Zinc in PDB 8aq0: Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C

Enzymatic activity of Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C

All present enzymatic activity of Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C:
3.5.1.87;

Protein crystallography data

The structure of Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C, PDB code: 8aq0 was solved by H.J.Rozeboom, C.Mayer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.23 / 2.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 132.569, 42.047, 137.211, 90, 94.78, 90
R / Rfree (%) 17.3 / 23.8

Other elements in 8aq0:

The structure of Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C (pdb code 8aq0). 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 L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C, PDB code: 8aq0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8aq0

Go back to Zinc Binding Sites List in 8aq0
Zinc binding site 1 out of 4 in the Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C


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 L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:47.6
occ:0.44
 FE A:FE502 0.6 35.4 0.2
OD1 A:ASP98 2.0 40.9 1.0
O A:HOH636 2.1 32.8 1.0
N1 A:NV6505 2.2 60.7 1.0
NE2 A:HIS194 2.3 46.4 1.0
NE2 A:HIS87 2.4 41.9 1.0
O1 A:NV6505 2.6 53.4 1.0
C1 A:NV6505 2.7 66.8 1.0
CG A:ASP98 3.2 40.4 1.0
CE1 A:HIS194 3.2 47.6 1.0
CE1 A:HIS87 3.3 39.3 1.0
CD2 A:HIS194 3.3 47.4 1.0
CD2 A:HIS87 3.4 40.0 1.0
FE A:FE504 3.5 39.2 0.2
ZN A:ZN503 3.5 45.3 0.4
OE1 A:GLU132 3.7 47.0 1.0
OD2 A:ASP98 3.7 41.9 1.0
N2 A:NV6505 3.9 70.7 1.0
CD A:GLU132 4.0 43.4 1.0
N A:GLY99 4.0 42.4 1.0
ND1 A:HIS362 4.1 46.5 1.0
OE2 A:GLU132 4.1 44.7 1.0
OE2 A:GLU133 4.3 41.6 1.0
ND1 A:HIS194 4.4 43.0 1.0
OE1 A:GLN197 4.4 37.4 1.0
CG A:HIS194 4.4 44.3 1.0
ND1 A:HIS87 4.5 37.7 1.0
CE1 A:HIS362 4.5 47.7 1.0
CB A:ASP98 4.5 39.4 1.0
CA A:GLY99 4.5 40.6 1.0
C A:ASP98 4.5 38.9 1.0
CG A:HIS87 4.5 38.5 1.0
NE2 A:GLN197 4.6 35.5 1.0
O A:HOH604 4.7 38.4 1.0
CD A:GLU133 4.7 37.7 1.0
CA A:ASP98 4.7 37.3 1.0
OE1 A:GLU133 4.8 43.7 1.0
CD A:GLN197 4.8 38.1 1.0
CG A:GLU132 4.9 45.8 1.0
O A:GLY361 4.9 43.3 1.0

Zinc binding site 2 out of 4 in 8aq0

Go back to Zinc Binding Sites List in 8aq0
Zinc binding site 2 out of 4 in the Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C


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 L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:45.3
occ:0.44
 FE A:FE504 0.1 39.2 0.2
OD2 A:ASP98 2.0 41.9 1.0
O1 A:NV6505 2.0 53.4 1.0
OE2 A:GLU133 2.1 41.6 1.0
OE1 A:GLU133 2.1 43.7 1.0
NE2 A:HIS386 2.2 45.4 1.0
CD A:GLU133 2.4 37.7 1.0
C1 A:NV6505 2.6 66.8 1.0
CG A:ASP98 2.8 40.4 1.0
N1 A:NV6505 3.0 60.7 1.0
OD1 A:ASP98 3.1 40.9 1.0
CD2 A:HIS386 3.2 43.3 1.0
CE1 A:HIS386 3.2 41.5 1.0
ZN A:ZN501 3.5 47.6 0.4
N2 A:NV6505 3.7 70.7 1.0
NE2 A:GLN197 3.8 35.5 1.0
FE A:FE502 3.8 35.4 0.2
CG A:GLU133 3.9 38.6 1.0
OE1 A:GLU132 4.1 47.0 1.0
O A:HOH634 4.2 43.5 1.0
CB A:ASP98 4.2 39.4 1.0
ND1 A:HIS386 4.3 40.7 1.0
CG A:HIS386 4.3 40.5 1.0
C2 A:NV6505 4.4 72.5 1.0
CE1 A:HIS87 4.4 39.3 1.0
NE2 A:HIS87 4.5 41.9 1.0
CD2 B:HIS230 4.5 46.3 1.0
NE2 B:HIS230 4.6 45.8 1.0
CG A:GLN91 4.8 35.8 1.0
NE2 A:GLN91 4.8 30.9 1.0
CD A:GLN197 4.8 38.1 1.0
CB A:GLU133 4.9 36.4 1.0
O4 A:NV6505 5.0 68.8 1.0
OE1 A:GLN197 5.0 37.4 1.0

Zinc binding site 3 out of 4 in 8aq0

Go back to Zinc Binding Sites List in 8aq0
Zinc binding site 3 out of 4 in the Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C


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 L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:41.7
occ:0.44
 FE B:FE502 0.1 37.5 0.2
OD1 B:ASP98 2.1 40.9 1.0
N1 B:NV6505 2.1 55.9 1.0
NE2 B:HIS194 2.1 44.8 1.0
O B:HOH631 2.2 31.6 1.0
NE2 B:HIS87 2.2 45.5 1.0
CE1 B:HIS194 3.1 47.3 1.0
CD2 B:HIS194 3.1 44.1 1.0
CG B:ASP98 3.2 40.5 1.0
CD2 B:HIS87 3.2 43.2 1.0
CE1 B:HIS87 3.2 48.0 1.0
C1 B:NV6505 3.4 64.6 1.0
FE B:FE504 3.7 37.1 0.2
ZN B:ZN503 3.7 44.1 0.4
OE1 B:GLU132 3.8 46.4 1.0
OD2 B:ASP98 3.8 43.1 1.0
N B:GLY99 3.9 40.4 1.0
O1 B:NV6505 3.9 55.2 1.0
ND1 B:HIS362 4.1 35.8 1.0
CD B:GLU132 4.1 46.3 1.0
CA B:GLY99 4.2 37.8 1.0
ND1 B:HIS194 4.2 45.4 1.0
CG B:HIS194 4.3 43.7 1.0
OE2 B:GLU132 4.3 47.7 1.0
OE2 B:GLU133 4.4 45.0 1.0
N2 B:NV6505 4.4 68.6 1.0
ND1 B:HIS87 4.4 46.0 1.0
C B:ASP98 4.4 41.3 1.0
CG B:HIS87 4.4 45.3 1.0
O B:HOH604 4.4 33.6 1.0
CB B:ASP98 4.5 40.3 1.0
CE1 B:HIS362 4.5 37.8 1.0
OE1 B:GLN197 4.6 48.6 1.0
CA B:ASP98 4.7 38.6 1.0
NE2 B:GLN197 4.8 45.7 1.0
CD B:GLU133 4.9 43.0 1.0
CG B:GLU132 4.9 46.2 1.0
CD B:GLN197 5.0 48.7 1.0

Zinc binding site 4 out of 4 in 8aq0

Go back to Zinc Binding Sites List in 8aq0
Zinc binding site 4 out of 4 in the Crystal Structure of L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C


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 L-N-Carbamoylase From Sinorhizobium Meliloti Mutant L217G/F329C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:44.1
occ:0.44
 FE B:FE504 0.1 37.1 0.2
O1 B:NV6505 2.0 55.2 1.0
OD2 B:ASP98 2.0 43.1 1.0
OE1 B:GLU133 2.1 45.9 1.0
OE2 B:GLU133 2.1 45.0 1.0
NE2 B:HIS386 2.2 43.1 1.0
CD B:GLU133 2.4 43.0 1.0
C1 B:NV6505 2.7 64.6 1.0
N1 B:NV6505 2.9 55.9 1.0
CG B:ASP98 2.9 40.5 1.0
CE1 B:HIS386 3.2 42.6 1.0
CD2 B:HIS386 3.2 42.6 1.0
OD1 B:ASP98 3.2 40.9 1.0
FE B:FE502 3.6 37.5 0.2
ZN B:ZN501 3.7 41.7 0.4
CG B:GLU133 3.9 41.2 1.0
N2 B:NV6505 3.9 68.6 1.0
NE2 B:GLN197 3.9 45.7 1.0
O B:HOH622 4.1 33.8 1.0
OE1 B:GLU132 4.1 46.4 1.0
CB B:ASP98 4.3 40.3 1.0
ND1 B:HIS386 4.3 39.0 1.0
CG B:HIS386 4.4 40.7 1.0
CE1 B:HIS87 4.4 48.0 1.0
CD2 A:HIS230 4.5 51.8 1.0
NE2 A:HIS230 4.5 53.0 1.0
NE2 B:HIS87 4.6 45.5 1.0
C2 B:NV6505 4.6 81.6 1.0
CG B:GLN91 4.7 38.2 1.0
NE2 B:GLN91 4.8 37.3 1.0
CB B:GLU133 4.8 39.7 1.0
O B:HOH639 4.9 42.5 1.0
CD B:GLN197 4.9 48.7 1.0

Reference:

R.Rubini, S.C.Jansen, H.Beekhuis, H.J.Rozeboom, C.Mayer. Selecting Better Biocatalysts By Complementing Recoded Bacteria. Angew.Chem.Int.Ed.Engl. 13942 2022.
ISSN: ESSN 1521-3773
PubMed: 36342942
DOI: 10.1002/ANIE.202213942
Page generated: Wed Oct 30 17:57:54 2024

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