Zinc in PDB 8ori: Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)

Protein crystallography data

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic), PDB code: 8ori was solved by J.Loch, P.Worsztynowicz, J.Sliwiak, B.Imiolczyk, M.Grzechowiak, M.Gilski, M.Jaskolski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.42 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.2, 89.881, 169.797, 90, 90, 90
R / Rfree (%) 13 / 17.7

Other elements in 8ori:

The structure of Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) also contains other interesting chemical elements:

Chlorine (Cl) 10 atoms
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) (pdb code 8ori). 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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic), PDB code: 8ori:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8ori

Go back to Zinc Binding Sites List in 8ori
Zinc binding site 1 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:17.7
occ:0.50
 O A:HOH504 1.9 18.1 0.5
O A:HOH520 2.2 30.9 1.0
SG A:CYS134 2.3 13.9 0.5
SG A:CYS188 2.3 16.4 0.5
NZ A:LYS137 2.3 26.3 1.0
CE A:LYS137 3.1 21.6 1.0
OD2 A:ASP186 3.2 16.4 0.5
CB A:CYS134 3.3 14.3 0.5
CB A:CYS134 3.4 14.5 0.5
CB A:CYS188 3.4 16.8 0.5
CB A:CYS188 3.6 19.4 0.5
OD2 A:ASP186 3.7 21.3 0.5
CE A:LYS50 3.8 16.2 1.0
SG A:CYS188 3.9 18.4 0.5
CG A:ASP186 3.9 15.8 0.5
O A:HOH797 4.1 34.2 1.0
O A:HOH547 4.1 21.9 1.0
NZ A:LYS50 4.1 16.7 1.0
OD1 A:ASP186 4.2 18.6 0.5
SG A:CYS134 4.2 17.7 0.5
CG A:ASP186 4.3 18.9 0.5
O A:HOH779 4.3 11.5 0.5
O A:HOH503 4.4 20.3 0.8
N A:CYS188 4.5 16.9 0.5
CD A:LYS137 4.5 20.2 1.0
NE2 A:HIS138 4.5 15.7 1.0
N A:CYS188 4.5 17.9 0.5
OG A:SER47 4.5 17.5 0.8
CA A:CYS188 4.6 17.5 0.5
CA A:CYS134 4.7 12.7 0.5
CA A:CYS134 4.7 12.2 0.5
O A:HOH515 4.7 18.7 0.5
O A:HOH741 4.7 24.5 0.5
CA A:CYS188 4.7 19.2 0.5
CB A:ASP186 4.8 17.8 0.5
OD1 A:ASP186 4.9 18.1 0.5
CD2 A:HIS138 5.0 16.8 1.0
CB A:ASP186 5.0 15.2 0.5
CD1 A:ILE190 5.0 22.3 1.0

Zinc binding site 2 out of 4 in 8ori

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Zinc binding site 2 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:14.2
occ:0.50
 O B:HOH1086 1.6 22.1 0.5
O B:HOH805 1.8 20.9 0.6
O B:HOH1083 2.1 14.6 0.5
SG B:CYS134 2.3 13.0 0.5
SG B:CYS188 2.3 13.8 0.5
NZ B:LYS137 2.5 23.0 1.0
O B:HOH1083 3.0 19.6 0.5
CE B:LYS137 3.1 20.2 1.0
OD2 B:ASP186 3.3 15.7 0.5
CB B:CYS188 3.3 12.8 0.5
CB B:CYS134 3.3 12.2 0.5
CB B:CYS134 3.4 15.2 0.5
CB B:CYS188 3.4 17.1 0.5
OD2 B:ASP186 3.7 14.6 0.5
SG B:CYS188 3.7 17.0 0.5
CE B:LYS50 3.8 15.1 1.0
CG B:ASP186 3.9 13.4 0.5
NZ B:LYS50 4.1 14.6 1.0
O B:HOH1108 4.2 30.8 1.0
SG B:CYS134 4.2 17.1 0.5
OD1 B:ASP186 4.2 13.1 0.5
O B:HOH841 4.2 24.6 1.0
CG B:ASP186 4.3 13.6 0.5
NE2 B:HIS138 4.3 16.8 1.0
N B:CYS188 4.3 12.4 0.5
O B:HOH1078 4.3 6.5 0.5
N B:CYS188 4.3 15.2 0.5
OG B:SER47 4.4 14.1 0.8
CA B:CYS188 4.5 12.1 0.5
CD B:LYS137 4.5 19.3 1.0
O B:HOH808 4.5 17.3 0.8
CA B:CYS188 4.5 15.6 0.5
O B:HOH1078 4.6 14.1 0.5
CA B:CYS134 4.7 10.7 0.5
O A:HOH586 4.7 19.7 0.5
CA B:CYS134 4.7 13.0 0.5
OD1 B:ASP186 4.8 15.1 0.5
CD2 B:HIS138 4.9 14.4 1.0
CB B:ASP186 4.9 12.3 0.5
CD1 B:ILE190 4.9 19.8 1.0

Zinc binding site 3 out of 4 in 8ori

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Zinc binding site 3 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:16.2
occ:0.50
 O C:HOH779 1.8 20.6 0.5
O C:HOH508 1.9 16.5 0.5
O C:HOH537 2.1 15.6 0.5
SG C:CYS134 2.3 14.3 0.5
SG C:CYS188 2.3 14.8 0.5
NZ C:LYS137 2.5 24.9 1.0
O C:HOH632 3.0 22.9 0.5
CE C:LYS137 3.1 23.2 1.0
OD2 C:ASP186 3.3 14.4 0.5
CB C:CYS188 3.3 13.2 0.5
CB C:CYS134 3.3 12.4 0.5
CB C:CYS134 3.4 13.2 0.5
CB C:CYS188 3.5 16.4 0.5
OD2 C:ASP186 3.6 20.2 0.5
SG C:CYS188 3.8 15.5 0.5
CE C:LYS50 3.8 14.4 1.0
CG C:ASP186 3.9 12.6 0.5
OD1 C:ASP186 4.1 12.9 0.5
O C:HOH550 4.1 23.8 1.0
NZ C:LYS50 4.2 14.9 1.0
O C:HOH822 4.2 37.3 1.0
SG C:CYS134 4.2 15.7 0.5
CG C:ASP186 4.2 19.3 0.5
O C:HOH796 4.4 8.6 0.5
N C:CYS188 4.4 14.2 0.5
NE2 C:HIS138 4.4 16.2 1.0
N C:CYS188 4.4 16.4 0.5
OG C:SER47 4.4 16.3 0.8
CA C:CYS188 4.5 12.8 0.5
CD C:LYS137 4.5 19.8 1.0
O C:HOH527 4.5 22.9 1.0
O C:HOH796 4.6 17.0 0.5
CA C:CYS188 4.6 17.1 0.5
O D:HOH716 4.6 22.9 0.5
CA C:CYS134 4.7 11.3 0.5
CA C:CYS134 4.7 11.9 0.5
OD1 C:ASP186 4.8 19.4 0.5
CB C:ASP186 4.8 16.0 0.5
O C:HOH505 4.9 10.2 0.2
CD2 C:HIS138 4.9 13.7 1.0
CD1 C:ILE190 5.0 20.7 1.0

Zinc binding site 4 out of 4 in 8ori

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Zinc binding site 4 out of 4 in the Crystal Structure of Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic)


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 Rhizobium Etli L-Asparaginase Reaiv (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:15.2
occ:0.50
 O D:HOH821 1.7 19.5 0.5
O D:HOH503 1.7 13.4 0.5
O D:HOH536 2.0 14.4 0.5
SG D:CYS188 2.3 14.3 0.5
SG D:CYS134 2.3 13.3 0.5
NZ D:LYS137 2.5 26.6 1.0
O D:HOH643 3.0 20.7 0.5
CE D:LYS137 3.1 24.6 1.0
OD2 D:ASP186 3.2 14.1 0.5
CB D:CYS188 3.3 12.7 0.5
CB D:CYS134 3.3 11.5 0.5
CB D:CYS188 3.4 13.0 0.5
CB D:CYS134 3.4 14.9 0.5
SG D:CYS188 3.7 14.3 0.5
OD2 D:ASP186 3.7 17.4 0.5
CE D:LYS50 3.7 14.7 1.0
CG D:ASP186 3.9 13.2 0.5
O D:HOH819 4.1 28.7 1.0
NZ D:LYS50 4.1 13.4 1.0
SG D:CYS134 4.2 15.7 0.5
OD1 D:ASP186 4.2 13.0 0.5
O D:HOH544 4.2 26.0 1.0
CG D:ASP186 4.3 15.0 0.5
NE2 D:HIS138 4.4 14.9 1.0
OG D:SER47 4.4 14.3 0.8
N D:CYS188 4.4 13.2 0.5
N D:CYS188 4.4 13.6 0.5
O D:HOH807 4.4 6.2 0.5
CA D:CYS188 4.5 12.2 0.5
CA D:CYS188 4.5 13.3 0.5
O D:HOH504 4.5 16.2 0.8
CD D:LYS137 4.5 22.2 1.0
O D:HOH807 4.6 14.0 0.5
CA D:CYS134 4.7 10.4 0.5
CA D:CYS134 4.7 12.8 0.5
CB D:ASP186 4.9 13.8 0.5
OD1 D:ASP186 4.9 16.1 0.5
CD2 D:HIS138 4.9 14.9 1.0
CD1 D:ILE190 5.0 16.6 1.0

Reference:

J.I.Loch, P.Worsztynowicz, J.Sliwiak, M.Grzechowiak, B.Imiolczyk, K.Pokrywka, M.Chwastyk, M.Gilski, M.Jaskolski. Rhizobium Etli Has Two L-Asparaginases with Low Sequence Identity But Similar Structure and Catalytic Center. Acta Crystallogr D Struct V. 79 775 2023BIOL.
ISSN: ISSN 2059-7983
PubMed: 37494066
DOI: 10.1107/S2059798323005648
Page generated: Thu Oct 31 08:53:53 2024

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