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Zinc in PDB 1wpl: Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex

Enzymatic activity of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex

All present enzymatic activity of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex:
3.5.4.16;

Protein crystallography data

The structure of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex, PDB code: 1wpl was solved by N.Maita, K.Hatakeyama, K.Okada, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 121.720, 109.670, 130.270, 90.00, 97.85, 90.00
R / Rfree (%) 20.7 / 23.3

Other elements in 1wpl:

The structure of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex also contains other interesting chemical elements:

Sodium (Na) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex (pdb code 1wpl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex, PDB code: 1wpl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1wpl

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Zinc binding site 1 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1110

b:60.0
occ:1.00
 SG A:CYS132 2.3 36.5 1.0
SG A:CYS203 2.4 46.1 1.0
ND1 A:HIS135 2.4 27.5 1.0
CE1 A:HIS135 3.1 27.2 1.0
CB A:CYS132 3.3 29.2 1.0
CB A:CYS203 3.4 42.5 1.0
CG A:HIS135 3.5 25.9 1.0
CB A:HIS135 4.0 26.3 1.0
N A:HIS135 4.0 30.3 1.0
CB A:HIS134 4.2 30.7 1.0
NE2 A:HIS135 4.3 28.2 1.0
CD2 A:HIS135 4.5 27.0 1.0
CA A:HIS135 4.6 27.6 1.0
CA A:CYS132 4.7 28.7 1.0
C A:HIS134 4.8 31.5 1.0
CA A:CYS203 4.8 41.0 1.0
CA A:HIS134 4.8 30.1 1.0
N A:HIS134 4.9 28.6 1.0

Zinc binding site 2 out of 10 in 1wpl

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Zinc binding site 2 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1108

b:59.8
occ:1.00
 ND1 B:HIS135 2.2 30.3 1.0
SG B:CYS132 2.3 34.6 1.0
SG B:CYS203 2.4 42.9 1.0
CE1 B:HIS135 3.0 29.1 1.0
CG B:HIS135 3.4 27.9 1.0
CB B:CYS132 3.4 31.6 1.0
CB B:CYS203 3.5 41.1 1.0
CB B:HIS135 3.9 26.9 1.0
N B:HIS135 3.9 28.6 1.0
CB B:HIS134 4.0 33.3 1.0
NE2 B:HIS135 4.2 30.2 1.0
CD2 B:HIS135 4.4 28.3 1.0
CA B:HIS135 4.5 27.6 1.0
C B:HIS134 4.6 30.6 1.0
CA B:HIS134 4.6 30.9 1.0
CA B:CYS132 4.8 30.5 1.0
N B:HIS134 4.8 29.8 1.0
CG B:HIS134 4.8 37.8 1.0
ND1 B:HIS134 4.9 40.3 1.0
CA B:CYS203 5.0 40.4 1.0

Zinc binding site 3 out of 10 in 1wpl

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Zinc binding site 3 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1103

b:56.5
occ:1.00
 SG C:CYS132 2.3 36.8 1.0
ND1 C:HIS135 2.4 30.1 1.0
SG C:CYS203 2.6 44.5 1.0
CE1 C:HIS135 3.1 30.0 1.0
CB C:CYS132 3.3 29.4 1.0
CG C:HIS135 3.6 28.3 1.0
CB C:CYS203 3.6 40.9 1.0
CB C:HIS134 4.0 31.5 1.0
N C:HIS135 4.0 29.1 1.0
CB C:HIS135 4.0 26.7 1.0
NE2 C:HIS135 4.3 30.9 1.0
O C:HOH2015 4.5 18.3 1.0
CD2 C:HIS135 4.6 29.1 1.0
CA C:HIS135 4.6 27.0 1.0
CA C:HIS134 4.7 29.3 1.0
C C:HIS134 4.7 30.3 1.0
CA C:CYS132 4.7 28.4 1.0
N C:HIS134 4.8 28.4 1.0
CG C:HIS134 4.8 36.0 1.0
ND1 C:HIS134 4.8 38.4 1.0

Zinc binding site 4 out of 10 in 1wpl

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Zinc binding site 4 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1104

b:58.7
occ:1.00
 ND1 D:HIS135 2.3 27.2 1.0
SG D:CYS132 2.3 33.3 1.0
SG D:CYS203 2.4 39.3 1.0
CE1 D:HIS135 3.0 26.2 1.0
CB D:CYS132 3.3 28.3 1.0
CG D:HIS135 3.4 25.7 1.0
CB D:CYS203 3.5 39.5 1.0
N D:HIS135 3.9 26.0 1.0
CB D:HIS134 3.9 31.1 1.0
CB D:HIS135 3.9 24.6 1.0
NE2 D:HIS135 4.2 24.8 1.0
O D:HOH2004 4.3 18.1 1.0
CD2 D:HIS135 4.4 24.8 1.0
CA D:HIS135 4.5 24.1 1.0
C D:HIS134 4.5 28.6 1.0
CA D:HIS134 4.6 28.8 1.0
N D:HIS134 4.7 27.3 1.0
CA D:CYS132 4.7 27.0 1.0
CG D:HIS134 4.8 34.8 1.0
ND1 D:HIS134 4.8 36.7 1.0
CA D:CYS203 4.9 39.1 1.0

Zinc binding site 5 out of 10 in 1wpl

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Zinc binding site 5 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1102

b:46.6
occ:1.00
 ND1 E:HIS135 2.2 27.6 1.0
SG E:CYS203 2.3 39.9 1.0
SG E:CYS132 2.4 32.9 1.0
CE1 E:HIS135 3.0 28.2 1.0
CG E:HIS135 3.3 26.0 1.0
CB E:CYS132 3.4 30.1 1.0
CB E:CYS203 3.4 39.3 1.0
CB E:HIS135 3.8 24.0 1.0
N E:HIS135 3.9 25.9 1.0
CB E:HIS134 3.9 31.7 1.0
NE2 E:HIS135 4.1 29.4 1.0
CD2 E:HIS135 4.3 25.8 1.0
O E:HOH2012 4.4 24.3 1.0
CA E:HIS135 4.5 23.6 1.0
C E:HIS134 4.6 28.2 1.0
CA E:HIS134 4.7 28.6 1.0
CA E:CYS132 4.8 28.6 1.0
N E:HIS134 4.8 27.6 1.0
CG E:HIS134 4.8 35.9 1.0
CA E:CYS203 4.9 38.6 1.0
ND1 E:HIS134 4.9 39.0 1.0

Zinc binding site 6 out of 10 in 1wpl

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Zinc binding site 6 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1105

b:50.0
occ:1.00
 ND1 F:HIS135 2.2 27.6 1.0
SG F:CYS132 2.2 34.8 1.0
SG F:CYS203 2.5 37.7 1.0
CE1 F:HIS135 3.0 26.7 1.0
O F:HOH2023 3.1 7.5 1.0
CB F:CYS132 3.3 28.7 1.0
CG F:HIS135 3.3 26.4 1.0
CB F:CYS203 3.6 39.9 1.0
CB F:HIS135 3.8 25.3 1.0
N F:HIS135 3.8 29.1 1.0
CB F:HIS134 3.9 32.9 1.0
NE2 F:HIS135 4.2 26.1 1.0
CD2 F:HIS135 4.4 27.1 1.0
CA F:HIS135 4.5 27.1 1.0
C F:HIS134 4.6 30.8 1.0
CA F:HIS134 4.6 30.9 1.0
CA F:CYS132 4.7 28.1 1.0
O F:HOH2013 4.7 32.3 1.0
N F:HIS134 4.7 30.2 1.0
CG F:HIS134 4.8 37.3 1.0
ND1 F:HIS134 4.8 38.9 1.0
C F:CYS132 5.0 28.0 1.0

Zinc binding site 7 out of 10 in 1wpl

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Zinc binding site 7 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1101

b:57.6
occ:1.00
 ND1 G:HIS135 2.3 27.1 1.0
SG G:CYS132 2.4 34.5 1.0
SG G:CYS203 2.6 41.6 1.0
CE1 G:HIS135 2.9 25.5 1.0
CB G:CYS132 3.2 27.1 1.0
CG G:HIS135 3.5 25.6 1.0
CB G:CYS203 3.8 41.5 1.0
CB G:HIS134 3.8 31.4 1.0
N G:HIS135 4.0 26.2 1.0
CB G:HIS135 4.1 23.6 1.0
NE2 G:HIS135 4.2 24.0 1.0
CD2 G:HIS135 4.5 24.8 1.0
CA G:HIS134 4.5 29.7 1.0
ND1 G:HIS134 4.6 36.8 1.0
CG G:HIS134 4.6 35.2 1.0
C G:HIS134 4.6 28.4 1.0
N G:HIS134 4.6 30.3 1.0
CA G:HIS135 4.7 25.3 1.0
CA G:CYS132 4.7 27.6 1.0
C G:CYS132 5.0 27.4 1.0

Zinc binding site 8 out of 10 in 1wpl

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Zinc binding site 8 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1107

b:59.2
occ:1.00
 ND1 H:HIS135 2.3 27.4 1.0
SG H:CYS132 2.4 33.3 1.0
SG H:CYS203 2.5 42.7 1.0
CE1 H:HIS135 3.0 27.9 1.0
CB H:CYS132 3.3 28.8 1.0
CG H:HIS135 3.5 25.7 1.0
CB H:CYS203 3.6 41.2 1.0
O H:HOH2008 3.8 38.5 1.0
CB H:HIS134 3.9 30.8 1.0
N H:HIS135 4.0 27.8 1.0
CB H:HIS135 4.0 23.9 1.0
NE2 H:HIS135 4.2 29.2 1.0
CD2 H:HIS135 4.5 27.9 1.0
CA H:HIS135 4.6 26.0 1.0
C H:HIS134 4.7 29.7 1.0
CA H:HIS134 4.7 28.9 1.0
CA H:CYS132 4.7 28.1 1.0
CG H:HIS134 4.8 34.9 1.0
N H:HIS134 4.8 29.3 1.0
ND1 H:HIS134 4.9 36.7 1.0
CA H:CYS203 5.0 40.9 1.0

Zinc binding site 9 out of 10 in 1wpl

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Zinc binding site 9 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1109

b:51.7
occ:1.00
 ND1 I:HIS135 2.3 26.0 1.0
SG I:CYS132 2.4 33.8 1.0
SG I:CYS203 2.4 41.5 1.0
O J:HOH2016 2.8 1.0 1.0
CE1 I:HIS135 3.0 26.4 1.0
CB I:CYS132 3.2 29.9 1.0
CB I:CYS203 3.4 40.5 1.0
CG I:HIS135 3.5 26.2 1.0
CB I:HIS135 4.0 25.0 1.0
CB I:HIS134 4.1 31.9 1.0
N I:HIS135 4.1 28.4 1.0
NE2 I:HIS135 4.2 28.2 1.0
CD2 I:HIS135 4.5 27.1 1.0
CA I:HIS135 4.7 25.8 1.0
CA I:CYS132 4.7 30.2 1.0
C I:HIS134 4.8 30.6 1.0
CA I:HIS134 4.8 30.0 1.0
CA I:CYS203 4.9 39.8 1.0
N I:HIS134 4.9 28.2 1.0
CG I:HIS134 4.9 36.2 1.0
ND1 I:HIS134 4.9 37.5 1.0
ND1 I:HIS201 5.0 27.0 1.0

Zinc binding site 10 out of 10 in 1wpl

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Zinc binding site 10 out of 10 in the Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Inhibitory Form of Rat Gtp Cyclohydrolase I/Gfrp Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1106

b:56.4
occ:1.00
 ND1 J:HIS135 2.3 30.0 1.0
SG J:CYS132 2.4 34.6 1.0
SG J:CYS203 2.4 44.1 1.0
CE1 J:HIS135 3.0 29.7 1.0
CB J:CYS132 3.3 28.1 1.0
CB J:CYS203 3.4 42.0 1.0
CG J:HIS135 3.5 28.6 1.0
CB J:HIS135 4.0 25.9 1.0
N J:HIS135 4.0 28.6 1.0
CB J:HIS134 4.1 30.4 1.0
NE2 J:HIS135 4.2 28.9 1.0
CD2 J:HIS135 4.5 29.0 1.0
CA J:HIS135 4.6 26.9 1.0
C J:HIS134 4.7 30.8 1.0
CA J:CYS132 4.8 29.1 1.0
CA J:HIS134 4.8 29.4 1.0
N J:HIS134 4.9 29.6 1.0
CA J:CYS203 4.9 40.5 1.0
CG J:HIS134 4.9 35.9 1.0
ND1 J:HIS134 4.9 37.7 1.0

Reference:

N.Maita, K.Hatakeyama, K.Okada, T.Hakoshima. Structural Basis of Biopterin-Induced Inhibition of Gtp Cyclohydrolase I By Gfrp, Its Feedback Regulatory Protein J.Biol.Chem. V. 279 51534 2004.
ISSN: ISSN 0021-9258
PubMed: 15448133
DOI: 10.1074/JBC.M409440200
Page generated: Wed Dec 16 03:10:31 2020

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