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Calcium in PDB 6azq: Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841

Protein crystallography data

The structure of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841, PDB code: 6azq was solved by T.S.Peat, L.Esquirol, J.Newman, C.Scott, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.85 / 2.22
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.702, 87.303, 341.695, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 27.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 (pdb code 6azq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841, PDB code: 6azq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 6azq

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Calcium binding site 1 out of 5 in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca302

b:51.2
occ:1.00
 O G:ARG186 3.5 27.1 1.0
NH2 C:ARG161 3.7 50.1 1.0
C G:GLY187 3.8 26.8 1.0
O G:GLY187 3.9 29.6 1.0
CE1 G:TYR188 4.1 31.3 1.0
N G:TYR188 4.1 25.0 1.0
O G:HOH425 4.1 18.9 1.0
CD1 G:TYR188 4.2 32.4 1.0
CA G:GLY187 4.2 28.0 1.0
CZ G:TYR188 4.2 30.3 1.0
CG G:TYR188 4.4 31.0 1.0
CE2 G:TYR188 4.4 28.9 1.0
C G:ARG186 4.5 25.1 1.0
CD2 G:TYR188 4.5 30.9 1.0
CA G:TYR188 4.6 28.5 1.0
CB C:ASN158 4.6 28.8 1.0
NE2 C:GLN159 4.6 24.9 1.0
CZ C:ARG161 4.6 48.5 1.0
OE1 C:GLN159 4.6 25.1 1.0
OH G:TYR188 4.7 29.7 1.0
N G:GLY187 4.8 28.6 1.0
O C:HOH441 4.8 25.2 1.0
O C:ASN158 4.8 30.3 1.0
NH1 C:ARG161 4.9 49.3 1.0

Calcium binding site 2 out of 5 in 6azq

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Calcium binding site 2 out of 5 in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:50.8
occ:1.00
 O B:ARG186 3.4 32.0 1.0
NH1 F:ARG161 3.9 71.2 1.0
C B:GLY187 4.0 26.6 1.0
CE1 B:TYR188 4.0 27.7 1.0
CZ B:TYR188 4.0 25.4 1.0
CD1 B:TYR188 4.2 26.8 1.0
O B:GLY187 4.2 26.2 1.0
N B:TYR188 4.2 26.5 1.0
CE2 B:TYR188 4.2 25.4 1.0
CA B:GLY187 4.3 28.1 1.0
O B:HOH419 4.3 22.8 1.0
O B:HOH427 4.3 21.8 1.0
O B:HOH405 4.3 29.2 1.0
C B:ARG186 4.4 28.7 1.0
CG B:TYR188 4.4 27.5 1.0
CB F:ASN158 4.4 33.8 1.0
CD2 B:TYR188 4.4 27.6 1.0
NE2 F:GLN159 4.4 34.0 1.0
OH B:TYR188 4.5 26.4 1.0
OE1 F:GLN159 4.6 24.1 1.0
CA B:TYR188 4.7 26.9 1.0
O F:ASN158 4.7 30.4 1.0
N B:GLY187 4.7 29.5 1.0
CD F:GLN159 4.9 28.2 1.0
C F:ASN158 5.0 30.8 1.0

Calcium binding site 3 out of 5 in 6azq

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Calcium binding site 3 out of 5 in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:57.6
occ:1.00
 O C:HOH425 3.1 33.2 1.0
O C:ARG186 3.5 37.6 1.0
C C:GLY187 4.0 35.5 1.0
CE1 C:TYR188 4.1 28.7 1.0
O C:GLY187 4.1 33.8 1.0
CZ C:TYR188 4.2 29.6 1.0
N C:TYR188 4.2 33.8 1.0
CD1 C:TYR188 4.2 30.5 1.0
CA C:GLY187 4.3 35.2 1.0
CE2 C:TYR188 4.4 29.2 1.0
NH1 G:ARG161 4.4 58.1 1.0
CG C:TYR188 4.5 32.5 1.0
C C:ARG186 4.5 35.9 1.0
CD2 C:TYR188 4.5 29.7 1.0
CB G:ASN158 4.5 31.4 1.0
OH C:TYR188 4.7 28.9 1.0
NE2 G:GLN159 4.7 28.7 1.0
CA C:TYR188 4.7 35.7 1.0
NH2 G:ARG161 4.7 58.8 1.0
N C:GLY187 4.8 36.7 1.0
OE1 G:GLN159 4.9 31.3 1.0
CZ G:ARG161 4.9 59.6 1.0
O G:ASN158 5.0 34.2 1.0

Calcium binding site 4 out of 5 in 6azq

Go back to Calcium Binding Sites List in 6azq
Calcium binding site 4 out of 5 in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:67.7
occ:1.00
 OE2 C:GLU130 3.6 52.0 1.0
OE1 C:GLU130 3.7 49.9 1.0
CG2 C:ILE128 4.0 37.0 1.0
CD C:GLU130 4.0 49.5 1.0
CB C:ILE128 4.2 36.4 1.0
CD1 C:ILE128 4.4 39.1 1.0
CD1 C:ILE62 4.5 45.0 1.0
CG1 C:ILE128 4.9 37.9 1.0
SG C:CYS42 5.0 32.5 1.0

Calcium binding site 5 out of 5 in 6azq

Go back to Calcium Binding Sites List in 6azq
Calcium binding site 5 out of 5 in the Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural and Biochemical Characterization of A Non-Canonical Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:52.7
occ:1.00
 O F:ARG186 3.7 25.5 1.0
NH1 B:ARG161 3.8 64.1 1.0
CE1 F:TYR188 4.0 38.9 1.0
CZ F:TYR188 4.0 37.2 1.0
CD1 F:TYR188 4.2 38.1 1.0
C F:GLY187 4.2 30.2 1.0
CE2 F:TYR188 4.3 39.1 1.0
CB B:ASN158 4.3 28.0 1.0
O F:GLY187 4.3 33.1 1.0
N F:TYR188 4.4 33.6 1.0
CG F:TYR188 4.5 37.8 1.0
CZ B:ARG161 4.5 64.7 1.0
OH F:TYR188 4.5 41.1 1.0
CD2 F:TYR188 4.5 37.2 1.0
CA F:GLY187 4.5 29.6 1.0
NE2 B:GLN159 4.6 29.7 1.0
C F:ARG186 4.6 28.4 1.0
O B:ASN158 4.7 26.3 1.0
NH2 B:ARG161 4.7 53.8 1.0
OE1 B:GLN159 4.8 27.2 1.0
CA F:TYR188 4.8 35.4 1.0
OD1 F:ASN158 4.9 37.8 1.0
C B:ASN158 5.0 29.2 1.0
O F:ILE162 5.0 41.6 1.0

Reference:

L.Esquirol, T.S.Peat, M.Wilding, D.Lucent, N.G.French, C.J.Hartley, J.Newman, C.Scott. Structural and Biochemical Characterization of the Biuret Hydrolase (Biuh) From the Cyanuric Acid Catabolism Pathway of Rhizobium Leguminasorum Bv. Viciae 3841. Plos One V. 13 92736 2018.
ISSN: ESSN 1932-6203
PubMed: 29425231
DOI: 10.1371/JOURNAL.PONE.0192736
Page generated: Mon Jul 15 16:38:47 2024

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