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Nickel in PDB 3la4: Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis)

Enzymatic activity of Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis)

All present enzymatic activity of Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis):
3.5.1.5;

Protein crystallography data

The structure of Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis), PDB code: 3la4 was solved by K.Ponnuraj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.05
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 138.565, 138.565, 198.355, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 20.1

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis) (pdb code 3la4). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis), PDB code: 3la4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 3la4

Go back to Nickel Binding Sites List in 3la4
Nickel binding site 1 out of 2 in the Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni841

b:10.7
occ:0.95
OQ1 A:KCX490 2.1 11.0 1.0
NE2 A:HIS409 2.1 13.7 1.0
NE2 A:HIS407 2.2 9.8 1.0
O4 A:PO4843 2.2 26.0 0.8
OD1 A:ASP633 2.2 14.6 1.0
O2 A:PO4843 2.4 28.7 0.6
P A:PO4843 2.8 26.6 0.6
CE1 A:HIS409 3.0 13.2 1.0
CX A:KCX490 3.1 13.6 1.0
CG A:ASP633 3.1 14.7 1.0
CE1 A:HIS407 3.1 12.7 1.0
CD2 A:HIS407 3.1 12.4 1.0
CD2 A:HIS409 3.1 12.7 1.0
OD2 A:ASP633 3.4 12.9 1.0
OQ2 A:KCX490 3.5 12.6 1.0
O1 A:PO4843 3.6 28.2 0.8
NI A:NI842 3.7 16.5 1.0
O3 A:PO4843 4.0 29.4 0.6
ND1 A:HIS409 4.1 13.4 1.0
CG2 A:THR442 4.2 10.7 1.0
ND1 A:HIS407 4.2 11.8 1.0
CG A:HIS407 4.2 12.7 1.0
CG A:HIS409 4.2 13.7 1.0
O A:ALA636 4.3 20.5 1.0
NZ A:KCX490 4.3 10.9 1.0
CB A:ASP633 4.3 13.6 1.0
CB A:ALA636 4.4 14.9 1.0
O A:ALA440 4.5 11.1 1.0
CA A:ASP633 4.6 13.6 1.0
CD2 A:HIS545 4.9 11.7 1.0
NE2 A:HIS545 5.0 13.3 1.0

Nickel binding site 2 out of 2 in 3la4

Go back to Nickel Binding Sites List in 3la4
Nickel binding site 2 out of 2 in the Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of the First Plant Urease From Jack Bean (Canavalia Ensiformis) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni842

b:16.5
occ:1.00
OQ2 A:KCX490 2.1 12.6 1.0
O4 A:PO4843 2.1 26.0 0.8
ND1 A:HIS519 2.2 16.5 1.0
O1 A:PO4843 2.2 28.2 0.8
NE2 A:HIS545 2.2 13.3 1.0
P A:PO4843 2.6 26.6 0.6
CE1 A:HIS519 3.0 14.5 1.0
CX A:KCX490 3.1 13.6 1.0
CD2 A:HIS545 3.1 11.7 1.0
CE1 A:HIS545 3.2 13.0 1.0
CG A:HIS519 3.2 15.2 1.0
O A:GLY550 3.3 13.2 1.0
OQ1 A:KCX490 3.4 11.0 1.0
O3 A:PO4843 3.5 29.4 0.6
NE2 A:HIS492 3.6 13.9 1.0
CB A:HIS519 3.7 14.5 1.0
NI A:NI841 3.7 10.7 0.9
O2 A:PO4843 3.8 28.7 0.6
CD2 A:HIS492 4.0 13.6 1.0
NE2 A:HIS519 4.1 16.2 1.0
CE1 A:HIS407 4.2 12.7 1.0
CD2 A:HIS519 4.3 15.3 1.0
ND1 A:HIS545 4.3 12.8 1.0
CG A:HIS545 4.3 12.2 1.0
C A:GLY550 4.4 14.7 1.0
NE2 A:HIS407 4.4 9.8 1.0
NZ A:KCX490 4.4 10.9 1.0
OD2 A:ASP633 4.5 12.9 1.0
O2 A:PO4844 4.6 28.4 0.5
CE1 A:HIS492 4.7 12.7 1.0
CA A:HIS519 4.8 14.8 1.0
CE A:KCX490 4.9 12.4 1.0

Reference:

A.Balasubramanian, K.Ponnuraj. Crystal Structure of the First Plant Urease From Jack Bean: 83 Years of Journey From Its First Crystal to Molecular Structure J.Mol.Biol. V. 400 274 2010.
ISSN: ISSN 0022-2836
PubMed: 20471401
DOI: 10.1016/J.JMB.2010.05.009
Page generated: Fri Sep 25 08:26:45 2020
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