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Zinc in PDB 3ic1: Crystal Structure of Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae

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

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

Protein crystallography data

The structure of Crystal Structure of Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 3ic1 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) 40.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.697, 95.751, 185.426, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 25

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae (pdb code 3ic1). 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 Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 3ic1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ic1

Go back to Zinc Binding Sites List in 3ic1
Zinc binding site 1 out of 4 in the Crystal Structure of Zinc-Bound 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 Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:32.5
occ:1.00
 OD1 A:ASP100 2.0 31.4 1.0
OE2 A:GLU163 2.1 32.8 1.0
NE2 A:HIS67 2.2 31.1 1.0
O A:HOH482 2.2 30.2 1.0
OE1 A:GLU163 2.6 35.0 1.0
CD A:GLU163 2.7 34.5 1.0
CG A:ASP100 2.9 29.6 1.0
CD2 A:HIS67 3.1 30.6 1.0
OD2 A:ASP100 3.2 31.0 1.0
CE1 A:HIS67 3.2 30.6 1.0
O A:HOH382 3.4 47.7 1.0
OE1 A:GLU134 3.6 42.7 1.0
OE2 A:GLU135 3.6 41.1 1.0
ZN A:ZN1002 3.6 30.7 0.5
CG A:GLU163 4.2 34.2 1.0
CD A:GLU134 4.2 42.8 1.0
CD A:GLU135 4.2 40.4 1.0
ND1 A:HIS67 4.3 29.7 1.0
CG A:HIS67 4.3 30.8 1.0
CB A:ASP100 4.3 29.8 1.0
CG A:MET101 4.3 28.7 1.0
CB A:MET101 4.4 29.2 1.0
SD A:MET101 4.4 31.9 1.0
OE2 A:GLU134 4.5 47.3 1.0
CA A:ASP100 4.6 29.9 1.0
C A:ASP100 4.7 29.9 1.0
OE1 A:GLU135 4.7 38.3 1.0
CD A:PRO164 4.8 35.4 1.0
CB A:GLU163 4.9 33.9 1.0
N A:MET101 4.9 29.3 1.0
O A:ASP100 4.9 30.2 1.0

Zinc binding site 2 out of 4 in 3ic1

Go back to Zinc Binding Sites List in 3ic1
Zinc binding site 2 out of 4 in the Crystal Structure of Zinc-Bound 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 Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:30.7
occ:0.50
 OD2 A:ASP100 2.0 31.0 1.0
OE2 A:GLU135 2.0 41.1 1.0
OE1 A:GLU135 2.1 38.3 1.0
O A:HOH482 2.1 30.2 1.0
NE2 A:HIS349 2.2 39.5 1.0
CD A:GLU135 2.4 40.4 1.0
CE1 A:HIS349 3.0 40.4 1.0
CG A:ASP100 3.1 29.6 1.0
CD2 A:HIS349 3.3 37.8 1.0
ZN A:ZN1001 3.6 32.5 1.0
OD1 A:ASP100 3.6 31.4 1.0
O A:HOH382 3.8 47.7 1.0
CG A:GLU135 3.9 41.9 1.0
O A:HOH419 4.1 25.8 1.0
ND1 A:HIS349 4.2 41.0 1.0
CB A:ASP100 4.2 29.8 1.0
OE1 A:GLU134 4.4 42.7 1.0
CG A:HIS349 4.4 38.3 1.0
NE2 A:HIS67 4.7 31.1 1.0
CE1 A:HIS67 4.8 30.6 1.0
CG1 A:VAL71 4.8 30.1 1.0
CB A:GLU135 4.9 42.5 1.0
CD1 A:ILE348 5.0 37.8 1.0

Zinc binding site 3 out of 4 in 3ic1

Go back to Zinc Binding Sites List in 3ic1
Zinc binding site 3 out of 4 in the Crystal Structure of Zinc-Bound 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 3 of Crystal Structure of Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:41.4
occ:0.40
 OE2 B:GLU135 2.0 44.7 1.0
OE1 B:GLU135 2.0 42.5 1.0
OD1 B:ASP100 2.0 38.1 1.0
O B:HOH479 2.1 35.0 1.0
CD B:GLU135 2.2 43.1 1.0
NE2 B:HIS349 2.2 44.7 1.0
CE1 B:HIS349 3.0 46.9 1.0
CG B:ASP100 3.1 35.7 1.0
CD2 B:HIS349 3.3 44.3 1.0
ZN B:ZN1001 3.4 36.2 1.0
OD2 B:ASP100 3.5 31.1 1.0
CG B:GLU135 3.6 43.6 1.0
O B:HOH480 3.7 55.0 1.0
OE1 B:GLU134 4.1 40.1 1.0
O B:HOH476 4.1 38.1 1.0
ND1 B:HIS349 4.2 46.0 1.0
OG1 B:THR325 4.3 38.0 1.0
CB B:ASP100 4.3 34.5 1.0
CG B:HIS349 4.4 44.8 1.0
O B:HOH392 4.5 43.8 1.0
NE2 B:HIS67 4.6 31.5 1.0
CE1 B:HIS67 4.6 30.6 1.0
CB B:GLU135 4.6 42.4 1.0
CG1 B:VAL71 4.8 35.5 1.0
OE2 B:GLU163 4.9 32.8 1.0

Zinc binding site 4 out of 4 in 3ic1

Go back to Zinc Binding Sites List in 3ic1
Zinc binding site 4 out of 4 in the Crystal Structure of Zinc-Bound 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 4 of Crystal Structure of Zinc-Bound Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:36.2
occ:1.00
 O B:HOH479 1.9 35.0 1.0
OE2 B:GLU163 2.0 32.8 1.0
OD2 B:ASP100 2.0 31.1 1.0
NE2 B:HIS67 2.1 31.5 1.0
OE1 B:GLU163 2.6 34.6 1.0
CD B:GLU163 2.7 34.6 1.0
CG B:ASP100 3.0 35.7 1.0
CE1 B:HIS67 3.0 30.6 1.0
OD1 B:ASP100 3.2 38.1 1.0
CD2 B:HIS67 3.2 32.1 1.0
ZN B:ZN1002 3.4 41.4 0.4
OE1 B:GLU134 3.6 40.1 1.0
OE2 B:GLU135 3.7 44.7 1.0
O B:HOH392 3.8 43.8 1.0
CG B:GLU163 4.2 35.2 1.0
ND1 B:HIS67 4.2 30.8 1.0
CG B:MET101 4.2 32.8 1.0
CD B:GLU135 4.2 43.1 1.0
CG B:HIS67 4.3 32.9 1.0
CD B:GLU134 4.3 41.0 1.0
CB B:ASP100 4.4 34.5 1.0
SD B:MET101 4.4 33.3 1.0
CB B:MET101 4.4 32.9 1.0
O B:THR325 4.6 36.2 1.0
OE1 B:GLU135 4.6 42.5 1.0
C B:ASP100 4.7 34.4 1.0
CD B:PRO164 4.7 33.6 1.0
CA B:ASP100 4.8 35.0 1.0
CB B:GLU163 4.8 33.9 1.0
OE2 B:GLU134 4.9 40.7 1.0
N B:MET101 4.9 33.8 1.0
O B:ASP100 4.9 34.8 1.0
OG1 B:THR325 4.9 38.0 1.0
CG B:GLU135 4.9 43.6 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: Sat Oct 26 06:56:19 2024

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