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Zinc in PDB 3isz: Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae

Enzymatic activity of Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae

All present enzymatic activity of Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae:
3.5.1.18;

Protein crystallography data

The structure of Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 3isz was solved by B.P.Nocek, D.M.Gillner, R.C.Holz, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.86 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.176, 95.709, 181.179, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae (pdb code 3isz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 3isz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3isz

Go back to Zinc Binding Sites List in 3isz
Zinc binding site 1 out of 2 in the Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae


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 Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:24.9
occ:1.00
OD1 A:ASP100 2.0 23.7 1.0
OE2 A:GLU163 2.0 19.4 1.0
O A:HOH572 2.0 21.8 1.0
NE2 A:HIS67 2.2 18.3 1.0
OE1 A:GLU163 2.6 20.8 1.0
CD A:GLU163 2.6 23.2 1.0
CG A:ASP100 2.8 22.9 1.0
OD2 A:ASP100 3.0 27.0 1.0
CD2 A:HIS67 3.1 15.4 1.0
CE1 A:HIS67 3.2 18.1 1.0
OE1 A:GLU134 3.7 24.8 1.0
OE2 A:GLU135 3.8 29.5 1.0
O A:HOH455 4.0 40.0 1.0
CG A:GLU163 4.1 23.3 1.0
CG A:MET101 4.2 17.2 1.0
CD A:GLU134 4.2 25.4 1.0
CB A:ASP100 4.3 19.3 1.0
ND1 A:HIS67 4.3 17.5 1.0
CG A:HIS67 4.3 16.0 1.0
CB A:MET101 4.3 17.0 1.0
SD A:MET101 4.3 18.6 1.0
CD A:GLU135 4.5 28.9 1.0
O A:THR325 4.6 24.9 1.0
OE2 A:GLU134 4.6 26.2 1.0
C A:ASP100 4.6 18.3 1.0
CA A:ASP100 4.6 18.7 1.0
CD A:PRO164 4.7 20.1 1.0
CB A:GLU163 4.8 21.5 1.0
N A:MET101 4.9 18.1 1.0
O A:ASP100 4.9 18.0 1.0
CG A:GLU134 4.9 23.7 1.0

Zinc binding site 2 out of 2 in 3isz

Go back to Zinc Binding Sites List in 3isz
Zinc binding site 2 out of 2 in the Crystal Structure of Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae


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 Mono-Zinc Form of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:39.2
occ:1.00
OD1 B:ASP100 2.0 39.4 1.0
OE1 B:GLU163 2.1 35.9 1.0
NE2 B:HIS67 2.1 31.6 1.0
O B:HOH420 2.2 40.6 1.0
OE2 B:GLU163 2.7 29.8 1.0
CD B:GLU163 2.7 29.6 1.0
CE1 B:HIS67 3.0 30.5 1.0
CG B:ASP100 3.0 37.3 1.0
OD2 B:ASP100 3.2 40.0 1.0
CD2 B:HIS67 3.2 31.9 1.0
CG B:MET101 3.8 36.4 1.0
OE2 B:GLU135 3.9 56.8 1.0
OE1 B:GLU134 3.9 42.5 1.0
O B:HOH424 4.0 47.9 1.0
ND1 B:HIS67 4.1 33.1 1.0
CG B:GLU163 4.2 29.3 1.0
CG B:HIS67 4.3 30.1 1.0
SD B:MET101 4.4 36.3 1.0
CB B:ASP100 4.4 37.1 1.0
CB B:MET101 4.4 35.1 1.0
CD B:GLU134 4.4 44.0 1.0
CD B:GLU135 4.5 54.3 1.0
C B:ASP100 4.7 36.8 1.0
O B:HOH464 4.7 30.0 1.0
CA B:ASP100 4.8 37.3 1.0
OE2 B:GLU134 4.8 42.5 1.0
O B:THR325 4.8 37.3 1.0
CD B:PRO164 4.8 29.3 1.0
CB B:GLU163 4.8 28.2 1.0
O B:ASP100 4.9 37.9 1.0
N B:MET101 5.0 36.1 1.0

Reference:

B.P.Nocek, D.M.Gillner, Y.Fan, R.C.Holz, A.Joachimiak. Structural Basis For Catalysis By the Mono- and Dimetalated Forms of the Dape-Encoded N-Succinyl-L,L-Diaminopimelic Acid Desuccinylase. J.Mol.Biol. V. 397 617 2010.
ISSN: ISSN 0022-2836
PubMed: 20138056
DOI: 10.1016/J.JMB.2010.01.062
Page generated: Wed Dec 16 04:27:01 2020

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