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Zinc in PDB 4a7z: Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M

Enzymatic activity of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M

All present enzymatic activity of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M:
4.2.1.110;

Protein crystallography data

The structure of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M, PDB code: 4a7z was solved by M.Claesson, Y.Lindqvist, S.Madrid, T.Sandalova, R.Fiskesund, S.Yu, G.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.33 / 2.60
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 132.220, 82.670, 97.910, 90.00, 90.00, 90.00
R / Rfree (%) 19.376 / 26.694

Other elements in 4a7z:

The structure of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M (pdb code 4a7z). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M, PDB code: 4a7z:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4a7z

Go back to Zinc Binding Sites List in 4a7z
Zinc binding site 1 out of 3 in the Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn950

b:28.4
occ:1.00
 O2 A:AY9954 1.8 31.4 1.0
NE2 A:HIS337 2.0 24.3 1.0
O3 A:AY9954 2.1 30.3 1.0
NE2 A:HIS215 2.1 23.8 1.0
NE2 A:HIS295 2.1 27.0 1.0
C2 A:AY9954 2.6 32.3 1.0
C3 A:AY9954 2.7 32.0 1.0
CD2 A:HIS337 2.8 24.1 1.0
CE1 A:HIS295 3.1 28.3 1.0
CE1 A:HIS215 3.1 22.8 1.0
CE1 A:HIS337 3.1 23.9 1.0
CD2 A:HIS295 3.2 26.6 1.0
CD2 A:HIS215 3.2 23.7 1.0
OH A:TYR35 3.7 26.0 1.0
C1 A:AY9954 3.9 33.9 1.0
CG A:HIS337 4.0 23.7 1.0
C4 A:AY9954 4.1 33.6 1.0
ND1 A:HIS337 4.1 23.6 1.0
CE1 A:PHE294 4.1 29.8 1.0
NH2 A:ARG156 4.1 23.8 1.0
ND1 A:HIS295 4.2 28.8 1.0
ND1 A:HIS215 4.2 22.4 1.0
OH A:TYR414 4.2 31.3 1.0
NE2 A:HIS155 4.2 28.7 1.0
CG A:HIS295 4.3 27.9 1.0
CG A:HIS215 4.3 22.8 1.0
CE1 A:TYR35 4.6 27.4 1.0
CZ A:TYR35 4.6 26.5 1.0
CZ A:PHE294 4.8 31.5 1.0
O5 A:AY9954 4.8 36.2 1.0
CE1 A:HIS155 4.8 27.2 1.0
CE2 A:TYR414 4.9 29.3 1.0
CD1 A:PHE294 4.9 28.8 1.0
C5 A:AY9954 5.0 36.0 1.0

Zinc binding site 2 out of 3 in 4a7z

Go back to Zinc Binding Sites List in 4a7z
Zinc binding site 2 out of 3 in the Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn951

b:70.8
occ:1.00
 O A:GLU349 2.4 28.3 1.0
OE2 A:GLU351 2.5 26.9 1.0
OE1 A:GLU351 2.6 27.8 1.0
OD1 A:ASP347 2.6 25.1 1.0
OD1 A:ASP343 2.6 24.0 1.0
OD1 A:ASP345 2.6 23.1 1.0
CD A:GLU351 2.9 26.8 1.0
CG A:ASP345 3.4 23.1 1.0
CG A:ASP347 3.5 26.1 1.0
C A:GLU349 3.6 27.4 1.0
CG A:ASP343 3.6 24.4 1.0
NZ A:LYS373 3.6 25.4 1.0
OD2 A:ASP345 3.7 23.1 1.0
CG A:GLU349 3.9 32.1 1.0
N A:ASP345 3.9 22.2 1.0
OD2 A:ASP347 4.0 26.4 1.0
N A:ASP347 4.1 25.9 1.0
N A:GLU349 4.1 27.9 1.0
N A:ILE344 4.2 21.6 1.0
N A:GLY346 4.2 23.6 1.0
OD2 A:ASP343 4.3 25.6 1.0
CA A:ASP343 4.3 22.5 1.0
CA A:GLU349 4.4 28.2 1.0
N A:GLU351 4.4 23.4 1.0
CG A:GLU351 4.4 25.8 1.0
C A:ASP343 4.4 22.5 1.0
CB A:ASP347 4.4 26.9 1.0
CA A:ASP345 4.5 22.8 1.0
CB A:ASP345 4.5 23.0 1.0
N A:ASP350 4.5 25.7 1.0
C A:ASP345 4.5 23.8 1.0
C A:ASP350 4.5 23.7 1.0
CB A:ASP343 4.5 23.5 1.0
CA A:ASP350 4.6 24.0 1.0
CA A:ASP347 4.6 27.0 1.0
CB A:GLU349 4.7 30.4 1.0
O A:HOH2078 4.8 17.9 1.0
N A:GLY348 4.8 27.0 1.0
OE2 A:GLU349 4.9 34.3 1.0
C A:ASP347 4.9 27.2 1.0
CD A:GLU349 4.9 34.3 1.0
C A:ILE344 4.9 22.1 1.0
CE A:LYS373 5.0 26.5 1.0

Zinc binding site 3 out of 3 in 4a7z

Go back to Zinc Binding Sites List in 4a7z
Zinc binding site 3 out of 3 in the Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex of Bifunctional Aldos-2-Ulose Dehydratase with the Reaction Intermediate Ascopyrone M within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn952

b:33.1
occ:1.00
 OE2 A:GLU639 1.9 25.2 1.0
NE2 A:HIS709 2.0 21.2 1.0
NE2 A:HIS632 2.2 21.7 1.0
NE2 A:HIS630 2.2 22.2 1.0
O A:HOH2151 2.5 15.3 1.0
CD2 A:HIS709 2.9 21.7 1.0
CD A:GLU639 2.9 24.4 1.0
CE1 A:HIS632 3.0 21.4 1.0
CE1 A:HIS709 3.0 21.8 1.0
CD2 A:HIS630 3.1 22.2 1.0
CE1 A:HIS630 3.2 22.8 1.0
CD2 A:HIS632 3.2 21.5 1.0
OE1 A:GLU639 3.2 24.7 1.0
O2 A:AY9955 3.9 50.2 1.0
C1 A:AY9955 4.0 50.1 1.0
CG A:HIS709 4.1 22.5 1.0
C2 A:AY9955 4.1 50.0 1.0
ND1 A:HIS632 4.1 21.8 1.0
ND1 A:HIS709 4.1 22.5 1.0
CG A:HIS632 4.2 21.6 1.0
CG A:GLU639 4.2 23.8 1.0
ND1 A:HIS630 4.2 23.4 1.0
CG A:HIS630 4.2 22.9 1.0
CE1 A:HIS641 4.6 23.4 1.0
C3 A:AY9955 4.9 49.7 1.0
CE A:MET653 4.9 25.6 1.0

Reference:

M.Claesson, Y.Lindqvist, S.Madrid, T.Sandalova, R.Fiskesund, S.Yu, G.Schneider. Crystal Structure of Bifunctional Aldos-2-Ulose Dehydratase/Isomerase From Phanerochaete Chrysosporium with the Reaction Intermediate Ascopyrone M. J.Mol.Biol. V. 417 279 2012.
ISSN: ISSN 0022-2836
PubMed: 22330145
DOI: 10.1016/J.JMB.2012.02.001
Page generated: Wed Dec 16 05:02:36 2020

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