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Zinc in PDB 2qqu: Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose

Enzymatic activity of Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose

All present enzymatic activity of Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose:
3.2.1.26;

Protein crystallography data

The structure of Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqu 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) 18.66 / 2.84
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 106.271, 106.271, 50.434, 90.00, 90.00, 120.00
R / Rfree (%) 19.4 / 25.3

Other elements in 2qqu:

The structure of Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Cell-Wall Invertase (D239A) From Arabidopsis Thaliana in Complex with Sucrose (pdb code 2qqu). 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 (D239A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qqu

Go back to Zinc Binding Sites List in 2qqu
Zinc binding site 1 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D239A) 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 (D239A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1020

b:71.7
occ:1.00
 NE2 A:HIS243 2.3 28.1 1.0
CD2 A:HIS243 3.2 28.1 1.0
CE1 A:HIS243 3.3 27.5 1.0
O A:THR241 4.0 32.1 1.0
NH2 A:ARG272 4.3 27.1 1.0
OE1 A:GLN396 4.4 36.9 1.0
ND1 A:HIS243 4.4 28.2 1.0
CG A:HIS243 4.4 28.4 1.0
O6 A:MAN753 4.4 54.7 1.0
NH1 A:ARG272 4.8 26.7 1.0
CZ A:ARG272 4.9 26.5 1.0
CB A:THR241 5.0 33.0 1.0
C A:THR241 5.0 32.1 1.0

Zinc binding site 2 out of 4 in 2qqu

Go back to Zinc Binding Sites List in 2qqu
Zinc binding site 2 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D239A) 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 (D239A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1021

b:56.6
occ:1.00
 NE2 A:HIS474 2.3 37.6 1.0
CE1 A:HIS474 3.1 37.1 1.0
CD2 A:HIS474 3.4 37.3 1.0
ND1 A:HIS474 4.3 37.6 1.0
CG A:HIS474 4.5 37.6 1.0
OH A:TYR443 4.7 44.7 1.0

Zinc binding site 3 out of 4 in 2qqu

Go back to Zinc Binding Sites List in 2qqu
Zinc binding site 3 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D239A) 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 (D239A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1022

b:79.6
occ:1.00
 NE2 A:HIS194 2.1 42.7 1.0
OD1 A:ASP196 2.6 43.6 1.0
CB A:MET266 2.8 59.4 1.0
N A:MET266 3.0 59.6 1.0
CE1 A:HIS194 3.0 42.4 1.0
CD2 A:HIS194 3.2 42.8 1.0
CG A:ASP196 3.3 43.4 1.0
OD2 A:ASP196 3.3 45.6 1.0
CA A:MET266 3.5 59.3 1.0
CG A:PRO260 4.1 48.4 1.0
C A:LYS265 4.1 59.9 1.0
CG A:MET266 4.1 59.9 1.0
ND1 A:HIS194 4.2 42.6 1.0
O A:TYR195 4.2 41.7 1.0
CG A:HIS194 4.3 42.7 1.0
CG A:LYS265 4.4 60.3 1.0
CA A:LYS265 4.4 60.0 1.0
C A:MET266 4.4 58.9 1.0
N A:ASP267 4.5 58.2 1.0
CB A:ASP196 4.7 41.9 1.0

Zinc binding site 4 out of 4 in 2qqu

Go back to Zinc Binding Sites List in 2qqu
Zinc binding site 4 out of 4 in the Crystal Structure of A Cell-Wall Invertase (D239A) 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 (D239A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1023

b:78.7
occ:1.00
 NE2 A:HIS170 2.2 42.5 1.0
CD2 A:HIS170 2.8 41.8 1.0
CE1 A:HIS170 3.3 42.0 1.0
CG A:HIS170 4.0 42.0 1.0
C8 A:NAG790 4.1 52.2 1.0
ND1 A:HIS170 4.3 41.5 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: Wed Dec 16 03:50:55 2020

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