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Zinc in PDB 4h2k: Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae

Enzymatic activity of Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae:
3.5.1.18;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 4h2k was solved by B.Nocek, R.Jedrzejczak, M.Makowska-Grzyska, A.Starus, R.Holz, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.667, 44.721, 92.481, 90.00, 92.90, 90.00
R / Rfree (%) 19.4 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae (pdb code 4h2k). 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 the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae, PDB code: 4h2k:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4h2k

Go back to Zinc Binding Sites List in 4h2k
Zinc binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain 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 the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:22.4
occ:1.00
 OD1 A:ASP100 2.0 25.8 1.0
O A:HOH1101 2.0 13.6 1.0
OE1 A:GLU163 2.1 23.4 1.0
NE2 A:HIS67 2.1 22.1 1.0
OE2 A:GLU163 2.6 19.7 1.0
CD A:GLU163 2.7 21.4 1.0
CG A:ASP100 2.9 25.4 1.0
CE1 A:HIS67 3.0 16.9 1.0
OD2 A:ASP100 3.2 27.5 1.0
CD2 A:HIS67 3.2 18.4 1.0
ZN A:ZN1002 3.4 26.5 0.8
OE1 A:GLU134 3.5 30.9 1.0
OE2 A:GLU135 3.7 36.8 1.0
CD A:GLU134 4.1 35.1 1.0
CG A:GLU163 4.2 22.5 1.0
CG A:MET101 4.2 19.7 1.0
ND1 A:HIS67 4.2 18.5 1.0
CG A:HIS67 4.3 19.6 1.0
CB A:ASP100 4.3 23.7 1.0
CD A:GLU135 4.4 31.9 1.0
CB A:MET101 4.4 19.1 1.0
SD A:MET101 4.5 20.7 1.0
OE2 A:GLU134 4.5 36.6 1.0
C A:ASP100 4.7 20.3 1.0
CA A:ASP100 4.7 22.9 1.0
OE1 A:GLU135 4.8 36.4 1.0
CB A:GLU163 4.8 21.5 1.0
CD A:PRO164 4.9 22.7 1.0
O A:ASP100 4.9 17.0 1.0
CG A:GLU134 5.0 30.0 1.0
N A:MET101 5.0 19.9 1.0

Zinc binding site 2 out of 4 in 4h2k

Go back to Zinc Binding Sites List in 4h2k
Zinc binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain 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 the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:26.5
occ:0.75
 OD2 A:ASP100 1.9 27.5 1.0
OE2 A:GLU135 2.0 36.8 1.0
NE2 A:HIS238 2.2 22.3 1.0
O A:HOH1101 2.2 13.6 1.0
CD A:GLU135 2.6 31.9 1.0
OE1 A:GLU135 2.7 36.4 1.0
CG A:ASP100 2.9 25.4 1.0
CE1 A:HIS238 3.0 29.6 1.0
CD2 A:HIS238 3.3 26.3 1.0
ZN A:ZN1001 3.4 22.4 1.0
OD1 A:ASP100 3.4 25.8 1.0
CG A:GLU135 4.1 28.9 1.0
O A:HOH1132 4.1 21.7 1.0
OE1 A:GLU134 4.1 30.9 1.0
CB A:ASP100 4.2 23.7 1.0
ND1 A:HIS238 4.3 30.8 1.0
CG A:HIS238 4.4 24.7 1.0
NE2 A:HIS67 4.6 22.1 1.0
CE1 A:HIS67 4.7 16.9 1.0
CG1 A:VAL71 4.8 26.8 1.0
OE1 A:GLU163 4.9 23.4 1.0
O A:HOH1151 4.9 39.8 1.0
O A:HOH1113 5.0 22.4 1.0

Zinc binding site 3 out of 4 in 4h2k

Go back to Zinc Binding Sites List in 4h2k
Zinc binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain 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 3 of Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:22.6
occ:1.00
 OD1 B:ASP100 1.9 21.6 1.0
NE2 B:HIS67 2.0 22.4 1.0
O B:HOH1101 2.1 23.7 1.0
OE1 B:GLU163 2.1 21.6 1.0
OE2 B:GLU163 2.7 29.2 1.0
CD B:GLU163 2.7 24.1 1.0
CG B:ASP100 2.9 22.5 1.0
CE1 B:HIS67 3.0 17.3 1.0
CD2 B:HIS67 3.1 20.5 1.0
OD2 B:ASP100 3.2 28.7 1.0
ZN B:ZN1002 3.4 27.9 0.8
OE1 B:GLU134 3.4 28.0 1.0
OE2 B:GLU135 3.7 28.2 1.0
CD B:GLU134 4.1 25.5 1.0
ND1 B:HIS67 4.1 18.6 1.0
CG B:HIS67 4.2 18.8 1.0
CG B:GLU163 4.2 23.7 1.0
CG B:MET101 4.3 20.1 1.0
CD B:GLU135 4.3 29.8 1.0
CB B:ASP100 4.4 24.0 1.0
OE2 B:GLU134 4.4 30.1 1.0
CB B:MET101 4.4 20.1 1.0
SD B:MET101 4.5 21.1 1.0
C B:ASP100 4.6 20.0 1.0
OE1 B:GLU135 4.7 29.9 1.0
CA B:ASP100 4.7 23.4 1.0
CB B:GLU163 4.8 23.5 1.0
N B:MET101 4.9 18.2 1.0
CD B:PRO164 4.9 25.9 1.0
O B:ASP100 4.9 20.0 1.0

Zinc binding site 4 out of 4 in 4h2k

Go back to Zinc Binding Sites List in 4h2k
Zinc binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain 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 4 of Crystal Structure of the Catalytic Domain of Succinyl-Diaminopimelate Desuccinylase From Haemophilus Influenzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1002

b:27.9
occ:0.75
 O B:HOH1101 2.0 23.7 1.0
OE2 B:GLU135 2.0 28.2 1.0
OD2 B:ASP100 2.1 28.7 1.0
NE2 B:HIS238 2.2 29.1 1.0
OE1 B:GLU135 2.6 29.9 1.0
CD B:GLU135 2.6 29.8 1.0
CG B:ASP100 3.0 22.5 1.0
CE1 B:HIS238 3.2 33.2 1.0
CD2 B:HIS238 3.2 28.0 1.0
ZN B:ZN1001 3.4 22.6 1.0
OD1 B:ASP100 3.4 21.6 1.0
O B:HOH1105 4.0 23.4 1.0
CG B:GLU135 4.1 27.4 1.0
OE1 B:GLU134 4.2 28.0 1.0
CB B:ASP100 4.3 24.0 1.0
ND1 B:HIS238 4.3 33.3 1.0
CG B:HIS238 4.4 31.3 1.0
O B:HOH1187 4.6 42.5 1.0
NE2 B:HIS67 4.6 22.4 1.0
CE1 B:HIS67 4.7 17.3 1.0
CG1 B:VAL71 4.9 24.5 1.0
CD1 B:ILE237 4.9 30.9 1.0

Reference:

B.Nocek, A.Starus, M.Makowska-Grzyska, B.Gutierrez, S.Sanchez, R.Jedrzejczak, J.C.Mack, K.W.Olsen, A.Joachimiak, R.C.Holz. The Dimerization Domain in Dape Enzymes Is Required For Catalysis. Plos One V. 9 93593 2014.
ISSN: ESSN 1932-6203
PubMed: 24806882
DOI: 10.1371/JOURNAL.PONE.0093593
Page generated: Sat Oct 26 23:50:12 2024

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