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Nickel in PDB 3wd7: Type III Polyketide Synthase

Enzymatic activity of Type III Polyketide Synthase

All present enzymatic activity of Type III Polyketide Synthase:
2.3.1.159;

Protein crystallography data

The structure of Type III Polyketide Synthase, PDB code: 3wd7 was solved by T.Mori, Y.Shimokawa, T.Matsui, R.Kato, S.Sugio, H.Morita, I.Abe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.52 / 2.35
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 105.999, 105.999, 346.548, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Type III Polyketide Synthase (pdb code 3wd7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 9 binding sites of Nickel where determined in the Type III Polyketide Synthase, PDB code: 3wd7:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Nickel binding site 1 out of 9 in 3wd7

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Nickel binding site 1 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni402

b:32.0
occ:1.00
 OD2 A:ASP207 2.0 30.3 1.0
ND1 A:HIS205 2.1 33.4 1.0
OD1 A:ASP207 2.2 31.4 1.0
O A:HOH643 2.3 34.0 1.0
O A:HOH635 2.3 36.0 1.0
ND1 A:HIS266 2.4 33.8 1.0
CG A:ASP207 2.4 30.3 1.0
CE1 A:HIS205 3.1 32.5 1.0
CG A:HIS205 3.1 34.3 1.0
CE1 A:HIS266 3.3 32.1 1.0
CB A:HIS205 3.4 29.5 1.0
CG A:HIS266 3.4 32.8 1.0
CB A:HIS266 3.8 26.1 1.0
CB A:ASP207 3.9 31.1 1.0
CA A:HIS266 4.0 29.0 1.0
O A:HOH663 4.1 40.0 1.0
O A:VAL265 4.1 30.3 1.0
O A:HOH654 4.1 35.4 1.0
CA A:HIS205 4.2 32.9 1.0
NE2 A:HIS205 4.2 31.5 1.0
CD2 A:HIS205 4.2 33.0 1.0
NE2 A:HIS266 4.4 31.1 1.0
OH A:TYR86 4.5 51.9 1.0
CD2 A:HIS266 4.5 29.6 1.0
N A:SER208 4.6 28.9 1.0
CA A:ASP207 4.8 34.0 1.0
O A:HOH585 4.8 35.6 1.0
C A:HIS205 4.9 32.3 1.0
N A:ASP207 4.9 33.6 1.0
N A:LEU267 4.9 33.5 1.0
N A:HIS266 4.9 27.6 1.0
C A:VAL265 4.9 30.0 1.0
C A:ASP207 5.0 31.1 1.0

Nickel binding site 2 out of 9 in 3wd7

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Nickel binding site 2 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni403

b:57.5
occ:1.00
 O A:HOH602 2.0 46.6 1.0
NE2 A:HIS329 2.1 40.7 1.0
OE1 A:GLU333 2.2 49.6 1.0
O A:HOH580 2.6 46.4 1.0
O A:HOH666 2.9 42.4 1.0
CE1 A:HIS329 3.0 37.2 1.0
CD2 A:HIS329 3.1 38.0 1.0
CD A:GLU333 3.3 46.4 1.0
OE1 A:GLU348 3.8 33.1 1.0
OE2 A:GLU333 3.8 46.1 1.0
ND1 A:HIS329 4.1 39.3 1.0
CG A:HIS329 4.2 35.4 1.0
CD A:GLU348 4.5 35.4 1.0
CG A:GLU333 4.6 42.3 1.0
NZ A:LYS352 4.6 45.3 1.0
OE2 A:GLU348 4.6 36.2 1.0
CB A:GLU333 4.8 31.9 1.0
O A:HOH637 4.9 37.8 1.0

Nickel binding site 3 out of 9 in 3wd7

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Nickel binding site 3 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni404

b:35.2
occ:1.00
 NE2 A:HIS-2 2.1 35.8 1.0
O A:HOH609 2.2 38.6 1.0
O A:HOH568 2.3 36.7 1.0
CE1 A:HIS-2 2.9 32.5 1.0
CD2 A:HIS-2 3.2 34.7 1.0
ND1 A:HIS-2 4.1 36.4 1.0
CG A:HIS-2 4.2 33.4 1.0

Nickel binding site 4 out of 9 in 3wd7

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Nickel binding site 4 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni405

b:41.2
occ:1.00
 NE2 A:HIS-3 2.0 37.2 1.0
CD2 A:HIS-3 2.9 37.1 1.0
CE1 A:HIS-3 3.0 38.0 1.0
ND1 A:HIS-3 4.1 38.5 1.0
CG A:HIS-3 4.1 37.9 1.0
CA B:GLY291 4.8 40.0 1.0

Nickel binding site 5 out of 9 in 3wd7

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Nickel binding site 5 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni406

b:31.4
occ:1.00
 O A:HOH675 2.0 26.9 1.0
NE2 A:HIS-7 2.0 33.6 1.0
O A:MET-11 2.2 33.9 1.0
N A:MET-11 2.3 32.3 1.0
SD A:MET-11 2.5 34.6 1.0
CE1 A:HIS-7 2.9 31.4 1.0
C A:MET-11 2.9 34.3 1.0
CA A:MET-11 3.0 34.1 1.0
CD2 A:HIS-7 3.1 33.3 1.0
CG A:MET-11 3.5 37.7 1.0
CE A:MET-11 3.7 35.9 1.0
CB A:MET-11 3.7 35.1 1.0
ND1 A:HIS-7 4.1 34.5 1.0
CG A:HIS-7 4.2 35.5 1.0
N A:ARG-10 4.2 37.5 1.0
CA A:ARG-10 4.9 34.9 1.0

Nickel binding site 6 out of 9 in 3wd7

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Nickel binding site 6 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni407

b:49.9
occ:1.00
 O A:HOH627 2.0 53.3 1.0
NE2 A:HIS-5 2.1 48.9 1.0
O A:HOH553 2.1 39.7 1.0
O A:HOH669 2.3 44.3 1.0
CE1 A:HIS-5 2.9 47.0 1.0
CD2 A:HIS-5 3.1 43.1 1.0
ND1 A:HIS-5 4.0 48.0 1.0
CG A:HIS-5 4.1 43.8 1.0

Nickel binding site 7 out of 9 in 3wd7

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Nickel binding site 7 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni408

b:48.2
occ:1.00
 O A:HOH668 2.0 50.8 1.0
O A:HOH594 2.1 37.6 1.0
NE2 A:HIS-4 2.1 39.8 1.0
NE2 A:HIS-6 2.2 40.0 1.0
CE1 A:HIS-4 2.9 33.8 1.0
CE1 A:HIS-6 3.0 33.9 1.0
CD2 A:HIS-4 3.2 33.7 1.0
CD2 A:HIS-6 3.3 35.9 1.0
ND1 A:HIS-4 4.1 34.6 1.0
ND1 A:HIS-6 4.2 34.0 1.0
CG A:HIS-4 4.3 39.6 1.0
CG A:HIS-6 4.3 38.4 1.0

Nickel binding site 8 out of 9 in 3wd7

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Nickel binding site 8 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni402

b:64.9
occ:1.00
 O B:HOH604 2.1 44.6 1.0
OE1 B:GLU333 2.2 49.6 1.0
NE2 B:HIS329 2.2 41.3 1.0
O B:HOH638 2.7 41.7 1.0
O B:HOH616 2.7 48.7 1.0
CE1 B:HIS329 3.1 44.5 1.0
CD B:GLU333 3.2 46.5 1.0
CD2 B:HIS329 3.2 41.7 1.0
OE2 B:GLU333 3.5 46.5 1.0
OE1 B:GLU348 3.7 37.7 1.0
ND1 B:HIS329 4.2 44.5 1.0
CG B:HIS329 4.3 40.1 1.0
CD B:GLU348 4.4 39.2 1.0
CG B:GLU333 4.5 43.6 1.0
OE2 B:GLU348 4.5 38.3 1.0
NZ B:LYS352 4.6 40.9 1.0
CB B:GLU333 4.9 37.3 1.0

Nickel binding site 9 out of 9 in 3wd7

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Nickel binding site 9 out of 9 in the Type III Polyketide Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Type III Polyketide Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni403

b:41.7
occ:1.00
 OD2 B:ASP207 2.0 42.1 1.0
O B:HOH532 2.2 39.6 1.0
ND1 B:HIS205 2.2 38.5 1.0
ND1 B:HIS266 2.2 42.1 1.0
O B:HOH565 2.3 43.2 1.0
OD1 B:ASP207 2.4 43.6 1.0
CG B:ASP207 2.5 42.4 1.0
CE1 B:HIS266 3.1 38.7 1.0
CE1 B:HIS205 3.1 41.5 1.0
CG B:HIS205 3.2 43.1 1.0
CG B:HIS266 3.3 40.6 1.0
CB B:HIS205 3.5 42.2 1.0
CB B:HIS266 3.6 33.4 1.0
CA B:HIS266 3.9 38.7 1.0
O B:VAL265 4.0 42.3 1.0
CB B:ASP207 4.0 42.9 1.0
NE2 B:HIS205 4.2 45.3 1.0
CD2 B:HIS205 4.3 45.3 1.0
NE2 B:HIS266 4.3 41.3 1.0
CA B:HIS205 4.3 46.6 1.0
O B:HOH622 4.3 43.9 1.0
CD2 B:HIS266 4.4 41.6 1.0
N B:SER208 4.6 41.5 1.0
C B:VAL265 4.7 38.6 1.0
N B:HIS266 4.7 35.8 1.0
OH B:TYR86 4.8 57.9 1.0
CA B:ASP207 4.9 45.9 1.0
C B:HIS205 4.9 46.4 1.0
N B:LEU267 4.9 41.1 1.0
C B:HIS266 5.0 40.4 1.0
N B:ASP207 5.0 42.0 1.0

Reference:

T.Mori, Y.Shimokawa, T.Matsui, K.Kinjo, R.Kato, H.Noguchi, S.Sugio, H.Morita, I.Abe. Cloning, Characterization, and Crystal Structure Analysis of Novel Type III Polyketide Synthases From Citrus Microcarpa To Be Published.
Page generated: Wed Oct 9 17:54:03 2024

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