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Zinc in PDB 2qqw: Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose

Enzymatic activity of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose

All present enzymatic activity of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose:
3.2.1.26;

Protein crystallography data

The structure of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqw was solved by W.Lammens, K.Le Roy, A.Van Laere, A.Rabijns, W.Van Den Ende, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.57 / 2.80
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 105.877, 105.877, 50.479, 90.00, 90.00, 120.00
R / Rfree (%) 18.8 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose (pdb code 2qqw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qqw

Go back to Zinc Binding Sites List in 2qqw
Zinc binding site 1 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:65.7
occ:1.00
 NE2 A:HIS474 2.2 41.9 1.0
CE1 A:HIS474 3.1 40.7 1.0
CD2 A:HIS474 3.2 41.1 1.0
ND2 A:ASN441 4.1 54.9 1.0
ND1 A:HIS474 4.2 41.6 1.0
CG A:HIS474 4.3 41.0 1.0
CD1 A:LEU382 4.5 48.9 1.0
OH A:TYR443 5.0 46.4 1.0

Zinc binding site 2 out of 4 in 2qqw

Go back to Zinc Binding Sites List in 2qqw
Zinc binding site 2 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:71.0
occ:1.00
 NE2 A:HIS194 2.3 49.4 1.0
OD1 A:ASP196 2.3 48.9 1.0
OD2 A:ASP196 2.4 48.6 1.0
CG A:ASP196 2.7 48.6 1.0
CD2 A:HIS194 2.9 49.3 1.0
CE1 A:HIS194 3.5 49.4 1.0
O A:TYR195 4.2 48.2 1.0
CB A:ASP196 4.2 48.2 1.0
CG A:HIS194 4.2 48.4 1.0
CG A:PRO260 4.3 57.5 1.0
ND1 A:HIS194 4.4 49.2 1.0
C A:TYR195 4.9 48.0 1.0
CA A:ASP196 5.0 48.3 1.0

Zinc binding site 3 out of 4 in 2qqw

Go back to Zinc Binding Sites List in 2qqw
Zinc binding site 3 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1103

b:75.7
occ:1.00
 CE1 A:HIS243 2.4 32.7 1.0
NE2 A:HIS243 3.1 32.0 1.0
ND1 A:HIS243 3.5 33.3 1.0
O A:THR241 4.1 39.9 1.0
NH2 A:ARG272 4.3 35.0 1.0
CD2 A:HIS243 4.4 33.1 1.0
OE1 A:GLN396 4.5 38.5 1.0
CG A:HIS243 4.6 35.0 1.0
O6 A:MAN753 4.8 65.5 1.0
CB A:THR241 5.0 40.4 1.0

Zinc binding site 4 out of 4 in 2qqw

Go back to Zinc Binding Sites List in 2qqw
Zinc binding site 4 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Cell-Wall Invertase (D23A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1104

b:83.9
occ:1.00
 OD2 A:ASP64 2.3 41.1 1.0
CG A:ASP64 3.0 41.6 1.0
OD1 A:ASP64 3.0 41.4 1.0
CB A:ASP64 4.4 41.4 1.0

Reference:

W.Lammens, K.Le Roy, A.Van Laere, A.Rabijns, W.Van Den Ende. Crystal Structures of Arabidopsis Thaliana Cell-Wall Invertase Mutants in Complex with Sucrose. J.Mol.Biol. V. 377 378 2008.
ISSN: ISSN 0022-2836
PubMed: 18258263
DOI: 10.1016/J.JMB.2007.12.074
Page generated: Thu Oct 17 03:33:55 2024

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