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Zinc in PDB 1is8: Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn

Enzymatic activity of Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn

All present enzymatic activity of Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn:
3.5.4.16;

Protein crystallography data

The structure of Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn, PDB code: 1is8 was solved by N.Maita, K.Okada, K.Hatakeyama, T.Hakoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 123.900, 111.430, 125.910, 90.00, 97.32, 90.00
R / Rfree (%) 21.9 / 24.5

Other elements in 1is8:

The structure of Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn also contains other interesting chemical elements:

Potassium (K) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn (pdb code 1is8). 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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn, PDB code: 1is8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1is8

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Zinc binding site 1 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3102

b:53.2
occ:1.00
 ND1 A:HIS135 2.1 34.1 1.0
SG A:CYS132 2.2 35.4 1.0
SG A:CYS203 2.4 52.2 1.0
O A:HOH3107 2.8 19.4 1.0
CE1 A:HIS135 2.8 31.6 1.0
CG A:HIS135 3.3 32.8 1.0
CB A:CYS203 3.4 52.1 1.0
CB A:CYS132 3.6 36.2 1.0
CB A:HIS135 3.9 32.2 1.0
NE2 A:HIS135 4.0 31.4 1.0
N A:HIS135 4.2 34.5 1.0
CB A:HIS134 4.2 39.1 1.0
CD2 A:HIS135 4.3 31.9 1.0
O A:HOH3112 4.4 27.7 1.0
CA A:HIS135 4.7 32.6 1.0
C A:HIS134 4.8 36.9 1.0
CA A:CYS203 4.8 53.2 1.0
ND1 A:HIS134 4.8 48.7 1.0
O A:HOH3117 4.8 30.3 1.0
CA A:HIS134 4.9 36.7 1.0
CA A:CYS132 4.9 34.6 1.0
N A:HIS134 5.0 36.5 1.0

Zinc binding site 2 out of 10 in 1is8

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Zinc binding site 2 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3109

b:54.6
occ:1.00
 SG B:CYS132 2.1 37.1 1.0
ND1 B:HIS135 2.1 28.3 1.0
O B:HOH3110 2.1 5.8 1.0
SG B:CYS203 2.3 45.4 1.0
CE1 B:HIS135 2.9 29.2 1.0
CG B:HIS135 3.2 30.4 1.0
CB B:CYS203 3.2 50.4 1.0
CB B:CYS132 3.5 34.1 1.0
CB B:HIS135 3.7 31.1 1.0
NE2 B:HIS135 4.0 29.1 1.0
N B:HIS135 4.1 34.1 1.0
O B:HOH3111 4.1 11.8 1.0
CD2 B:HIS135 4.2 29.0 1.0
CB B:HIS134 4.3 40.4 1.0
CA B:HIS135 4.5 32.4 1.0
CA B:CYS203 4.7 51.6 1.0
C B:HIS134 4.7 36.4 1.0
CA B:CYS132 4.8 32.8 1.0
CA B:HIS134 4.9 37.6 1.0
ND1 B:HIS134 4.9 47.8 1.0
N B:HIS134 4.9 37.0 1.0

Zinc binding site 3 out of 10 in 1is8

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Zinc binding site 3 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn3107

b:55.1
occ:1.00
 ND1 C:HIS135 2.2 35.8 1.0
SG C:CYS132 2.3 40.4 1.0
O C:HOH3108 2.3 13.5 1.0
SG C:CYS203 2.4 50.4 1.0
CE1 C:HIS135 3.0 38.5 1.0
CB C:CYS203 3.1 52.4 1.0
CG C:HIS135 3.2 34.2 1.0
CB C:CYS132 3.4 34.4 1.0
CB C:HIS135 3.6 34.1 1.0
N C:HIS135 4.0 34.7 1.0
NE2 C:HIS135 4.1 38.8 1.0
CD2 C:HIS135 4.2 36.8 1.0
CB C:HIS134 4.3 39.7 1.0
CA C:HIS135 4.4 34.4 1.0
CA C:CYS203 4.6 53.6 1.0
C C:HIS134 4.7 37.9 1.0
CA C:CYS132 4.8 33.2 1.0
O D:HOH3110 4.9 26.2 1.0
CA C:HIS134 4.9 38.5 1.0
N C:HIS134 5.0 38.4 1.0

Zinc binding site 4 out of 10 in 1is8

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Zinc binding site 4 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn3108

b:73.0
occ:1.00
 ND1 D:HIS135 2.1 29.8 1.0
SG D:CYS132 2.2 40.6 1.0
SG D:CYS203 2.5 51.6 1.0
O D:HOH3109 2.8 38.8 1.0
CE1 D:HIS135 2.8 30.5 1.0
CG D:HIS135 3.2 29.5 1.0
CB D:CYS203 3.3 54.3 1.0
CB D:CYS132 3.6 36.5 1.0
CB D:HIS135 3.8 31.9 1.0
N D:HIS135 4.0 34.8 1.0
NE2 D:HIS135 4.0 31.9 1.0
CB D:HIS134 4.2 39.3 1.0
CD2 D:HIS135 4.2 30.2 1.0
CA D:HIS135 4.5 33.3 1.0
O D:HOH3115 4.6 48.0 1.0
C D:HIS134 4.7 36.6 1.0
CA D:CYS203 4.8 56.3 1.0
CA D:HIS134 4.8 37.0 1.0
ND1 D:HIS134 4.8 44.6 1.0
CA D:CYS132 4.9 37.0 1.0
N D:HIS134 4.9 36.7 1.0
CG D:HIS134 5.0 42.6 1.0

Zinc binding site 5 out of 10 in 1is8

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Zinc binding site 5 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn3105

b:57.8
occ:1.00
 O E:HOH3107 2.2 17.6 1.0
ND1 E:HIS135 2.2 34.1 1.0
SG E:CYS132 2.2 40.2 1.0
SG E:CYS203 2.3 50.2 1.0
CE1 E:HIS135 3.0 35.0 1.0
CB E:CYS203 3.1 52.8 1.0
CG E:HIS135 3.2 33.2 1.0
CB E:CYS132 3.5 36.0 1.0
CB E:HIS135 3.7 32.6 1.0
N E:HIS135 4.1 36.0 1.0
NE2 E:HIS135 4.1 35.0 1.0
CD2 E:HIS135 4.2 33.3 1.0
CB E:HIS134 4.4 41.1 1.0
O E:HOH3110 4.5 33.6 1.0
CA E:HIS135 4.5 34.5 1.0
CA E:CYS203 4.5 54.1 1.0
O A:HOH3109 4.6 33.3 1.0
C E:HIS134 4.8 38.5 1.0
CA E:CYS132 4.9 36.8 1.0
C E:CYS203 5.0 57.6 1.0

Zinc binding site 6 out of 10 in 1is8

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Zinc binding site 6 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn3110

b:62.3
occ:1.00
 SG F:CYS132 2.2 44.5 1.0
ND1 F:HIS135 2.2 37.4 1.0
O F:HOH3111 2.4 18.3 1.0
SG F:CYS203 2.4 52.7 1.0
CE1 F:HIS135 2.9 38.2 1.0
CB F:CYS203 3.2 53.8 1.0
CG F:HIS135 3.4 35.7 1.0
CB F:CYS132 3.5 37.8 1.0
CB F:HIS135 3.9 34.4 1.0
NE2 F:HIS135 4.1 37.9 1.0
N F:HIS135 4.1 37.0 1.0
CB F:HIS134 4.3 41.4 1.0
CD2 F:HIS135 4.3 36.8 1.0
CA F:HIS135 4.6 35.5 1.0
CA F:CYS203 4.7 54.9 1.0
O F:HOH3120 4.8 28.0 1.0
CA F:CYS132 4.8 36.7 1.0
C F:HIS134 4.8 39.8 1.0
ND1 F:HIS134 4.9 49.4 1.0
CA F:HIS134 4.9 39.3 1.0

Zinc binding site 7 out of 10 in 1is8

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Zinc binding site 7 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn3103

b:56.2
occ:1.00
 ND1 G:HIS135 2.2 36.0 1.0
SG G:CYS132 2.2 40.1 1.0
O G:HOH3104 2.3 16.1 1.0
SG G:CYS203 2.4 51.4 1.0
CE1 G:HIS135 2.9 36.8 1.0
CG G:HIS135 3.2 35.2 1.0
CB G:CYS203 3.2 52.6 1.0
CB G:CYS132 3.4 36.4 1.0
CB G:HIS135 3.7 35.0 1.0
N G:HIS135 4.0 37.1 1.0
NE2 G:HIS135 4.1 36.0 1.0
CB G:HIS134 4.2 42.1 1.0
CD2 G:HIS135 4.2 35.5 1.0
O G:HOH3111 4.4 35.5 1.0
CA G:HIS135 4.5 35.4 1.0
O G:HOH3106 4.6 22.4 1.0
CA G:CYS203 4.7 54.1 1.0
C G:HIS134 4.7 39.1 1.0
CA G:CYS132 4.8 35.3 1.0
CA G:HIS134 4.9 39.1 1.0
ND1 G:HIS134 4.9 49.4 1.0
N G:HIS134 4.9 38.4 1.0

Zinc binding site 8 out of 10 in 1is8

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Zinc binding site 8 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn3104

b:49.8
occ:1.00
 ND1 H:HIS135 2.1 31.7 1.0
SG H:CYS203 2.3 49.1 1.0
O H:HOH3105 2.3 9.9 1.0
SG H:CYS132 2.4 40.8 1.0
CE1 H:HIS135 2.9 32.1 1.0
CG H:HIS135 3.2 32.5 1.0
CB H:CYS203 3.2 51.4 1.0
CB H:CYS132 3.6 34.2 1.0
CB H:HIS135 3.7 33.5 1.0
NE2 H:HIS135 4.0 31.4 1.0
N H:HIS135 4.1 35.0 1.0
O H:HOH3120 4.1 27.5 1.0
CD2 H:HIS135 4.2 31.2 1.0
CB H:HIS134 4.3 39.8 1.0
CA H:HIS135 4.5 33.9 1.0
CA H:CYS203 4.7 53.6 1.0
C H:HIS134 4.8 37.1 1.0
CA H:CYS132 5.0 33.2 1.0
CA H:HIS134 5.0 37.8 1.0

Zinc binding site 9 out of 10 in 1is8

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Zinc binding site 9 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn3101

b:50.2
occ:1.00
 SG I:CYS203 1.8 43.9 1.0
SG I:CYS132 1.9 34.3 1.0
ND1 I:HIS135 2.2 32.9 1.0
CE1 I:HIS135 3.0 32.0 1.0
CB I:CYS203 3.1 51.7 1.0
CG I:HIS135 3.3 30.4 1.0
CB I:CYS132 3.4 32.1 1.0
O I:HOH3102 3.5 78.6 1.0
CB I:HIS135 3.8 29.5 1.0
NE2 I:HIS135 4.1 29.4 1.0
N I:HIS135 4.1 30.1 1.0
CD2 I:HIS135 4.3 29.6 1.0
CB I:HIS134 4.3 34.7 1.0
O I:HOH3111 4.4 21.8 1.0
CA I:CYS203 4.5 52.5 1.0
CA I:HIS135 4.6 29.8 1.0
O J:HOH3112 4.7 29.2 1.0
CA I:CYS132 4.8 32.7 1.0
C I:HIS134 4.9 34.0 1.0
C I:CYS203 5.0 56.0 1.0
CA I:HIS134 5.0 33.3 1.0

Zinc binding site 10 out of 10 in 1is8

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Zinc binding site 10 out of 10 in the Crystal Structure of Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn


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 Rat Gtpchi/Gfrp Stimulatory Complex Plus Zn within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn3106

b:53.1
occ:1.00
 ND1 J:HIS135 2.2 29.2 1.0
SG J:CYS132 2.3 33.6 1.0
O J:HOH3117 2.4 16.1 1.0
SG J:CYS203 2.4 46.2 1.0
O J:HOH3107 2.7 46.3 1.0
CE1 J:HIS135 2.9 27.4 1.0
CG J:HIS135 3.4 27.9 1.0
CB J:CYS203 3.5 50.7 1.0
CB J:CYS132 3.6 34.0 1.0
CB J:HIS135 3.9 28.4 1.0
NE2 J:HIS135 4.1 29.3 1.0
N J:HIS135 4.1 31.3 1.0
CB J:HIS134 4.2 38.7 1.0
O J:HOH3116 4.2 22.9 1.0
CD2 J:HIS135 4.4 29.2 1.0
CA J:HIS135 4.7 30.7 1.0
C J:HIS134 4.8 34.7 1.0
ND1 J:HIS134 4.8 45.9 1.0
CA J:HIS134 4.9 35.7 1.0
CA J:CYS203 4.9 52.3 1.0
CA J:CYS132 4.9 33.9 1.0
CG J:HIS134 5.0 43.2 1.0
N J:HIS134 5.0 36.7 1.0

Reference:

N.Maita, K.Okada, K.Hatakeyama, T.Hakoshima. Crystal Structure of the Stimulatory Complex of Gtp Cyclohydrolase I and Its Feedback Regulatory Protein Gfrp. Proc.Natl.Acad.Sci.Usa V. 99 1212 2002.
ISSN: ISSN 0027-8424
PubMed: 11818540
DOI: 10.1073/PNAS.022646999
Page generated: Wed Dec 16 02:53:06 2020

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