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Nickel in PDB 1ysj: Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family

Enzymatic activity of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family

All present enzymatic activity of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family:
3.5.1.14;

Protein crystallography data

The structure of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family, PDB code: 1ysj was solved by G.Minasov, L.Shuvalova, J.S.Brunzelle, F.R.Collart, W.F.Anderson, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 233.854, 42.157, 75.449, 90.00, 106.71, 90.00
R / Rfree (%) 18.2 / 24.7

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family (pdb code 1ysj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family, PDB code: 1ysj:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 1ysj

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Nickel binding site 1 out of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family


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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni381

b:35.1
occ:1.00
 O A:HOH383 1.9 39.7 1.0
NE2 A:HIS100 2.0 38.8 1.0
NE2 A:HIS158 2.2 46.2 1.0
O A:HOH489 2.3 29.5 0.5
SG A:CYS98 2.5 47.0 1.0
CD2 A:HIS100 3.0 39.6 1.0
CE1 A:HIS100 3.1 43.1 1.0
CD2 A:HIS158 3.1 42.8 1.0
CE1 A:HIS158 3.2 44.1 1.0
NI A:NI382 3.3 42.6 1.0
CB A:CYS98 3.5 43.3 1.0
OE1 A:GLU133 3.6 53.9 1.0
OE2 A:GLU134 3.6 49.7 1.0
O A:CYS98 3.9 42.9 1.0
OD2 A:ASP73 4.1 59.4 1.0
ND1 A:HIS100 4.2 45.0 1.0
CG A:HIS100 4.2 42.8 1.0
O A:HOH385 4.2 49.4 1.0
ND1 A:HIS158 4.3 43.0 1.0
CG A:HIS158 4.3 46.4 1.0
CD A:GLU133 4.3 58.9 1.0
O A:HOH518 4.5 47.5 0.5
CD A:GLU134 4.5 46.9 1.0
CE1 A:HIS103 4.6 42.9 1.0
C A:CYS98 4.6 43.6 1.0
CA A:CYS98 4.6 44.4 1.0
OE2 A:GLU133 4.8 61.0 1.0
OE1 A:GLU134 4.9 43.0 1.0
OE1 A:GLU325 4.9 59.4 1.0
CG A:ASP73 4.9 53.2 1.0

Nickel binding site 2 out of 4 in 1ysj

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Nickel binding site 2 out of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family


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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni382

b:42.6
occ:1.00
 NE2 A:HIS350 2.3 50.8 1.0
O A:HOH385 2.3 49.4 1.0
OE2 A:GLU134 2.4 49.7 1.0
OE1 A:GLU134 2.4 43.0 1.0
O A:HOH383 2.5 39.7 1.0
SG A:CYS98 2.6 47.0 1.0
CD A:GLU134 2.8 46.9 1.0
CD2 A:HIS350 3.2 49.2 1.0
CE1 A:HIS350 3.3 50.1 1.0
NI A:NI381 3.3 35.1 1.0
CB A:CYS98 3.4 43.3 1.0
O A:HOH384 3.5 46.0 1.0
O A:HOH518 4.1 47.5 0.5
OE1 A:GLU133 4.1 53.9 1.0
CG A:GLU134 4.3 45.4 1.0
NE2 A:HIS100 4.3 38.8 1.0
CD1 A:LEU77 4.4 46.1 1.0
CG A:HIS350 4.4 46.3 1.0
ND1 A:HIS350 4.4 50.8 1.0
CE1 A:HIS100 4.6 43.1 1.0
O A:HOH452 4.8 29.4 1.0
CA A:CYS98 4.8 44.4 1.0
O A:HOH386 4.9 42.7 1.0
NE2 A:HIS158 4.9 46.2 1.0
O A:HOH489 5.0 29.5 0.5

Nickel binding site 3 out of 4 in 1ysj

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Nickel binding site 3 out of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni381

b:36.2
occ:1.00
 O B:HOH383 2.1 31.1 1.0
NE2 B:HIS158 2.1 49.5 1.0
NE2 B:HIS100 2.3 42.6 1.0
SG B:CYS98 2.4 45.0 1.0
O B:HOH493 2.4 21.3 0.5
CE1 B:HIS158 3.1 45.8 1.0
CD2 B:HIS100 3.1 40.9 1.0
CD2 B:HIS158 3.1 44.2 1.0
NI B:NI382 3.3 39.7 1.0
CE1 B:HIS100 3.4 44.2 1.0
CB B:CYS98 3.5 43.3 1.0
O B:HOH535 3.5 32.0 0.5
OE1 B:GLU133 3.6 56.0 1.0
OE1 B:GLU134 3.7 50.8 1.0
O B:CYS98 3.8 42.9 1.0
OD2 B:ASP73 4.0 49.8 1.0
O B:HOH386 4.1 44.5 1.0
ND1 B:HIS158 4.2 44.0 1.0
CG B:HIS158 4.3 43.6 1.0
CG B:HIS100 4.3 44.3 1.0
ND1 B:HIS100 4.4 44.8 1.0
CD B:GLU133 4.4 58.3 1.0
CE1 B:HIS103 4.5 44.4 1.0
C B:CYS98 4.5 43.7 1.0
CA B:CYS98 4.6 43.4 1.0
CD B:GLU134 4.6 52.2 1.0
CG B:ASP73 4.9 48.1 1.0

Nickel binding site 4 out of 4 in 1ysj

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Nickel binding site 4 out of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni382

b:39.7
occ:1.00
 O B:HOH386 2.2 44.5 1.0
NE2 B:HIS350 2.3 44.4 1.0
SG B:CYS98 2.4 45.0 1.0
OE1 B:GLU134 2.4 50.8 1.0
OE2 B:GLU134 2.5 55.3 1.0
O B:HOH383 2.6 31.1 1.0
CD B:GLU134 2.8 52.2 1.0
CD2 B:HIS350 3.2 47.3 1.0
NI B:NI381 3.3 36.2 1.0
CE1 B:HIS350 3.3 41.0 1.0
CB B:CYS98 3.3 43.3 1.0
O B:HOH384 3.7 55.8 1.0
OE1 B:GLU133 4.1 56.0 1.0
O B:HOH535 4.2 32.0 0.5
NE2 B:HIS100 4.3 42.6 1.0
CG B:GLU134 4.3 47.1 1.0
CG B:HIS350 4.3 47.3 1.0
ND1 B:HIS350 4.4 45.3 1.0
CD1 B:LEU77 4.4 49.0 1.0
CA B:CYS98 4.7 43.4 1.0
O B:HOH460 4.8 38.6 1.0
NE2 B:HIS158 4.8 49.5 1.0
CE1 B:HIS100 4.8 44.2 1.0
O B:HOH385 4.9 46.8 1.0
O B:HOH493 4.9 21.3 0.5

Reference:

G.Minasov, L.Shuvalova, J.S.Brunzelle, F.R.Collart, W.F.Anderson. Structure of Bacillus Subtilis Yxep Protein, A Dinuclear Metal Binding Peptidase From M20 Family To Be Published.
Page generated: Wed Oct 9 16:33:32 2024

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