Atomistry » Zinc » PDB 8f1b-8fgl » 8f8o
Atomistry »
  Zinc »
    PDB 8f1b-8fgl »
      8f8o »

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: Fri Aug 22 09:53:44 2025

Last articles

Zn in 8TH9
Zn in 8TGP
Zn in 8TAU
Zn in 8TBX
Zn in 8TAR
Zn in 8TB2
Zn in 8T7P
Zn in 8T83
Zn in 8T75
Zn in 8T59
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy