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Cobalt in PDB 1gqi: Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase

Enzymatic activity of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase

All present enzymatic activity of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase:
3.2.1.139;

Protein crystallography data

The structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase, PDB code: 1gqi 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 / 1.48
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.912, 74.682, 87.587, 115.18, 93.14, 109.33
R / Rfree (%) 13.3 / 16.8

Other elements in 1gqi:

The structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 1gqi

Go back to Cobalt Binding Sites List in 1gqi
Cobalt binding site 1 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1719

b:11.4
occ:0.50
 OG1 A:THR629 3.1 9.6 1.0
O A:HOH2760 3.2 11.8 1.0
O A:HOH2888 3.3 11.4 1.0
O A:HOH2624 3.3 14.5 1.0
O A:ALA625 3.8 8.5 1.0
CA A:MET502 3.8 7.4 1.0
CB A:THR629 3.8 7.7 1.0
CB A:MET502 3.8 9.1 1.0
CA A:MET626 3.8 7.9 1.0
N A:MET626 3.9 7.9 1.0
C A:ALA625 4.0 7.8 1.0
CG A:MET502 4.0 9.6 1.0
CG A:MET626 4.0 8.8 1.0
CG2 A:THR629 4.3 9.6 1.0
N A:MET502 4.4 8.2 1.0
O A:HOH2763 4.4 11.4 1.0
CB A:MET626 4.5 7.4 1.0
CB A:ALA625 4.5 7.5 1.0
CG1 A:VAL505 4.6 11.2 1.0
O A:HOH2770 4.9 22.9 1.0
CA A:ALA625 4.9 7.6 1.0
C A:MET626 5.0 6.5 1.0
C A:GLN501 5.0 9.1 1.0

Cobalt binding site 2 out of 8 in 1gqi

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


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

b:10.3
occ:0.50
 O A:HOH2793 3.0 14.9 1.0
O A:HOH2598 3.0 8.6 1.0
ND2 A:ASN452 3.3 9.9 1.0
CB A:ASN452 3.6 5.5 1.0
CB A:PRO457 3.6 7.6 1.0
CA A:GLY7 3.6 8.0 1.0
CG A:PRO457 3.6 8.1 1.0
NE2 A:GLN460 3.7 12.8 1.0
CD A:ARG641 3.8 9.0 1.0
CG A:ASN452 4.0 7.8 1.0
CA A:PRO457 4.1 6.0 1.0
N A:GLY7 4.1 8.5 1.0
CG A:ARG641 4.2 8.5 1.0
OE1 A:GLN644 4.4 14.9 1.0
O A:ASP6 4.4 9.6 1.0
CD A:GLN460 4.4 8.7 1.0
C A:ASP6 4.4 9.4 1.0
OE1 A:GLN460 4.5 7.5 1.0
CD A:PRO457 4.8 7.3 1.0
O A:HOH2011 4.8 14.7 1.0
C A:GLY7 4.8 7.3 1.0
N A:PRO457 4.8 6.5 1.0
CA A:ASN452 4.9 5.7 1.0

Cobalt binding site 3 out of 8 in 1gqi

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


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

b:15.8
occ:0.50
 O A:HOH2819 3.2 24.3 1.0
NH1 A:ARG673 3.3 15.9 1.0
ND2 A:ASN607 3.4 11.0 1.0
CD1 A:TRP609 3.7 9.8 1.0
CD A:ARG673 3.8 15.2 1.0
NE2 A:GLN610 4.1 19.3 1.0
OD1 A:ASN607 4.2 11.0 1.0
CG A:ASN607 4.2 9.8 1.0
CB A:ARG673 4.3 14.3 1.0
CG A:ARG673 4.3 15.5 1.0
CZ A:ARG673 4.3 14.4 1.0
CG A:GLN610 4.4 10.3 1.0
CG A:TRP609 4.5 8.7 1.0
NE A:ARG673 4.5 15.5 1.0
CD A:GLN610 4.6 14.0 1.0
NE1 A:TRP609 4.6 10.5 1.0
CB A:TRP609 4.6 9.3 1.0
CD A:PRO674 4.9 18.4 1.0

Cobalt binding site 4 out of 8 in 1gqi

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


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

b:14.8
occ:0.50
 O A:HOH2890 2.8 19.9 1.0
O A:HOH2889 3.0 27.9 1.0
O B:HOH2855 3.2 22.0 1.0
ND2 A:ASN162 3.3 9.5 1.0
ND2 A:ASN164 3.3 9.1 1.0
CD1 A:TRP702 3.7 8.7 1.0
CB A:VAL166 3.9 7.3 1.0
CG1 A:VAL166 3.9 7.5 1.0
OD1 A:ASN164 4.0 8.4 1.0
NE1 A:TRP702 4.1 9.2 1.0
CG A:ASN164 4.1 7.5 1.0
CG A:ASN162 4.3 7.1 1.0
CG2 A:VAL166 4.5 7.8 1.0
O A:HOH2864 4.5 25.9 1.0
CB A:ASN162 4.6 6.5 1.0
O A:HOH2265 4.8 15.3 1.0
CG A:TRP702 4.9 7.4 1.0
OG B:SER707 4.9 12.6 1.0
O B:HOH2849 5.0 13.7 1.0

Cobalt binding site 5 out of 8 in 1gqi

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1719

b:11.6
occ:0.50
 OG1 B:THR629 3.1 10.5 1.0
O B:HOH2751 3.2 12.4 1.0
O B:HOH2874 3.3 11.5 1.0
O B:HOH2621 3.3 14.0 1.0
CA B:MET502 3.8 8.7 1.0
O B:ALA625 3.8 8.7 1.0
CB B:MET502 3.8 8.6 1.0
CA B:MET626 3.8 7.3 1.0
CB B:THR629 3.8 8.7 1.0
N B:MET626 3.9 8.0 1.0
O B:HOH2626 3.9 40.0 1.0
CG B:MET502 4.0 8.9 1.0
C B:ALA625 4.0 7.7 1.0
CG B:MET626 4.0 6.4 0.5
CG B:MET626 4.1 10.7 0.5
CG2 B:THR629 4.3 10.0 1.0
N B:MET502 4.4 7.7 1.0
O B:HOH2755 4.4 12.3 1.0
CB B:ALA625 4.5 8.0 1.0
CB B:MET626 4.5 7.6 1.0
CG1 B:VAL505 4.6 12.0 1.0
CA B:ALA625 4.9 7.5 1.0
O B:HOH2764 4.9 21.5 1.0
C B:MET626 5.0 6.6 1.0

Cobalt binding site 6 out of 8 in 1gqi

Go back to Cobalt Binding Sites List in 1gqi
Cobalt binding site 6 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase


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

b:10.5
occ:0.50
 O B:HOH2786 3.0 15.4 1.0
O B:HOH2591 3.0 8.9 1.0
ND2 B:ASN452 3.4 8.8 1.0
CB B:ASN452 3.6 5.5 1.0
CA B:GLY7 3.6 8.9 1.0
CB B:PRO457 3.6 7.5 1.0
CG B:PRO457 3.7 8.2 1.0
NE2 B:GLN460 3.7 12.0 1.0
CD B:ARG641 3.7 10.0 1.0
CG B:ASN452 4.0 6.8 1.0
CA B:PRO457 4.1 7.0 1.0
N B:GLY7 4.1 9.1 1.0
CG B:ARG641 4.1 9.0 1.0
O B:ASP6 4.4 10.5 1.0
C B:ASP6 4.4 10.2 1.0
CD B:GLN460 4.4 8.6 1.0
OE1 B:GLN460 4.4 9.1 1.0
OE1 B:GLN644 4.5 15.6 1.0
CD B:PRO457 4.8 8.1 1.0
O B:HOH2010 4.8 13.9 1.0
C B:GLY7 4.8 7.7 1.0
N B:PRO457 4.8 7.0 1.0
CA B:ASN452 4.9 5.1 1.0

Cobalt binding site 7 out of 8 in 1gqi

Go back to Cobalt Binding Sites List in 1gqi
Cobalt binding site 7 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase


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

b:14.3
occ:0.50
 O B:HOH2876 2.8 19.4 1.0
O B:HOH2875 3.0 28.9 1.0
O A:HOH2872 3.1 25.2 1.0
ND2 B:ASN162 3.3 9.5 1.0
ND2 B:ASN164 3.4 10.3 1.0
CD1 B:TRP702 3.7 9.4 1.0
CB B:VAL166 3.9 7.2 1.0
CG1 B:VAL166 3.9 9.4 1.0
OD1 B:ASN164 4.0 7.9 1.0
NE1 B:TRP702 4.1 9.9 1.0
CG B:ASN164 4.1 7.4 1.0
CG B:ASN162 4.3 6.9 1.0
CG2 B:VAL166 4.5 8.1 1.0
O B:HOH2850 4.5 26.9 1.0
CB B:ASN162 4.6 6.2 1.0
O B:HOH2264 4.8 15.1 1.0
OG A:SER707 4.9 12.4 1.0
CG B:TRP702 4.9 7.7 1.0
O A:HOH2862 5.0 16.3 1.0

Cobalt binding site 8 out of 8 in 1gqi

Go back to Cobalt Binding Sites List in 1gqi
Cobalt binding site 8 out of 8 in the Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase


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

b:16.6
occ:0.50
 O B:HOH2811 3.2 29.5 1.0
ND2 B:ASN607 3.3 13.3 1.0
NH1 B:ARG673 3.4 18.3 1.0
CD1 B:TRP609 3.7 10.9 1.0
CD B:ARG673 3.8 18.6 1.0
OD1 B:ASN607 4.2 12.1 1.0
CG B:ASN607 4.2 12.0 1.0
NE2 B:GLN610 4.2 16.2 1.0
CB B:ARG673 4.4 19.1 1.0
CG B:ARG673 4.4 18.6 1.0
CZ B:ARG673 4.4 17.3 1.0
CG B:TRP609 4.5 9.9 1.0
CG B:GLN610 4.5 11.3 1.0
NE1 B:TRP609 4.6 12.5 1.0
NE B:ARG673 4.6 18.1 1.0
CB B:TRP609 4.6 10.6 1.0
CD B:GLN610 4.6 12.5 1.0
CD B:PRO674 5.0 21.6 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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