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Zinc in PDB 8f8o: Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids

Enzymatic activity of Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids

All present enzymatic activity of Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids:
3.5.1.18;

Protein crystallography data

The structure of Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids, PDB code: 8f8o was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, I.Dubrovska, S.Pshenychnyi, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases(Csbid), Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.659, 102.533, 145.491, 90, 90, 90
R / Rfree (%) 18.9 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids (pdb code 8f8o). 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 Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids, PDB code: 8f8o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8f8o

Go back to Zinc Binding Sites List in 8f8o
Zinc binding site 1 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids


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 Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:43.4
occ:1.00
 O4 A:SIN403 2.0 38.6 1.0
OE2 A:GLU164 2.0 42.5 1.0
OD1 A:ASP101 2.0 50.4 1.0
NE2 A:HIS68 2.0 49.7 1.0
OE1 A:GLU164 2.5 47.0 1.0
CD A:GLU164 2.6 40.2 1.0
CE1 A:HIS68 3.0 49.2 1.0
C4 A:SIN403 3.0 46.8 1.0
CD2 A:HIS68 3.1 44.2 1.0
CG A:ASP101 3.1 45.6 1.0
C3 A:SIN403 3.5 42.3 1.0
OD2 A:ASP101 3.5 52.6 1.0
ZN A:ZN402 3.8 43.3 1.0
OE2 A:GLU136 3.8 42.1 1.0
OE2 A:GLU135 3.9 38.2 1.0
O3 A:SIN403 4.0 47.3 1.0
CG A:GLU164 4.1 38.5 1.0
ND1 A:HIS68 4.1 44.6 1.0
CG A:HIS68 4.2 43.6 1.0
CG A:MSE102 4.2 39.1 1.0
SE A:MSE102 4.3 41.7 1.0
CD A:GLU135 4.3 38.9 1.0
OE1 A:GLU135 4.3 43.1 1.0
CB A:MSE102 4.3 40.7 1.0
CB A:ASP101 4.3 45.6 1.0
CD A:GLU136 4.6 38.9 1.0
C A:ASP101 4.6 44.8 1.0
CA A:ASP101 4.6 42.9 1.0
CD A:PRO165 4.7 42.1 1.0
O A:ASP101 4.7 37.2 1.0
CB A:GLU164 4.7 40.3 1.0
OHN A:2OP404 4.8 40.9 1.0
N A:MSE102 4.9 40.0 1.0
CA A:GLU164 5.0 40.0 1.0
C2 A:SIN403 5.0 43.4 1.0

Zinc binding site 2 out of 4 in 8f8o

Go back to Zinc Binding Sites List in 8f8o
Zinc binding site 2 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids


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 Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:43.3
occ:1.00
 OE2 A:GLU136 2.0 42.1 1.0
OD2 A:ASP101 2.0 52.6 1.0
O3 A:SIN403 2.0 47.3 1.0
NE2 A:HIS350 2.1 50.0 1.0
O4 A:SIN403 2.4 38.6 1.0
C4 A:SIN403 2.5 46.8 1.0
OE1 A:GLU136 2.5 36.9 1.0
CD A:GLU136 2.6 38.9 1.0
CE1 A:HIS350 3.0 51.5 1.0
CG A:ASP101 3.0 45.6 1.0
CD2 A:HIS350 3.1 50.3 1.0
OD1 A:ASP101 3.4 50.4 1.0
ZN A:ZN401 3.8 43.4 1.0
O A:HOH564 3.9 37.8 1.0
C3 A:SIN403 4.0 42.3 1.0
CG A:GLU136 4.1 39.5 1.0
ND1 A:HIS350 4.1 49.7 1.0
CG A:HIS350 4.2 52.1 1.0
CB A:ASP101 4.3 45.6 1.0
NE2 B:HIS195 4.4 37.1 1.0
CD2 B:HIS195 4.4 38.5 1.0
OHN A:2OP404 4.4 40.9 1.0
CA A:2OP404 4.4 49.5 1.0
OE2 A:GLU135 4.5 38.2 1.0
CG1 A:VAL72 4.5 50.2 1.0
NE2 A:HIS68 4.7 49.7 1.0
ND2 B:ASN246 4.7 44.3 1.0
C2 A:SIN403 4.7 43.4 1.0
CE1 A:HIS68 4.8 49.2 1.0

Zinc binding site 3 out of 4 in 8f8o

Go back to Zinc Binding Sites List in 8f8o
Zinc binding site 3 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids


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 Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:46.1
occ:1.00
 OE2 B:GLU164 2.0 44.6 1.0
O3 B:SIN403 2.0 46.4 1.0
OD1 B:ASP101 2.0 45.9 1.0
NE2 B:HIS68 2.0 49.7 1.0
CD B:GLU164 2.6 44.7 1.0
OE1 B:GLU164 2.6 47.3 1.0
C4 B:SIN403 2.9 39.5 1.0
CE1 B:HIS68 2.9 52.0 1.0
CG B:ASP101 3.0 43.8 1.0
CD2 B:HIS68 3.0 49.2 1.0
C3 B:SIN403 3.3 44.8 1.0
OD2 B:ASP101 3.4 45.2 1.0
OE2 B:GLU136 3.7 39.7 1.0
ZN B:ZN402 3.8 45.5 1.0
OE2 B:GLU135 4.0 38.4 1.0
O4 B:SIN403 4.0 43.1 1.0
ND1 B:HIS68 4.1 47.2 1.0
CG B:GLU164 4.1 39.8 1.0
CG B:MSE102 4.1 45.8 1.0
CG B:HIS68 4.1 46.4 1.0
CB B:ASP101 4.3 44.9 1.0
SE B:MSE102 4.3 46.6 1.0
CD B:GLU135 4.4 41.3 1.0
CB B:MSE102 4.4 46.2 1.0
OE1 B:GLU135 4.4 43.1 1.0
CD B:GLU136 4.6 44.5 1.0
CA B:ASP101 4.6 45.5 1.0
CD B:PRO165 4.6 48.3 1.0
C B:ASP101 4.6 44.9 1.0
OHN B:2OP404 4.7 44.0 1.0
CB B:GLU164 4.8 44.1 1.0
C2 B:SIN403 4.8 41.2 1.0
O B:ASP101 4.9 41.8 1.0
N B:MSE102 5.0 45.4 1.0

Zinc binding site 4 out of 4 in 8f8o

Go back to Zinc Binding Sites List in 8f8o
Zinc binding site 4 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids


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 Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:45.5
occ:1.00
 OE2 B:GLU136 2.0 39.7 1.0
NE2 B:HIS350 2.0 43.6 1.0
O4 B:SIN403 2.0 43.1 1.0
OD2 B:ASP101 2.0 45.2 1.0
O3 B:SIN403 2.2 46.4 1.0
C4 B:SIN403 2.4 39.5 1.0
OE1 B:GLU136 2.5 36.6 1.0
CD B:GLU136 2.5 44.5 1.0
CE1 B:HIS350 2.9 46.2 1.0
CG B:ASP101 3.0 43.8 1.0
CD2 B:HIS350 3.1 43.2 1.0
OD1 B:ASP101 3.4 45.9 1.0
ZN B:ZN401 3.8 46.1 1.0
O B:HOH590 3.8 41.9 1.0
C3 B:SIN403 3.9 44.8 1.0
CG B:GLU136 4.0 42.4 1.0
ND1 B:HIS350 4.1 40.9 1.0
CG B:HIS350 4.2 43.6 1.0
NE2 A:HIS195 4.2 43.5 1.0
CB B:ASP101 4.3 44.9 1.0
CG1 B:VAL72 4.3 46.2 1.0
CD2 A:HIS195 4.4 42.7 1.0
CA B:2OP404 4.4 41.8 1.0
OHN B:2OP404 4.5 44.0 1.0
ND2 A:ASN246 4.6 38.5 1.0
OE2 B:GLU135 4.6 38.4 1.0
CE1 B:HIS68 4.6 52.0 1.0
C2 B:SIN403 4.7 41.2 1.0
NE2 B:HIS68 4.7 49.7 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, I.Dubrovska, S.Pshenychnyi, K.J.F.Satchell, Center For Structural Biology Of Infectious Diseases (Csbid). Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic and L-Lactic Acids To Be Published.
Page generated: Wed Oct 30 20:14:25 2024

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