Zinc in PDB 8apz: Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti

Enzymatic activity of Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti

All present enzymatic activity of Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti:
3.5.1.87;

Protein crystallography data

The structure of Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti, PDB code: 8apz 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) 43.22 / 1.75
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 133.25, 41.801, 133.996, 90, 94.08, 90
R / Rfree (%) 15 / 18.6

Other elements in 8apz:

The structure of Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 8apz

Go back to Zinc Binding Sites List in 8apz
Zinc binding site 1 out of 4 in the Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti


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 Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.7
occ:0.40
 FE A:FE502 0.1 15.4 0.3
OD1 A:ASP98 2.0 18.3 1.0
NE A:ORD505 2.1 24.6 1.0
NE2 A:HIS87 2.1 17.2 1.0
O A:HOH739 2.1 20.6 1.0
NE2 A:HIS194 2.1 19.2 1.0
CD A:ORD505 2.5 31.9 1.0
CD2 A:HIS87 3.1 17.7 1.0
CE1 A:HIS194 3.1 20.0 1.0
CE1 A:HIS87 3.1 17.5 1.0
CD2 A:HIS194 3.1 18.7 1.0
CG A:ASP98 3.3 18.5 1.0
FE A:FE504 3.6 19.4 0.3
ZN A:ZN503 3.6 19.6 0.4
OE1 A:GLU132 3.6 28.1 1.0
N A:GLY99 3.8 19.5 1.0
OD2 A:ASP98 3.9 19.5 1.0
CG A:ORD505 4.0 32.5 1.0
CD A:GLU132 4.0 25.1 1.0
CA A:GLY99 4.1 18.9 1.0
OE2 A:GLU133 4.2 25.6 1.0
ND1 A:HIS362 4.2 21.9 1.0
ND1 A:HIS194 4.2 20.6 1.0
ND1 A:HIS87 4.2 17.0 1.0
CG A:HIS87 4.2 17.1 1.0
CG A:HIS194 4.3 19.0 1.0
OE2 A:GLU132 4.3 30.2 1.0
C A:ASP98 4.3 18.0 1.0
NE2 A:GLN197 4.4 20.6 1.0
CB A:ASP98 4.5 18.5 1.0
CB A:ORD505 4.5 37.5 1.0
O A:HOH607 4.5 19.1 1.0
CE1 A:HIS362 4.6 22.6 1.0
CA A:ASP98 4.6 19.1 1.0
CD A:GLU133 4.7 25.8 1.0
OE1 A:GLN197 4.7 21.4 1.0
OE1 A:GLU133 4.8 26.4 1.0
CG A:GLU132 4.8 22.4 1.0
CD A:GLN197 4.9 21.0 1.0
OG A:SER86 5.0 19.8 1.0
O A:ASP98 5.0 18.2 1.0

Zinc binding site 2 out of 4 in 8apz

Go back to Zinc Binding Sites List in 8apz
Zinc binding site 2 out of 4 in the Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti


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 Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:19.6
occ:0.40
 FE A:FE504 0.1 19.4 0.3
OD2 A:ASP98 2.0 19.5 1.0
NE A:ORD505 2.0 24.6 1.0
OE2 A:GLU133 2.1 25.6 1.0
NE2 A:HIS386 2.1 20.7 1.0
OE1 A:GLU133 2.1 26.4 1.0
CD A:GLU133 2.5 25.8 1.0
CD A:ORD505 2.8 31.9 1.0
CG A:ASP98 2.8 18.5 1.0
CD2 A:HIS386 3.0 20.7 1.0
OD1 A:ASP98 3.1 18.3 1.0
CE1 A:HIS386 3.1 20.8 1.0
CG A:ORD505 3.3 32.5 1.0
FE A:FE502 3.6 15.4 0.3
ZN A:ZN501 3.6 15.7 0.4
NE2 A:GLN197 3.7 20.6 1.0
O A:HOH696 4.0 18.0 1.0
CG A:GLU133 4.0 23.5 1.0
OE1 A:GLU132 4.1 28.1 1.0
CG A:HIS386 4.2 18.8 1.0
CE1 A:HIS87 4.2 17.5 1.0
CB A:ASP98 4.2 18.5 1.0
ND1 A:HIS386 4.2 19.9 1.0
CB A:ORD505 4.3 37.5 1.0
NE2 A:HIS87 4.4 17.2 1.0
CD2 B:HIS230 4.5 22.2 1.0
NE2 B:HIS230 4.5 23.7 1.0
CG A:GLN91 4.5 18.4 1.0
NE2 A:GLN91 4.7 17.4 1.0
CA A:ORD505 4.7 43.9 1.0
O A:HOH712 4.8 18.2 1.0
CD A:GLN197 4.8 21.0 1.0

Zinc binding site 3 out of 4 in 8apz

Go back to Zinc Binding Sites List in 8apz
Zinc binding site 3 out of 4 in the Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti


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 Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:14.2
occ:0.40
 FE B:FE502 0.1 13.9 0.3
NE B:ORD505 2.0 25.4 1.0
O B:HOH762 2.0 17.7 1.0
OD1 B:ASP98 2.1 18.0 1.0
NE2 B:HIS87 2.1 14.7 1.0
NE2 B:HIS194 2.1 17.8 1.0
CD B:ORD505 2.9 36.9 1.0
CD2 B:HIS87 3.0 15.4 1.0
CE1 B:HIS87 3.1 15.6 1.0
CE1 B:HIS194 3.1 18.0 1.0
CD2 B:HIS194 3.1 17.4 1.0
CG B:ASP98 3.3 18.8 1.0
FE B:FE504 3.5 18.6 0.3
ZN B:ZN503 3.6 19.0 0.4
OE1 B:GLU132 3.7 22.1 1.0
N B:GLY99 3.7 17.8 1.0
OD2 B:ASP98 3.9 19.9 1.0
CG B:ORD505 3.9 33.0 1.0
CD B:GLU132 4.0 22.9 1.0
CA B:GLY99 4.1 19.0 1.0
ND1 B:HIS362 4.1 17.2 1.0
ND1 B:HIS87 4.2 14.9 1.0
OE2 B:GLU133 4.2 20.3 1.0
CG B:HIS87 4.2 15.4 1.0
ND1 B:HIS194 4.2 18.2 1.0
CG B:HIS194 4.3 17.4 1.0
OE2 B:GLU132 4.3 25.3 1.0
C B:ASP98 4.3 18.7 1.0
NE2 B:GLN197 4.5 19.9 1.0
CB B:ASP98 4.5 19.3 1.0
CE1 B:HIS362 4.6 18.4 1.0
O B:HOH610 4.6 19.9 1.0
CA B:ASP98 4.6 18.3 1.0
CD B:GLU133 4.7 18.4 1.0
OE1 B:GLN197 4.8 20.9 1.0
OE1 B:GLU133 4.8 23.9 1.0
CB B:ORD505 4.8 43.2 1.0
CG B:GLU132 4.8 19.0 1.0
CD B:GLN197 4.9 20.0 1.0
OG B:SER86 4.9 18.3 1.0

Zinc binding site 4 out of 4 in 8apz

Go back to Zinc Binding Sites List in 8apz
Zinc binding site 4 out of 4 in the Crystal Structure of Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti


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 Wild-Type L-N-Carbamoylase From Sinorhizobium Meliloti within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:19.0
occ:0.40
 FE B:FE504 0.1 18.6 0.3
OD2 B:ASP98 2.0 19.9 1.0
NE B:ORD505 2.0 25.4 1.0
OE2 B:GLU133 2.1 20.3 1.0
OE1 B:GLU133 2.1 23.9 1.0
NE2 B:HIS386 2.2 20.2 1.0
CD B:ORD505 2.3 36.9 1.0
CD B:GLU133 2.5 18.4 1.0
CG B:ASP98 2.9 18.8 1.0
OD1 B:ASP98 3.1 18.0 1.0
CD2 B:HIS386 3.1 21.0 1.0
CE1 B:HIS386 3.2 20.0 1.0
CG B:ORD505 3.5 33.0 1.0
FE B:FE502 3.6 13.9 0.3
ZN B:ZN501 3.6 14.2 0.4
NE2 B:GLN197 3.7 19.9 1.0
CG B:GLU133 4.0 17.5 1.0
O B:HOH755 4.0 17.8 1.0
OE1 B:GLU132 4.1 22.1 1.0
CE1 B:HIS87 4.2 15.6 1.0
CG B:HIS386 4.3 19.4 1.0
CB B:ASP98 4.3 19.3 1.0
ND1 B:HIS386 4.3 19.2 1.0
NE2 B:HIS87 4.3 14.7 1.0
CD2 A:HIS230 4.5 21.7 1.0
CG B:GLN91 4.5 16.5 1.0
CB B:ORD505 4.5 43.2 1.0
NE2 A:HIS230 4.5 23.2 1.0
NE2 B:GLN91 4.6 15.4 1.0
N B:ORD505 4.6 44.9 1.0
CA B:ORD505 4.6 43.8 1.0
O B:HOH703 4.7 18.9 1.0
CD B:GLN197 4.8 20.0 1.0
CB B:GLU133 5.0 18.4 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 17:56:54 2024

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