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Cobalt in PDB 1gqj: Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Xylobiose

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

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

Protein crystallography data

The structure of Structure of Pseudomonas Cellulosa Alpha-D-Glucuronidase Complexed with Xylobiose, PDB code: 1gqj 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 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 69.561, 74.609, 87.450, 115.23, 93.15, 109.17
R / Rfree (%) 17.2 / 22.1

Cobalt Binding Sites:

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

Cobalt binding site 1 out of 8 in 1gqj

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


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

b:22.4
occ:0.50
 OG1 A:THR629 2.9 15.3 1.0
O A:HOH2583 3.2 18.6 1.0
O A:HOH2475 3.4 21.6 1.0
O A:HOH2683 3.5 18.3 1.0
CB A:THR629 3.6 15.6 1.0
O A:ALA625 3.7 14.6 1.0
CB A:MET502 3.8 17.0 1.0
CA A:MET502 3.8 16.9 1.0
CA A:MET626 3.8 16.0 1.0
CG A:MET502 3.8 15.4 1.0
C A:ALA625 3.9 15.0 1.0
N A:MET626 3.9 15.3 1.0
CG2 A:THR629 4.0 14.0 1.0
CG A:MET626 4.2 20.4 1.0
O A:HOH2585 4.2 22.9 1.0
N A:MET502 4.3 17.5 1.0
CB A:ALA625 4.5 15.3 1.0
CB A:MET626 4.5 15.7 1.0
CG1 A:VAL505 4.6 17.4 1.0
O A:HOH2592 4.6 27.8 1.0
CA A:ALA625 4.8 15.1 1.0
C A:MET626 4.9 15.8 1.0

Cobalt binding site 2 out of 8 in 1gqj

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


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

b:20.4
occ:0.50
 O A:HOH2613 2.8 20.0 1.0
O A:HOH2454 3.1 14.7 1.0
ND2 A:ASN452 3.3 12.0 1.0
CB A:ASN452 3.4 15.7 1.0
CA A:GLY7 3.5 15.7 1.0
CB A:PRO457 3.6 13.8 1.0
CG A:PRO457 3.6 12.6 1.0
NE2 A:GLN460 3.7 15.4 1.0
CD A:ARG641 3.7 16.6 1.0
CG A:ASN452 3.9 15.1 1.0
CA A:PRO457 4.0 13.8 1.0
N A:GLY7 4.0 16.6 1.0
CG A:ARG641 4.1 14.9 1.0
C A:ASP6 4.3 16.9 1.0
O A:ASP6 4.4 16.9 1.0
CD A:GLN460 4.4 11.3 1.0
OE1 A:GLN644 4.4 19.2 1.0
OE1 A:GLN460 4.4 14.7 1.0
O A:HOH2009 4.7 22.7 1.0
C A:GLY7 4.8 14.8 1.0
CD A:PRO457 4.8 12.9 1.0
N A:PRO457 4.8 13.7 1.0
CA A:ASN452 4.8 15.4 1.0
O A:GLY7 5.0 14.6 1.0

Cobalt binding site 3 out of 8 in 1gqj

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


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

b:22.4
occ:0.50
 NH1 A:ARG673 3.3 28.4 1.0
ND2 A:ASN607 3.4 21.5 1.0
CD1 A:TRP609 3.7 19.7 1.0
CD A:ARG673 3.7 26.9 1.0
OD1 A:ASN607 4.0 19.1 1.0
O A:HOH2231 4.1 43.5 1.0
CG A:ASN607 4.1 20.9 1.0
NE2 A:GLN610 4.2 19.6 1.0
CG A:ARG673 4.3 28.1 1.0
CZ A:ARG673 4.3 27.8 1.0
CB A:ARG673 4.4 27.1 1.0
NE A:ARG673 4.4 27.9 1.0
CG A:TRP609 4.5 17.5 1.0
CD A:GLN610 4.5 19.4 1.0
CG A:GLN610 4.5 16.6 1.0
CB A:TRP609 4.5 16.7 1.0
NE1 A:TRP609 4.6 20.9 1.0
CD A:PRO674 5.0 28.8 1.0

Cobalt binding site 4 out of 8 in 1gqj

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


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 Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1724

b:23.9
occ:0.50
 O A:HOH2684 2.7 31.5 1.0
ND2 A:ASN162 3.1 14.8 1.0
ND2 A:ASN164 3.4 14.0 1.0
CD1 A:TRP702 3.5 20.2 1.0
CB A:VAL166 3.8 15.1 1.0
CG1 A:VAL166 3.8 15.2 1.0
OD1 A:ASN164 3.9 13.0 1.0
NE1 A:TRP702 4.0 18.8 1.0
CG A:ASN164 4.1 13.6 1.0
CG A:ASN162 4.2 14.6 1.0
CB A:ASN162 4.4 13.7 1.0
CG2 A:VAL166 4.5 16.5 1.0
CG A:TRP702 4.8 18.0 1.0
O A:HOH2185 4.8 18.9 1.0
O B:HOH2673 4.9 19.6 1.0
O A:VAL166 4.9 15.2 1.0
OG B:SER707 4.9 20.5 1.0

Cobalt binding site 5 out of 8 in 1gqj

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


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

b:22.1
occ:0.50
 OG1 B:THR629 3.1 16.8 1.0
O B:HOH2698 3.2 17.8 1.0
O B:HOH2594 3.2 21.3 1.0
O B:HOH2479 3.3 20.4 1.0
O B:ALA625 3.7 16.2 1.0
CB B:THR629 3.7 17.4 1.0
CA B:MET626 3.8 17.1 1.0
CA B:MET502 3.8 16.4 1.0
CG B:MET502 3.8 17.9 1.0
CB B:MET502 3.8 16.9 1.0
C B:ALA625 3.8 15.9 1.0
N B:MET626 3.9 16.8 1.0
CG B:MET626 4.1 15.0 0.5
CG B:MET626 4.1 18.7 0.5
CG2 B:THR629 4.2 16.7 1.0
O B:HOH2596 4.3 20.1 1.0
N B:MET502 4.4 17.7 1.0
CB B:ALA625 4.5 16.2 1.0
CB B:MET626 4.5 17.0 1.0
CG1 B:VAL505 4.6 18.3 1.0
O B:HOH2203 4.8 35.9 1.0
CA B:ALA625 4.8 15.5 1.0
O B:HOH2603 4.9 31.1 1.0
C B:MET626 4.9 17.5 1.0
O B:HOH2246 5.0 22.2 1.0

Cobalt binding site 6 out of 8 in 1gqj

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


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

b:19.9
occ:0.50
 O B:HOH2622 2.9 16.8 1.0
O B:HOH2452 3.1 15.5 1.0
ND2 B:ASN452 3.3 14.8 1.0
CB B:ASN452 3.5 14.2 1.0
CG B:PRO457 3.6 15.3 1.0
CA B:GLY7 3.6 15.6 1.0
CB B:PRO457 3.6 15.9 1.0
CD B:ARG641 3.7 15.7 1.0
NE2 B:GLN460 3.8 15.9 1.0
CG B:ASN452 3.9 14.3 1.0
CA B:PRO457 4.0 15.3 1.0
N B:GLY7 4.1 16.0 1.0
CG B:ARG641 4.1 15.4 1.0
OE1 B:GLN644 4.4 18.7 1.0
C B:ASP6 4.4 17.1 1.0
CD B:GLN460 4.4 16.3 1.0
O B:ASP6 4.5 16.9 1.0
OE1 B:GLN460 4.5 15.1 1.0
O B:HOH2011 4.6 20.4 1.0
CD B:PRO457 4.7 14.9 1.0
C B:GLY7 4.8 14.8 1.0
N B:PRO457 4.8 14.9 1.0
CA B:ASN452 4.9 14.3 1.0
O B:GLY7 5.0 14.0 1.0

Cobalt binding site 7 out of 8 in 1gqj

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


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

b:20.9
occ:0.50
 O B:HOH2699 2.7 27.6 1.0
ND2 B:ASN162 3.2 17.8 1.0
ND2 B:ASN164 3.4 16.0 1.0
CD1 B:TRP702 3.6 17.9 1.0
CB B:VAL166 3.8 15.4 1.0
CG1 B:VAL166 3.8 14.5 1.0
OD1 B:ASN164 4.0 15.9 1.0
NE1 B:TRP702 4.0 18.4 1.0
CG B:ASN164 4.1 16.8 1.0
CG B:ASN162 4.3 15.6 1.0
CG2 B:VAL166 4.4 15.7 1.0
CB B:ASN162 4.5 15.0 1.0
CG B:TRP702 4.8 18.6 1.0
O B:HOH2198 4.8 23.6 1.0
O A:HOH2662 4.8 20.0 1.0
OG A:SER707 4.9 20.4 1.0
O B:VAL166 4.9 14.2 1.0
CA B:VAL166 5.0 14.8 1.0

Cobalt binding site 8 out of 8 in 1gqj

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


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 Xylobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1724

b:23.1
occ:0.50
 NH1 B:ARG673 3.2 30.3 1.0
ND2 B:ASN607 3.5 19.8 1.0
CD1 B:TRP609 3.6 20.1 1.0
CD B:ARG673 3.7 27.7 1.0
CZ B:ARG673 4.2 28.9 1.0
OD1 B:ASN607 4.2 19.4 1.0
CG B:ARG673 4.3 29.3 1.0
CG B:ASN607 4.3 20.9 1.0
CB B:ARG673 4.3 29.9 1.0
NE B:ARG673 4.4 28.6 1.0
CG B:TRP609 4.4 17.5 1.0
NE2 B:GLN610 4.4 19.5 1.0
NE1 B:TRP609 4.5 21.4 1.0
CB B:TRP609 4.6 18.9 1.0
CG B:GLN610 4.6 18.5 1.0
CD B:GLN610 4.7 21.0 1.0
CD B:PRO674 4.7 30.9 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 14:17:14 2024

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