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Chlorine in PDB 2q3e: Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose

Enzymatic activity of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose

All present enzymatic activity of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose:
1.1.1.22;

Protein crystallography data

The structure of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose, PDB code: 2q3e was solved by K.L.Kavanagh, K.Guo, G.Bunkoczi, P.Savitsky, E.Pilka, C.Bhatia, C.Smee, G.Berridge, F.Von Delft, J.Wiegelt, C.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) 49.09 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 115.990, 184.132, 170.943, 90.00, 109.23, 90.00
R / Rfree (%) 17.2 / 20.5

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose (pdb code 2q3e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose, PDB code: 2q3e:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 2q3e

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Chlorine binding site 1 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl3001

b:21.6
occ:1.00
 O A:HOH3037 3.3 26.2 1.0
N A:MET419 3.4 32.1 1.0
CG A:MET419 3.6 31.2 1.0
CB A:MET419 3.6 32.7 1.0
N A:ASP418 3.8 34.2 1.0
CE3 A:TRP417 3.9 32.2 1.0
CB A:TRP417 4.0 31.2 1.0
CA A:MET419 4.1 32.1 1.0
SD A:MET419 4.2 36.1 1.0
C A:TRP417 4.3 32.9 1.0
C A:ASP418 4.4 32.2 1.0
CB A:ASP418 4.4 33.2 1.0
CA A:ASP418 4.4 33.4 1.0
CA A:TRP417 4.5 29.9 1.0
CD2 A:TRP417 4.6 32.6 1.0
CG A:TRP417 4.6 30.7 1.0
CG A:PRO369 4.7 31.7 1.0
CZ3 A:TRP417 4.8 30.2 1.0

Chlorine binding site 2 out of 12 in 2q3e

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Chlorine binding site 2 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl3009

b:29.6
occ:1.00
 O B:HOH3081 3.3 39.3 1.0
N B:MET419 3.6 32.1 1.0
CB B:MET419 3.6 33.6 1.0
CG B:MET419 3.6 29.6 1.0
N B:ASP418 3.8 32.6 1.0
CE3 B:TRP417 3.9 32.1 1.0
CB B:TRP417 4.0 32.6 1.0
SD B:MET419 4.2 36.8 1.0
CA B:MET419 4.2 32.7 1.0
C B:TRP417 4.4 33.5 1.0
CA B:TRP417 4.5 31.6 1.0
CA B:ASP418 4.5 33.9 1.0
C B:ASP418 4.5 32.5 1.0
CD2 B:TRP417 4.5 33.5 1.0
CB B:ASP418 4.5 33.5 1.0
CG B:PRO369 4.6 31.5 1.0
CG B:TRP417 4.6 33.1 1.0
CZ3 B:TRP417 4.8 32.3 1.0
CB B:PRO369 5.0 33.1 1.0

Chlorine binding site 3 out of 12 in 2q3e

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Chlorine binding site 3 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl3005

b:25.4
occ:1.00
 O C:HOH3067 3.2 28.6 1.0
CG C:MET419 3.5 31.6 1.0
N C:MET419 3.5 31.7 1.0
CB C:MET419 3.7 33.0 1.0
N C:ASP418 3.8 32.9 1.0
CB C:TRP417 3.9 31.7 1.0
CE3 C:TRP417 3.9 32.6 1.0
SD C:MET419 4.1 37.0 1.0
CA C:MET419 4.2 32.4 1.0
C C:TRP417 4.3 33.0 1.0
CB C:ASP418 4.4 32.8 1.0
CA C:ASP418 4.4 32.9 1.0
C C:ASP418 4.4 32.3 1.0
CA C:TRP417 4.5 31.5 1.0
CD2 C:TRP417 4.5 33.2 1.0
CG C:TRP417 4.6 33.2 1.0
CG C:PRO369 4.6 31.0 1.0
CZ3 C:TRP417 4.9 31.6 1.0
CB C:PRO369 5.0 33.4 1.0

Chlorine binding site 4 out of 12 in 2q3e

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Chlorine binding site 4 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl3006

b:30.6
occ:1.00
 O D:HOH3057 3.1 33.8 1.0
N D:MET419 3.6 30.5 1.0
CG D:MET419 3.6 31.0 1.0
CB D:MET419 3.7 32.2 1.0
N D:ASP418 3.8 32.2 1.0
CE3 D:TRP417 3.9 32.9 1.0
CB D:TRP417 4.0 31.2 1.0
SD D:MET419 4.1 35.2 1.0
CA D:MET419 4.3 32.2 1.0
CB D:ASP418 4.3 32.7 1.0
C D:TRP417 4.4 33.3 1.0
CA D:ASP418 4.4 32.1 1.0
C D:ASP418 4.5 31.6 1.0
CA D:TRP417 4.5 31.3 1.0
CD2 D:TRP417 4.6 34.2 1.0
CG D:TRP417 4.6 32.0 1.0
CG D:PRO369 4.7 30.8 1.0
CZ3 D:TRP417 4.9 31.6 1.0

Chlorine binding site 5 out of 12 in 2q3e

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Chlorine binding site 5 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl3011

b:29.7
occ:1.00
 O E:HOH3190 3.1 35.0 1.0
N E:MET419 3.6 31.8 1.0
CB E:MET419 3.7 32.8 1.0
CG E:MET419 3.7 32.5 1.0
N E:ASP418 3.8 30.8 1.0
CE3 E:TRP417 4.0 33.5 1.0
CB E:TRP417 4.0 30.5 1.0
SD E:MET419 4.2 36.8 1.0
CA E:MET419 4.2 32.4 1.0
CB E:ASP418 4.4 33.6 1.0
C E:TRP417 4.4 32.5 1.0
CA E:ASP418 4.4 32.7 1.0
C E:ASP418 4.5 31.3 1.0
CA E:TRP417 4.5 31.2 1.0
CD2 E:TRP417 4.6 32.3 1.0
CG E:PRO369 4.6 31.0 1.0
CG E:TRP417 4.7 29.2 1.0
CZ3 E:TRP417 4.9 29.7 1.0

Chlorine binding site 6 out of 12 in 2q3e

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Chlorine binding site 6 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl3004

b:26.8
occ:1.00
 O F:HOH3033 3.5 29.1 1.0
N F:MET419 3.5 31.6 1.0
CB F:MET419 3.6 33.2 1.0
CG F:MET419 3.6 30.1 1.0
N F:ASP418 3.9 31.0 1.0
CE3 F:TRP417 4.0 31.0 1.0
CA F:MET419 4.1 32.3 1.0
CB F:TRP417 4.2 32.0 1.0
SD F:MET419 4.2 37.0 1.0
CB F:ASP418 4.3 32.8 1.0
C F:ASP418 4.4 31.6 1.0
C F:TRP417 4.4 32.0 1.0
CA F:ASP418 4.4 31.8 1.0
CA F:TRP417 4.6 31.4 1.0
CD2 F:TRP417 4.7 33.5 1.0
CG F:PRO369 4.7 30.5 1.0
CG F:TRP417 4.8 30.8 1.0
CZ3 F:TRP417 4.8 30.4 1.0

Chlorine binding site 7 out of 12 in 2q3e

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Chlorine binding site 7 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl3002

b:26.0
occ:1.00
 O G:HOH3081 3.1 30.3 1.0
N G:MET419 3.5 32.2 1.0
CG G:MET419 3.6 30.8 1.0
CB G:MET419 3.6 32.5 1.0
N G:ASP418 3.8 32.9 1.0
CE3 G:TRP417 4.0 30.1 1.0
CB G:TRP417 4.0 31.3 1.0
SD G:MET419 4.1 36.5 1.0
CA G:MET419 4.2 32.6 1.0
CB G:ASP418 4.3 32.6 1.0
C G:TRP417 4.4 32.4 1.0
CA G:ASP418 4.4 32.9 1.0
C G:ASP418 4.4 31.8 1.0
CA G:TRP417 4.5 31.7 1.0
CD2 G:TRP417 4.6 32.6 1.0
CG G:TRP417 4.7 30.9 1.0
CG G:PRO369 4.7 30.4 1.0
CZ3 G:TRP417 4.9 32.0 1.0

Chlorine binding site 8 out of 12 in 2q3e

Go back to Chlorine Binding Sites List in 2q3e
Chlorine binding site 8 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl3010

b:36.5
occ:1.00
 O H:HOH3052 3.2 38.3 1.0
N H:MET419 3.7 31.9 1.0
CG H:MET419 3.7 31.2 1.0
CE3 H:TRP417 3.8 31.5 1.0
CB H:MET419 3.8 32.5 1.0
N H:ASP418 3.8 32.8 1.0
CB H:TRP417 4.0 32.2 1.0
SD H:MET419 4.2 36.3 1.0
CB H:ASP418 4.3 33.2 1.0
CA H:MET419 4.4 32.8 1.0
C H:TRP417 4.4 34.1 1.0
CA H:ASP418 4.4 33.2 1.0
CD2 H:TRP417 4.5 35.4 1.0
CA H:TRP417 4.5 31.8 1.0
C H:ASP418 4.5 31.9 1.0
CG H:PRO369 4.6 31.1 1.0
CG H:TRP417 4.6 31.3 1.0
CZ3 H:TRP417 4.7 31.4 1.0
CB H:PRO369 5.0 33.0 1.0

Chlorine binding site 9 out of 12 in 2q3e

Go back to Chlorine Binding Sites List in 2q3e
Chlorine binding site 9 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Cl3003

b:29.1
occ:1.00
 O I:HOH3057 3.4 31.4 1.0
N I:MET419 3.5 32.6 1.0
CG I:MET419 3.5 31.9 1.0
CB I:MET419 3.6 33.5 1.0
N I:ASP418 3.9 32.6 1.0
CE3 I:TRP417 3.9 31.8 1.0
CB I:TRP417 4.0 31.6 1.0
SD I:MET419 4.1 37.2 1.0
CA I:MET419 4.1 33.2 1.0
C I:TRP417 4.4 33.0 1.0
C I:ASP418 4.4 32.1 1.0
CB I:ASP418 4.4 32.8 1.0
CA I:ASP418 4.4 32.8 1.0
CD2 I:TRP417 4.5 33.7 1.0
CA I:TRP417 4.5 31.7 1.0
CG I:TRP417 4.6 30.8 1.0
CG I:PRO369 4.6 30.6 1.0
CZ3 I:TRP417 4.8 30.6 1.0

Chlorine binding site 10 out of 12 in 2q3e

Go back to Chlorine Binding Sites List in 2q3e
Chlorine binding site 10 out of 12 in the Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Human Udp-Glucose Dehydrogenase Complexed with Nadh and Udp-Glucose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl3012

b:30.0
occ:1.00
 O J:HOH3060 3.4 33.1 1.0
N J:MET419 3.5 32.3 1.0
CG J:MET419 3.5 30.7 1.0
CB J:MET419 3.6 32.4 1.0
N J:ASP418 3.9 31.6 1.0
CE3 J:TRP417 3.9 32.3 1.0
CB J:TRP417 4.1 32.1 1.0
SD J:MET419 4.1 36.1 1.0
CA J:MET419 4.2 31.4 1.0
CB J:ASP418 4.4 32.0 1.0
C J:TRP417 4.4 32.6 1.0
CA J:ASP418 4.4 31.7 1.0
C J:ASP418 4.4 31.2 1.0
CD2 J:TRP417 4.6 33.3 1.0
CA J:TRP417 4.6 31.1 1.0
CG J:PRO369 4.7 30.1 1.0
CG J:TRP417 4.7 31.9 1.0
CZ3 J:TRP417 4.8 29.9 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 10:25:29 2024

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