND2 A:ASN607 3.4 17.8 1.0
CD A:ARG673 3.6 24.3 1.0
CD1 A:TRP609 3.7 17.7 1.0
CG A:ARG673 4.2 24.0 1.0
NE2 A:GLN610 4.2 24.3 1.0
CB A:ARG673 4.2 23.6 1.0
CZ A:ARG673 4.3 22.5 1.0
CG A:ASN607 4.3 18.6 1.0
NE A:ARG673 4.4 23.3 1.0
OD1 A:ASN607 4.4 14.5 1.0
CG A:TRP609 4.4 16.0 1.0
CG A:GLN610 4.5 21.0 1.0
CB A:TRP609 4.5 16.4 1.0
CD A:GLN610 4.6 23.4 1.0
NE1 A:TRP609 4.6 17.5 1.0
CD A:PRO674 5.0 25.9 1.0

Cobalt binding site 4 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1723

b:28.1
occ:0.50
 O A:HOH2650 2.7 22.5 1.0
ND2 A:ASN162 3.2 15.8 1.0
ND2 A:ASN164 3.3 17.8 1.0
CD1 A:TRP702 3.6 19.6 1.0
CB A:VAL166 3.8 15.3 1.0
OD1 A:ASN164 3.8 14.0 1.0
NE1 A:TRP702 3.9 18.2 1.0
CG A:ASN164 3.9 14.7 1.0
CG1 A:VAL166 3.9 16.6 1.0
CG A:ASN162 4.2 16.3 1.0
CB A:ASN162 4.4 14.9 1.0
O A:HOH2628 4.4 41.5 1.0
CG2 A:VAL166 4.5 16.6 1.0
OG B:SER707 4.8 18.8 1.0
CG A:TRP702 4.8 17.3 1.0
O A:VAL166 4.8 14.2 1.0
O A:HOH2157 4.9 25.0 1.0
O B:HOH2609 5.0 19.7 1.0
CA A:VAL166 5.0 14.6 1.0

Cobalt binding site 5 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1720

b:22.7
occ:0.50
 OG1 B:THR629 3.0 13.7 1.0
O B:HOH2528 3.2 20.1 1.0
O B:HOH2634 3.4 16.5 1.0
O B:HOH2428 3.4 23.6 1.0
CB B:THR629 3.7 14.5 1.0
O B:ALA625 3.7 14.5 1.0
CB B:MET502 3.7 15.6 1.0
CA B:MET626 3.8 14.7 1.0
CA B:MET502 3.8 16.0 1.0
CG B:MET502 3.8 18.1 1.0
C B:ALA625 3.8 14.7 1.0
N B:MET626 3.9 14.6 1.0
CG B:MET626 4.1 13.0 0.5
CG B:MET626 4.1 15.6 0.5
CG2 B:THR629 4.1 16.2 1.0
O B:HOH2530 4.2 19.2 1.0
N B:MET502 4.4 15.4 1.0
CB B:MET626 4.5 15.3 1.0
CB B:ALA625 4.5 14.9 1.0
CG1 B:VAL505 4.6 19.2 1.0
O B:HOH2162 4.7 34.9 1.0
O B:HOH2537 4.8 25.0 1.0
CA B:ALA625 4.8 14.8 1.0
C B:MET626 4.9 15.7 1.0
O B:HOH2203 5.0 19.8 1.0

Cobalt binding site 6 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1721

b:18.1
occ:0.50
 O B:HOH2402 3.0 13.3 1.0
O B:HOH2556 3.0 18.0 1.0
ND2 B:ASN452 3.3 14.9 1.0
CB B:ASN452 3.5 14.6 1.0
NE2 B:GLN460 3.6 19.2 1.0
CA B:GLY7 3.6 17.5 1.0
CB B:PRO457 3.7 14.0 1.0
CG B:PRO457 3.7 13.5 1.0
CD B:ARG641 3.9 16.1 1.0
CG B:ASN452 3.9 13.6 1.0
CA B:PRO457 4.0 13.4 1.0
N B:GLY7 4.1 18.0 1.0
CG B:ARG641 4.3 13.6 1.0
CD B:GLN460 4.3 18.4 1.0
OE1 B:GLN460 4.4 17.8 1.0
O B:ASP6 4.4 19.4 1.0
C B:ASP6 4.4 19.9 1.0
OE1 B:GLN644 4.5 17.6 1.0
O B:HOH2010 4.7 25.8 1.0
C B:GLY7 4.7 16.5 1.0
CD B:PRO457 4.8 12.3 1.0
N B:PRO457 4.8 12.9 1.0
CA B:ASN452 4.8 14.2 1.0
O B:GLY7 4.9 16.6 1.0

Cobalt binding site 7 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1722

b:28.4
occ:0.50
 O B:HOH2635 2.7 24.0 1.0
ND2 B:ASN162 3.1 18.0 1.0
ND2 B:ASN164 3.3 18.8 1.0
OD1 B:ASN164 3.7 15.2 1.0
CD1 B:TRP702 3.7 17.6 1.0
CB B:VAL166 3.8 13.8 1.0
CG B:ASN164 3.9 16.3 1.0
CG1 B:VAL166 4.0 16.3 1.0
CG B:ASN162 4.1 17.0 1.0
NE1 B:TRP702 4.1 18.0 1.0
CB B:ASN162 4.2 13.9 1.0
CG2 B:VAL166 4.4 16.9 1.0
O B:HOH2611 4.6 36.6 1.0
O B:VAL166 4.7 13.8 1.0
OG A:SER707 4.8 20.5 1.0
CA B:VAL166 4.9 14.4 1.0
CG B:TRP702 4.9 17.3 1.0
O B:HOH2152 5.0 26.6 1.0

Cobalt binding site 8 out of 8 in 1gqk

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1723

b:22.5
occ:0.50
 NH1 B:ARG673 3.3 26.0 1.0
ND2 B:ASN607 3.4 18.9 1.0
CD1 B:TRP609 3.7 18.2 1.0
CD B:ARG673 3.7 25.4 1.0
OD1 B:ASN607 4.2 15.7 1.0
NE2 B:GLN610 4.2 20.7 1.0
CG B:ASN607 4.2 17.0 1.0
CG B:ARG673 4.3 26.2 1.0
CZ B:ARG673 4.3 23.8 1.0
CB B:ARG673 4.3 26.1 1.0
NE B:ARG673 4.5 24.4 1.0
CG B:TRP609 4.5 16.6 1.0
CG B:GLN610 4.5 18.8 1.0
CD B:GLN610 4.6 21.4 1.0
CB B:TRP609 4.6 17.1 1.0
NE1 B:TRP609 4.6 17.9 1.0
CD B:PRO674 4.9 27.7 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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