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Zinc in PDB 2qqv: Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose

Enzymatic activity of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose

All present enzymatic activity of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose:
3.2.1.26;

Protein crystallography data

The structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqv 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) 19.63 / 3.01
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 107.131, 107.131, 50.832, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.7

Other elements in 2qqv:

The structure of Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Cell-Wall Invertase (E203A) From Arabidopsis Thaliana in Complex with Sucrose (pdb code 2qqv). 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 (E203A) From Arabidopsis Thaliana in Complex with Sucrose, PDB code: 2qqv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2qqv

Go back to Zinc Binding Sites List in 2qqv
Zinc binding site 1 out of 4 in the Crystal Structure of A Cell-Wall Invertase (E203A) 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 (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:95.0
occ:1.00
 NE2 A:HIS243 2.7 27.9 1.0
CD2 A:HIS243 3.3 27.9 1.0
CE1 A:HIS243 3.8 28.0 1.0
O A:THR241 4.1 31.6 1.0
NH2 A:ARG272 4.6 30.9 1.0
CG A:HIS243 4.6 28.6 1.0
OE1 A:GLN396 4.7 42.7 1.0
ND1 A:HIS243 4.8 28.2 1.0
CB A:THR241 4.9 32.0 1.0
NH1 A:ARG272 4.9 30.4 1.0

Zinc binding site 2 out of 4 in 2qqv

Go back to Zinc Binding Sites List in 2qqv
Zinc binding site 2 out of 4 in the Crystal Structure of A Cell-Wall Invertase (E203A) 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 (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:73.4
occ:1.00
 OD1 A:ASP64 2.3 39.1 1.0
CG A:ASP64 3.1 38.8 1.0
OD2 A:ASP64 3.2 39.1 1.0
CB A:ASP64 4.6 38.6 1.0

Zinc binding site 3 out of 4 in 2qqv

Go back to Zinc Binding Sites List in 2qqv
Zinc binding site 3 out of 4 in the Crystal Structure of A Cell-Wall Invertase (E203A) 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 (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1103

b:63.1
occ:1.00
 SG A:CYS204 2.3 36.1 1.0
CE A:LYS282 3.1 28.2 1.0
CB A:SER83 3.6 35.3 1.0
NZ A:LYS282 3.6 28.1 1.0
CB A:CYS204 3.8 35.0 1.0
OG A:SER83 4.2 35.3 1.0
CA A:CYS204 4.2 35.0 1.0
CB A:ASP149 4.2 37.0 1.0
CG A:ASP149 4.3 37.0 1.0
CD A:LYS282 4.4 28.4 1.0
N A:GLY84 4.5 35.4 1.0
O A:GLY84 4.5 35.4 1.0
OD2 A:ASP23 4.5 37.9 1.0
OD2 A:ASP149 4.5 37.1 1.0
O A:PRO24 4.5 37.1 1.0
OD1 A:ASP149 4.7 36.7 1.0
ND2 A:ASN25 4.7 36.8 1.0
CA A:SER83 4.8 35.3 1.0
C A:SER83 4.8 35.4 1.0
CB A:ASP23 4.9 37.4 1.0
CA A:ASP149 4.9 37.0 1.0
O A:ALA280 5.0 27.4 1.0

Zinc binding site 4 out of 4 in 2qqv

Go back to Zinc Binding Sites List in 2qqv
Zinc binding site 4 out of 4 in the Crystal Structure of A Cell-Wall Invertase (E203A) 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 (E203A) From Arabidopsis Thaliana in Complex with Sucrose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1104

b:65.0
occ:1.00
 OE2 A:GLU389 1.9 46.6 1.0
CD A:GLU389 3.0 46.8 1.0
CG A:GLU389 3.5 47.2 1.0
OE1 A:GLU389 4.1 46.6 1.0
CD A:PRO390 4.2 47.4 1.0
CG A:PRO390 4.4 47.4 1.0
CB A:GLU389 4.9 47.4 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 03:33:51 2024

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