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Chlorine in PDB 2qg4: Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate

Enzymatic activity of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate

All present enzymatic activity of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate:
1.1.1.22;

Protein crystallography data

The structure of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate, PDB code: 2qg4 was solved by K.L.Kavanagh, K.Guo, G.Bunkoczi, P.Savitsky, E.Pilka, C.Bhatia, F.Niesen, C.Smee, G.Berridge, F.Von Delft, J.Weigelt, C.H.Arrowsmith, M.Sundstrom, A.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.66 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 193.868, 193.868, 352.223, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.5

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate (pdb code 2qg4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate, PDB code: 2qg4:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 2qg4

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Chlorine binding site 1 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4002

b:10.1
occ:1.00
 O B:HOH5092 3.2 16.2 1.0
N B:MET419 3.5 13.7 1.0
CB B:MET419 3.6 14.5 1.0
CG B:MET419 3.6 11.8 1.0
O B:HOH5325 3.7 32.3 1.0
N B:ASP418 3.9 11.4 1.0
CE3 B:TRP417 3.9 7.7 1.0
CB B:TRP417 4.0 13.0 1.0
SD B:MET419 4.1 21.4 1.0
CA B:MET419 4.1 13.5 1.0
O B:HOH5287 4.2 21.2 1.0
C B:TRP417 4.4 13.5 1.0
CB B:ASP418 4.4 14.0 1.0
C B:ASP418 4.5 13.2 1.0
CA B:ASP418 4.5 12.4 1.0
CA B:TRP417 4.5 13.4 1.0
CD2 B:TRP417 4.5 10.2 1.0
CG B:PRO369 4.5 16.3 1.0
CG B:TRP417 4.7 15.3 1.0
CZ3 B:TRP417 4.7 13.2 1.0
CB B:PRO369 4.9 15.7 1.0

Chlorine binding site 2 out of 8 in 2qg4

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Chlorine binding site 2 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl4005

b:21.7
occ:1.00
 OG1 B:THR213 3.0 16.0 1.0
O B:HOH5379 3.2 28.9 1.0
NE1 B:TRP214 3.6 16.5 1.0
CB B:THR213 3.6 12.5 1.0
N B:THR213 3.6 13.6 1.0
CB B:ASP183 3.6 25.3 1.0
CA B:ASP183 3.6 23.3 1.0
CE2 B:TRP214 3.8 19.1 1.0
CZ2 B:TRP214 3.9 17.2 1.0
N B:ASP183 4.0 20.0 1.0
O B:GLY182 4.0 17.1 1.0
CB B:ASN212 4.1 15.3 1.0
O B:HOH5374 4.2 33.1 1.0
NH1 B:ARG141 4.2 17.8 1.0
CA B:THR213 4.2 13.8 1.0
C B:GLY182 4.2 17.8 1.0
CD1 B:TRP214 4.3 15.3 1.0
CD2 B:TRP214 4.5 16.7 1.0
C B:ASN212 4.6 13.3 1.0
CA B:ASN212 4.6 13.1 1.0
NH2 B:ARG141 4.7 21.1 1.0
CG B:ASN212 4.7 13.7 1.0
CH2 B:TRP214 4.8 18.1 1.0
CG B:TRP214 4.8 15.7 1.0
CZ B:ARG141 4.9 18.4 1.0
N B:TRP214 4.9 10.8 1.0
C B:ASP183 4.9 25.9 1.0
CG2 B:THR213 4.9 10.4 1.0

Chlorine binding site 3 out of 8 in 2qg4

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Chlorine binding site 3 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl4001

b:10.4
occ:1.00
 O D:HOH4143 3.1 17.6 1.0
O D:HOH4305 3.4 22.2 1.0
N D:MET419 3.6 14.4 1.0
CB D:MET419 3.6 16.1 1.0
CG D:MET419 3.7 11.3 1.0
CE3 D:TRP417 3.9 16.3 1.0
SD D:MET419 3.9 16.2 1.0
CB D:TRP417 4.0 16.0 1.0
N D:ASP418 4.0 12.2 1.0
CA D:MET419 4.3 14.5 1.0
O D:HOH4281 4.4 29.1 1.0
C D:TRP417 4.5 13.1 1.0
CB D:ASP418 4.5 13.0 1.0
CG D:PRO369 4.5 11.7 1.0
CD2 D:TRP417 4.5 18.7 1.0
CA D:ASP418 4.6 12.2 1.0
CA D:TRP417 4.6 15.6 1.0
C D:ASP418 4.6 12.4 1.0
CG D:TRP417 4.6 15.6 1.0
CZ3 D:TRP417 4.8 14.2 1.0
O D:HOH4385 4.8 53.3 1.0
CB D:PRO369 4.9 13.3 1.0

Chlorine binding site 4 out of 8 in 2qg4

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Chlorine binding site 4 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl4006

b:22.8
occ:1.00
 OG1 D:THR213 2.8 15.1 1.0
N D:THR213 3.5 11.0 1.0
CB D:THR213 3.5 10.5 1.0
CA D:ASP183 3.5 24.4 1.0
O D:HOH4378 3.6 39.4 1.0
NE1 D:TRP214 3.7 13.3 1.0
CB D:ASP183 3.8 24.3 1.0
CE2 D:TRP214 3.9 16.9 1.0
O D:GLY182 3.9 17.1 1.0
CB D:ASN212 3.9 17.3 1.0
N D:ASP183 3.9 22.2 1.0
CZ2 D:TRP214 4.0 10.8 1.0
C D:GLY182 4.1 19.6 1.0
CA D:THR213 4.1 11.7 1.0
CD1 D:TRP214 4.4 10.0 1.0
CA D:ASN212 4.4 17.9 1.0
C D:ASN212 4.4 17.1 1.0
CG D:ASN212 4.5 17.3 1.0
NH1 D:ARG141 4.6 15.7 1.0
CD2 D:TRP214 4.6 12.2 1.0
NH2 D:ARG141 4.8 17.1 1.0
C D:ASP183 4.8 24.8 1.0
N D:TRP214 4.8 12.1 1.0
CH2 D:TRP214 4.9 15.7 1.0
CG D:TRP214 4.9 7.1 1.0
CG2 D:THR213 4.9 9.8 1.0

Chlorine binding site 5 out of 8 in 2qg4

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Chlorine binding site 5 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl4003

b:11.2
occ:1.00
 O F:HOH5084 3.3 11.0 1.0
N F:MET419 3.5 11.2 1.0
CB F:MET419 3.6 15.0 1.0
CG F:MET419 3.7 16.6 1.0
N F:ASP418 3.8 9.8 1.0
CE3 F:TRP417 3.9 8.3 1.0
CB F:TRP417 4.0 11.0 1.0
CA F:MET419 4.1 14.5 1.0
SD F:MET419 4.2 20.4 1.0
C F:TRP417 4.3 10.1 1.0
CA F:ASP418 4.4 11.4 1.0
CB F:ASP418 4.4 12.0 1.0
C F:ASP418 4.4 11.9 1.0
CA F:TRP417 4.5 10.0 1.0
CD2 F:TRP417 4.6 13.2 1.0
CG F:PRO369 4.6 12.1 1.0
CG F:TRP417 4.7 13.2 1.0
CZ3 F:TRP417 4.8 9.9 1.0
O F:HOH5202 5.0 21.7 1.0

Chlorine binding site 6 out of 8 in 2qg4

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Chlorine binding site 6 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl4007

b:22.5
occ:1.00
 OG1 F:THR213 2.9 7.8 1.0
O F:HOH5381 3.2 36.6 1.0
N F:THR213 3.5 11.5 1.0
CA F:ASP183 3.6 21.7 1.0
CB F:THR213 3.6 10.3 1.0
CB F:ASP183 3.7 22.7 1.0
NE1 F:TRP214 3.7 12.2 1.0
CE2 F:TRP214 3.9 15.8 1.0
N F:ASP183 3.9 17.4 1.0
O F:GLY182 4.0 20.5 1.0
CZ2 F:TRP214 4.0 12.9 1.0
C F:GLY182 4.1 17.5 1.0
CA F:THR213 4.1 10.3 1.0
CB F:ASN212 4.2 12.7 1.0
NH1 F:ARG141 4.2 11.9 1.0
CD1 F:TRP214 4.3 9.9 1.0
C F:ASN212 4.5 9.8 1.0
CD2 F:TRP214 4.6 13.0 1.0
CA F:ASN212 4.6 12.7 1.0
NH2 F:ARG141 4.6 20.5 1.0
CG F:ASN212 4.8 10.8 1.0
C F:ASP183 4.8 24.2 1.0
CG F:TRP214 4.9 13.7 1.0
CZ F:ARG141 4.9 18.2 1.0
CH2 F:TRP214 4.9 12.9 1.0
N F:TRP214 4.9 8.5 1.0
CG2 F:THR213 4.9 8.0 1.0

Chlorine binding site 7 out of 8 in 2qg4

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Chlorine binding site 7 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl4004

b:11.0
occ:1.00
 O H:HOH4155 3.3 14.5 1.0
O H:HOH4353 3.5 38.9 1.0
N H:MET419 3.6 13.6 1.0
CB H:MET419 3.7 16.3 1.0
N H:ASP418 3.8 14.2 1.0
CG H:MET419 3.8 14.7 1.0
CE3 H:TRP417 3.9 9.8 1.0
CB H:TRP417 3.9 11.7 1.0
SD H:MET419 4.0 14.6 1.0
C H:TRP417 4.3 12.7 1.0
CA H:MET419 4.3 14.3 1.0
O H:HOH4272 4.3 35.9 1.0
CA H:TRP417 4.4 11.7 1.0
CA H:ASP418 4.4 14.9 1.0
CB H:ASP418 4.4 15.2 1.0
C H:ASP418 4.5 13.4 1.0
CD2 H:TRP417 4.5 12.1 1.0
CG H:TRP417 4.6 11.4 1.0
CG H:PRO369 4.7 8.1 1.0
CZ3 H:TRP417 4.8 10.8 1.0
O H:HOH4192 4.9 15.2 1.0

Chlorine binding site 8 out of 8 in 2qg4

Go back to Chlorine Binding Sites List in 2qg4
Chlorine binding site 8 out of 8 in the Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Human Udp-Glucose Dehydrogenase Product Complex with Udp-Glucuronate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl4008

b:22.6
occ:1.00
 OG1 H:THR213 2.8 5.7 1.0
N H:THR213 3.5 9.5 1.0
CA H:ASP183 3.5 24.3 1.0
CB H:THR213 3.5 7.2 1.0
NE1 H:TRP214 3.7 7.3 1.0
CB H:ASP183 3.7 23.1 1.0
O H:GLY182 3.9 21.9 1.0
CE2 H:TRP214 3.9 10.8 1.0
N H:ASP183 3.9 22.3 1.0
CB H:ASN212 4.0 15.4 1.0
C H:GLY182 4.0 21.1 1.0
CZ2 H:TRP214 4.1 8.5 1.0
CA H:THR213 4.1 8.3 1.0
CD1 H:TRP214 4.3 10.1 1.0
NH1 H:ARG141 4.4 13.3 1.0
C H:ASN212 4.5 13.2 1.0
CA H:ASN212 4.5 15.2 1.0
CG H:ASN212 4.6 14.3 1.0
CD2 H:TRP214 4.6 8.8 1.0
C H:ASP183 4.8 25.7 1.0
NH2 H:ARG141 4.8 12.8 1.0
N H:TRP214 4.8 9.7 1.0
CG H:TRP214 4.9 5.1 1.0
CG2 H:THR213 4.9 2.7 1.0
CH2 H:TRP214 4.9 12.1 1.0

Reference:

S.Egger, A.Chaikuad, K.L.Kavanagh, U.Oppermann, B.Nidetzky. Structure and Mechanism of Human Udp-Glucose 6-Dehydrogenase. J.Biol.Chem. V. 286 23877 2011.
ISSN: ISSN 0021-9258
PubMed: 21502315
DOI: 10.1074/JBC.M111.234682
Page generated: Sat Jul 20 10:41:15 2024

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