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Nickel in PDB 3i2b: The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase

Enzymatic activity of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase

All present enzymatic activity of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase:
4.2.3.12;

Protein crystallography data

The structure of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase, PDB code: 3i2b was solved by E.Ugochukwu, R.Cocking, E.Pilka, W.W.Yue, J.E.Bray, A.Chaikuad, T.Krojer, J.Muniz, F.Von Delft, C.Bountra, C.H.Arrowsmith, J.Weigelt, A.Edwards, U.Oppermann, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.94 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.290, 118.720, 234.980, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 24.6

Other elements in 3i2b:

The structure of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase (pdb code 3i2b). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase, PDB code: 3i2b:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in 3i2b

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Nickel binding site 1 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni146

b:33.8
occ:1.00
O A:HOH293 1.6 12.4 1.0
NE2 A:HIS24 1.9 14.9 1.0
NE2 A:HIS49 2.0 15.3 1.0
NE2 A:HIS51 2.1 16.3 1.0
CE1 A:HIS24 2.8 15.1 1.0
OE2 A:GLU134 2.9 20.6 1.0
CE1 A:HIS49 2.9 15.2 1.0
CD2 A:HIS24 3.0 16.4 1.0
CD2 A:HIS49 3.0 14.9 1.0
CD2 A:HIS51 3.0 14.5 1.0
CE1 A:HIS51 3.2 14.2 1.0
CD A:GLU134 3.9 19.7 1.0
ND1 A:HIS24 3.9 14.2 1.0
ND1 A:HIS49 4.0 14.5 1.0
CG A:HIS49 4.0 14.6 1.0
CG A:HIS24 4.1 14.4 1.0
CG A:HIS51 4.2 15.8 1.0
ND1 A:HIS51 4.3 15.0 1.0
CG A:GLU134 4.5 17.4 1.0
SG A:CYS43 4.7 20.1 1.0
OH A:TYR53 4.8 15.0 1.0
OE1 A:GLU134 4.9 20.7 1.0

Nickel binding site 2 out of 12 in 3i2b

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Nickel binding site 2 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni4

b:29.1
occ:1.00
O D:HOH154 1.6 28.6 1.0
NE2 D:HIS24 2.0 14.7 1.0
NE2 D:HIS49 2.1 15.1 1.0
NE2 D:HIS51 2.1 16.9 1.0
OE2 D:GLU134 2.7 21.6 1.0
CE1 D:HIS24 2.9 15.0 1.0
CD2 D:HIS51 3.0 15.0 1.0
CE1 D:HIS49 3.0 14.8 1.0
CD2 D:HIS49 3.1 14.4 1.0
CD2 D:HIS24 3.1 16.5 1.0
CE1 D:HIS51 3.2 13.5 1.0
O I:HOH198 3.2 34.6 1.0
CD D:GLU134 3.6 20.0 1.0
ND1 D:HIS24 4.0 14.2 1.0
ND1 D:HIS49 4.1 14.2 1.0
CG D:HIS49 4.2 14.9 1.0
CG D:HIS51 4.2 15.5 1.0
CG D:HIS24 4.2 14.7 1.0
ND1 D:HIS51 4.2 14.8 1.0
CG D:GLU134 4.3 17.8 1.0
OE1 D:GLU134 4.5 21.1 1.0
SG D:CYS43 4.7 20.4 1.0
OH D:TYR53 4.8 14.3 1.0
O D:HOH2 4.8 16.3 1.0
NE2 I:HIS90 5.0 16.4 1.0

Nickel binding site 3 out of 12 in 3i2b

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Nickel binding site 3 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni146

b:35.0
occ:1.00
O E:HOH152 1.9 21.0 1.0
NE2 E:HIS24 2.0 14.4 1.0
NE2 E:HIS49 2.0 14.6 1.0
NE2 E:HIS51 2.2 16.9 1.0
O E:HOH277 2.6 31.9 1.0
OE2 E:GLU134 2.8 20.6 1.0
CE1 E:HIS24 2.8 15.6 1.0
CE1 E:HIS49 2.9 15.2 1.0
CD2 E:HIS49 3.1 15.2 1.0
CD2 E:HIS24 3.1 16.5 1.0
CD2 E:HIS51 3.1 14.9 1.0
CE1 E:HIS51 3.2 14.2 1.0
CD E:GLU134 3.7 19.9 1.0
ND1 E:HIS24 4.0 14.3 1.0
ND1 E:HIS49 4.1 14.3 1.0
CG E:HIS24 4.1 14.8 1.0
CG E:HIS49 4.2 15.1 1.0
CG E:HIS51 4.3 15.4 1.0
ND1 E:HIS51 4.3 15.1 1.0
CG E:GLU134 4.4 17.6 1.0
OE1 E:GLU134 4.6 20.0 1.0
OH E:TYR53 4.7 14.9 1.0
SG E:CYS43 4.7 20.0 1.0

Nickel binding site 4 out of 12 in 3i2b

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Nickel binding site 4 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2

b:31.3
occ:1.00
O B:HOH275 1.6 30.4 1.0
NE2 B:HIS24 2.0 13.5 1.0
NE2 B:HIS49 2.0 14.6 1.0
NE2 B:HIS51 2.2 16.2 1.0
OE2 B:GLU134 2.8 20.6 1.0
CE1 B:HIS24 2.9 14.8 1.0
CE1 B:HIS49 2.9 15.6 1.0
CD2 B:HIS24 3.0 16.3 1.0
CD2 B:HIS51 3.1 14.5 1.0
CD2 B:HIS49 3.1 15.0 1.0
CE1 B:HIS51 3.2 14.5 1.0
CD B:GLU134 3.8 20.0 1.0
O B:HOH201 3.8 30.1 1.0
ND1 B:HIS24 4.0 14.2 1.0
ND1 B:HIS49 4.1 14.3 1.0
CG B:HIS24 4.1 14.9 1.0
CG B:HIS49 4.2 14.9 1.0
CG B:HIS51 4.2 15.2 1.0
ND1 B:HIS51 4.3 15.0 1.0
CG B:GLU134 4.4 17.9 1.0
OE1 B:GLU134 4.7 21.1 1.0
SG B:CYS43 4.7 21.2 1.0
OH B:TYR53 4.8 15.2 1.0

Nickel binding site 5 out of 12 in 3i2b

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Nickel binding site 5 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni3

b:29.6
occ:1.00
NE2 C:HIS49 2.0 13.6 1.0
O C:HOH159 2.1 26.2 1.0
NE2 C:HIS24 2.1 14.2 1.0
NE2 C:HIS51 2.1 17.1 1.0
OE2 C:GLU134 2.6 21.4 1.0
CE1 C:HIS49 2.9 15.2 1.0
CE1 C:HIS24 2.9 14.7 1.0
O C:HOH270 3.0 31.5 1.0
CD2 C:HIS49 3.0 14.4 1.0
CD2 C:HIS51 3.1 14.9 1.0
CE1 C:HIS51 3.1 13.9 1.0
CD2 C:HIS24 3.1 16.2 1.0
CD C:GLU134 3.6 19.7 1.0
ND1 C:HIS49 4.0 14.2 1.0
CG C:HIS49 4.1 14.9 1.0
ND1 C:HIS24 4.1 14.3 1.0
ND1 C:HIS51 4.2 14.6 1.0
CG C:HIS51 4.2 15.6 1.0
CG C:HIS24 4.2 15.3 1.0
OE1 C:GLU134 4.4 20.5 1.0
CG C:GLU134 4.4 17.1 1.0
SG C:CYS43 4.6 20.6 1.0
OH C:TYR53 4.8 14.3 1.0
O C:HOH148 4.8 13.8 1.0

Nickel binding site 6 out of 12 in 3i2b

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Nickel binding site 6 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni146

b:41.0
occ:1.00
NE2 F:HIS49 2.0 14.9 1.0
NE2 F:HIS24 2.0 14.3 1.0
NE2 F:HIS51 2.2 16.5 1.0
O F:HOH295 2.2 33.1 1.0
OE2 F:GLU134 2.8 20.3 1.0
O F:HOH203 2.8 29.3 1.0
CE1 F:HIS49 2.9 14.9 1.0
CE1 F:HIS24 2.9 15.3 1.0
CD2 F:HIS49 3.0 15.5 1.0
CD2 F:HIS51 3.1 15.1 1.0
CD2 F:HIS24 3.1 16.3 1.0
CE1 F:HIS51 3.2 14.7 1.0
CD F:GLU134 3.7 19.1 1.0
ND1 F:HIS49 4.0 14.4 1.0
ND1 F:HIS24 4.1 14.5 1.0
CG F:HIS49 4.1 14.9 1.0
CG F:HIS24 4.2 15.0 1.0
ND1 F:HIS51 4.3 14.8 1.0
CG F:HIS51 4.3 15.4 1.0
O F:HOH285 4.3 26.2 1.0
CG F:GLU134 4.4 17.1 1.0
SG F:CYS43 4.5 20.9 1.0
OE1 F:GLU134 4.5 19.7 1.0
OH F:TYR53 4.9 14.8 1.0

Nickel binding site 7 out of 12 in 3i2b

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Nickel binding site 7 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ni146

b:35.7
occ:1.00
O G:HOH155 1.7 12.8 1.0
NE2 G:HIS49 1.9 15.0 1.0
NE2 G:HIS24 2.0 14.3 1.0
NE2 G:HIS51 2.1 16.6 1.0
OE2 G:GLU134 2.8 20.6 1.0
CE1 G:HIS49 2.9 15.2 1.0
CE1 G:HIS24 2.9 15.5 1.0
CD2 G:HIS49 2.9 14.8 1.0
CD2 G:HIS51 3.0 14.4 1.0
CD2 G:HIS24 3.1 15.8 1.0
CE1 G:HIS51 3.1 13.8 1.0
CD G:GLU134 3.7 19.8 1.0
ND1 G:HIS49 4.0 14.3 1.0
O G:HOH205 4.0 35.5 1.0
CG G:HIS49 4.0 14.9 1.0
ND1 G:HIS24 4.0 15.2 1.0
CG G:HIS24 4.2 14.8 1.0
CG G:HIS51 4.2 15.6 1.0
ND1 G:HIS51 4.2 14.8 1.0
CG G:GLU134 4.4 17.4 1.0
SG G:CYS43 4.4 21.0 1.0
OE1 G:GLU134 4.6 20.1 1.0
OH G:TYR53 4.8 14.3 1.0
NE2 A:HIS90 5.0 16.1 1.0

Nickel binding site 8 out of 12 in 3i2b

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Nickel binding site 8 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ni146

b:36.9
occ:1.00
NE2 H:HIS24 2.0 14.0 1.0
NE2 H:HIS49 2.1 14.5 1.0
NE2 H:HIS51 2.1 16.8 1.0
O H:HOH152 2.2 22.4 1.0
OE2 H:GLU134 2.7 20.2 1.0
O E:HOH196 2.8 13.7 1.0
CE1 H:HIS24 2.9 15.9 1.0
CE1 H:HIS49 3.0 15.1 1.0
CD2 H:HIS51 3.1 14.9 1.0
CD2 H:HIS49 3.1 15.5 1.0
CD2 H:HIS24 3.2 16.4 1.0
CE1 H:HIS51 3.2 14.1 1.0
CD H:GLU134 3.7 19.3 1.0
ND1 H:HIS24 4.1 14.3 1.0
ND1 H:HIS49 4.1 14.3 1.0
CG H:HIS49 4.2 15.2 1.0
CG H:HIS51 4.2 15.4 1.0
CG H:HIS24 4.2 14.7 1.0
ND1 H:HIS51 4.2 14.7 1.0
CG H:GLU134 4.3 17.5 1.0
SG H:CYS43 4.5 20.4 1.0
OE1 H:GLU134 4.5 19.6 1.0
OH H:TYR53 4.8 15.0 1.0
O H:HOH218 5.0 16.9 1.0

Nickel binding site 9 out of 12 in 3i2b

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Nickel binding site 9 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ni146

b:31.4
occ:1.00
O I:HOH152 2.0 26.7 1.0
NE2 I:HIS49 2.0 14.7 1.0
NE2 I:HIS24 2.1 13.8 1.0
NE2 I:HIS51 2.2 16.7 1.0
O I:HOH273 2.6 22.7 1.0
OE2 I:GLU134 2.6 20.4 1.0
CE1 I:HIS24 2.9 15.2 1.0
CE1 I:HIS49 2.9 15.2 1.0
CD2 I:HIS49 3.0 15.2 1.0
CD2 I:HIS24 3.2 16.1 1.0
CD2 I:HIS51 3.2 14.1 1.0
CE1 I:HIS51 3.2 14.2 1.0
CD I:GLU134 3.7 19.4 1.0
ND1 I:HIS49 4.0 14.0 1.0
ND1 I:HIS24 4.1 14.4 1.0
CG I:HIS49 4.1 15.1 1.0
CG I:HIS24 4.2 14.9 1.0
ND1 I:HIS51 4.3 15.1 1.0
CG I:HIS51 4.3 15.5 1.0
CG I:GLU134 4.5 17.4 1.0
SG I:CYS43 4.5 19.4 1.0
OE1 I:GLU134 4.6 20.0 1.0
OH I:TYR53 4.9 14.4 1.0
NE2 D:HIS90 5.0 16.3 1.0

Nickel binding site 10 out of 12 in 3i2b

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Nickel binding site 10 out of 12 in the The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ni146

b:29.2
occ:1.00
O J:HOH157 2.0 38.0 1.0
NE2 J:HIS24 2.0 13.3 1.0
NE2 J:HIS49 2.0 14.6 1.0
NE2 J:HIS51 2.2 16.7 1.0
OE2 J:GLU134 2.8 20.5 1.0
CE1 J:HIS24 2.8 15.5 1.0
CE1 J:HIS49 3.0 15.2 1.0
O J:HOH272 3.0 25.1 1.0
CD2 J:HIS49 3.1 15.1 1.0
CD2 J:HIS51 3.1 14.2 1.0
CD2 J:HIS24 3.1 16.0 1.0
CE1 J:HIS51 3.2 13.8 1.0
CD J:GLU134 3.7 19.7 1.0
ND1 J:HIS24 4.0 14.8 1.0
ND1 J:HIS49 4.1 14.4 1.0
CG J:HIS49 4.2 14.8 1.0
CG J:HIS24 4.2 14.4 1.0
CG J:HIS51 4.2 15.6 1.0
ND1 J:HIS51 4.3 14.7 1.0
CG J:GLU134 4.4 17.4 1.0
SG J:CYS43 4.6 20.7 1.0
OE1 J:GLU134 4.6 20.9 1.0
O J:HOH156 4.8 27.3 1.0
OH J:TYR53 4.8 14.5 1.0
O J:HOH1 4.9 13.9 1.0

Reference:

E.Ugochukwu, R.Cocking, E.Pilka, W.W.Yue, J.E.Bray, A.Chaikuad, T.Krojer, J.Muniz, U.Oppermann. The Crystal Structure of Human 6 Pyruvoyl Tetrahydrobiopterin Synthase To Be Published.
Page generated: Wed Oct 9 17:22:58 2024

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