Zinc in PDB 7t1q: Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid

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

All present enzymatic activity of Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid:
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 Acid, PDB code: 7t1q was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, I.Dubrovska, S.Pshenychnyi, K.J.F.Satchell, 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) 29.71 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.323, 103.46, 145.157, 90, 90, 90
R / Rfree (%) 18.8 / 23.3

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 Acid (pdb code 7t1q). 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 Acid, PDB code: 7t1q:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7t1q

Go back to Zinc Binding Sites List in 7t1q
Zinc binding site 1 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid


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 Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:42.2
occ:1.00
 NE2 A:HIS68 2.0 48.6 1.0
OE2 A:GLU164 2.1 40.9 1.0
OD1 A:ASP101 2.1 57.5 1.0
O4 A:SIN401 2.1 40.2 1.0
OE1 A:GLU164 2.4 42.4 1.0
CD A:GLU164 2.6 39.5 1.0
CG A:ASP101 2.9 52.7 1.0
CE1 A:HIS68 3.0 48.7 1.0
CD2 A:HIS68 3.0 45.5 1.0
C4 A:SIN401 3.1 47.0 1.0
OD2 A:ASP101 3.3 56.2 1.0
OE2 A:GLU135 3.6 48.5 1.0
C3 A:SIN401 3.6 47.5 1.0
ZN A:ZN405 3.8 46.2 1.0
OE2 A:GLU136 3.9 45.3 1.0
O3 A:SIN401 4.1 41.0 1.0
CG A:GLU164 4.1 39.7 1.0
CD A:GLU135 4.1 49.2 1.0
ND1 A:HIS68 4.1 45.9 1.0
CG A:HIS68 4.2 44.5 1.0
CG A:MSE102 4.2 43.0 1.0
OE1 A:GLU135 4.2 52.9 1.0
CB A:ASP101 4.3 49.8 1.0
SE A:MSE102 4.3 42.8 1.0
CB A:MSE102 4.4 44.5 1.0
CD A:GLU136 4.5 48.9 1.0
CA A:ASP101 4.6 47.5 1.0
C A:ASP101 4.6 46.5 1.0
CD A:PRO165 4.7 45.2 1.0
CB A:GLU164 4.8 43.1 1.0
O A:ASP101 4.8 42.5 1.0
CA A:GLU164 5.0 42.0 1.0
OE1 A:GLU136 5.0 49.2 1.0
N A:MSE102 5.0 45.1 1.0

Zinc binding site 2 out of 4 in 7t1q

Go back to Zinc Binding Sites List in 7t1q
Zinc binding site 2 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid


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 Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:46.2
occ:1.00
 OE2 A:GLU136 2.1 45.3 1.0
O3 A:SIN401 2.1 41.0 1.0
OD2 A:ASP101 2.1 56.2 1.0
NE2 A:HIS350 2.1 60.0 1.0
OE1 A:GLU136 2.5 49.2 1.0
O4 A:SIN401 2.5 40.2 1.0
CD A:GLU136 2.6 48.9 1.0
C4 A:SIN401 2.6 47.0 1.0
CE1 A:HIS350 3.1 62.9 1.0
CD2 A:HIS350 3.1 58.3 1.0
CG A:ASP101 3.1 52.7 1.0
OD1 A:ASP101 3.6 57.5 1.0
ZN A:ZN404 3.8 42.2 1.0
O A:HOH557 4.0 50.8 1.0
C3 A:SIN401 4.0 47.5 1.0
CG A:GLU136 4.1 48.1 1.0
ND1 A:HIS350 4.2 64.1 1.0
CG A:HIS350 4.2 60.6 1.0
CB A:ASP101 4.4 49.8 1.0
OE2 A:GLU135 4.4 48.5 1.0
CD2 B:HIS195 4.4 53.4 1.0
NE2 B:HIS195 4.5 51.9 1.0
CG1 A:VAL72 4.6 54.9 1.0
CH3 A:ACT402 4.7 47.7 1.0
C2 A:SIN401 4.7 48.2 1.0
NE2 A:HIS68 4.8 48.6 1.0
ND2 B:ASN246 4.8 57.1 1.0
CE1 A:HIS68 4.8 48.7 1.0

Zinc binding site 3 out of 4 in 7t1q

Go back to Zinc Binding Sites List in 7t1q
Zinc binding site 3 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid


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 Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:43.8
occ:1.00
 NE2 B:HIS68 2.1 48.5 1.0
OD1 B:ASP101 2.1 52.6 1.0
O3 B:SIN401 2.1 43.3 1.0
OE2 B:GLU164 2.1 51.5 1.0
OE1 B:GLU164 2.6 43.8 1.0
CD B:GLU164 2.6 46.8 1.0
CG B:ASP101 3.0 46.8 1.0
C4 B:SIN401 3.0 42.8 1.0
CE1 B:HIS68 3.0 51.3 1.0
CD2 B:HIS68 3.1 46.7 1.0
OD2 B:ASP101 3.2 46.0 1.0
C3 B:SIN401 3.3 42.9 1.0
OE2 B:GLU135 3.7 54.0 1.0
ZN B:ZN404 3.9 44.3 1.0
OE2 B:GLU136 3.9 42.9 1.0
CG B:GLU164 4.1 43.2 1.0
O4 B:SIN401 4.1 45.8 1.0
CG B:MSE102 4.1 51.0 1.0
ND1 B:HIS68 4.1 51.0 1.0
CD B:GLU135 4.2 48.7 1.0
CG B:HIS68 4.2 48.2 1.0
SE B:MSE102 4.3 46.4 1.0
CB B:ASP101 4.3 47.6 1.0
OE1 B:GLU135 4.4 50.5 1.0
CB B:MSE102 4.4 49.8 1.0
CD B:GLU136 4.6 39.9 1.0
CA B:ASP101 4.7 48.5 1.0
CD B:PRO165 4.7 46.1 1.0
CB B:GLU164 4.7 45.2 1.0
C B:ASP101 4.7 49.9 1.0
C2 B:SIN401 4.8 43.2 1.0
OE1 B:GLU136 4.9 38.5 1.0

Zinc binding site 4 out of 4 in 7t1q

Go back to Zinc Binding Sites List in 7t1q
Zinc binding site 4 out of 4 in the Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid


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 Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:44.3
occ:1.00
 NE2 B:HIS350 2.0 48.2 1.0
OD2 B:ASP101 2.1 46.0 1.0
OE2 B:GLU136 2.1 42.9 1.0
O4 B:SIN401 2.1 45.8 1.0
O3 B:SIN401 2.4 43.3 1.0
OE1 B:GLU136 2.5 38.5 1.0
C4 B:SIN401 2.5 42.8 1.0
CD B:GLU136 2.6 39.9 1.0
CE1 B:HIS350 2.9 49.4 1.0
CD2 B:HIS350 3.0 48.9 1.0
CG B:ASP101 3.1 46.8 1.0
OD1 B:ASP101 3.7 52.6 1.0
O B:HOH617 3.8 46.9 1.0
ZN B:ZN403 3.9 43.8 1.0
C3 B:SIN401 3.9 42.9 1.0
ND1 B:HIS350 4.1 46.8 1.0
CG B:GLU136 4.1 39.9 1.0
CG B:HIS350 4.1 48.7 1.0
CD2 A:HIS195 4.2 46.3 1.0
NE2 A:HIS195 4.2 46.1 1.0
CB B:ASP101 4.3 47.6 1.0
CG1 B:VAL72 4.4 51.4 1.0
ND2 A:ASN246 4.5 46.0 1.0
OE2 B:GLU135 4.5 54.0 1.0
CE1 B:HIS68 4.7 51.3 1.0
C2 B:SIN401 4.7 43.2 1.0
NE2 B:HIS68 4.7 48.5 1.0
CH3 B:ACT402 4.8 48.9 1.0

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, I.Dubrovska, S.Pshenychnyi, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of the Succinyl-Diaminopimelate Desuccinylase (Dape) From Acinetobacter Baumannii in Complex with Succinic Acid. To Be Published.
Page generated: Wed Oct 30 11:24:32 2024

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