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Zinc in PDB 6igs: Crystal Structure of Hprt From F. Tularensis with Zinc

Enzymatic activity of Crystal Structure of Hprt From F. Tularensis with Zinc

All present enzymatic activity of Crystal Structure of Hprt From F. Tularensis with Zinc:
2.4.2.8;

Protein crystallography data

The structure of Crystal Structure of Hprt From F. Tularensis with Zinc, PDB code: 6igs was solved by G.C.Pavithra, S.V.Kundapura, U.A.Ramagopal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.24 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.764, 90.193, 113.707, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hprt From F. Tularensis with Zinc (pdb code 6igs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Hprt From F. Tularensis with Zinc, PDB code: 6igs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6igs

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Zinc binding site 1 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:32.6
occ:1.00
 OE2 A:GLU102 2.0 30.3 1.0
O A:HOH334 2.1 29.9 1.0
OD1 A:ASP103 2.1 27.5 1.0
O A:HOH312 2.3 34.4 1.0
O A:HOH305 2.3 31.9 1.0
O A:HOH318 2.5 24.4 1.0
CD A:GLU102 2.8 27.9 1.0
OE1 A:GLU102 3.0 28.6 1.0
CG A:ASP103 3.1 24.5 1.0
OD2 A:ASP103 3.5 27.2 1.0
O1 A:SO4201 3.7 33.5 1.0
N A:ASP103 4.1 20.6 1.0
CG A:GLU102 4.2 26.3 1.0
CB A:ASP103 4.4 22.2 1.0
N A:ILE104 4.4 23.5 1.0
O A:ILE104 4.4 23.9 1.0
CG1 A:VAL42 4.4 17.2 1.0
OG A:SER46 4.5 19.2 0.5
O A:VAL42 4.5 16.4 1.0
CA A:ASP103 4.7 21.9 1.0
O2 A:SO4201 4.8 43.0 1.0
CB A:VAL42 4.9 17.5 1.0
CB A:GLU102 4.9 24.9 1.0
S A:SO4201 4.9 34.6 1.0
CG2 A:ILE104 4.9 29.9 1.0
CA A:GLU102 5.0 21.3 1.0

Zinc binding site 2 out of 8 in 6igs

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Zinc binding site 2 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn204

b:86.6
occ:1.00
 ND1 A:HIS109 1.9 56.6 1.0
OE2 A:GLU139 1.9 55.2 1.0
NE2 A:HIS112 2.3 57.6 1.0
CE1 A:HIS109 2.8 57.0 1.0
CE1 A:HIS112 2.9 55.2 1.0
CG A:HIS109 2.9 50.3 1.0
CD A:GLU139 3.0 62.9 1.0
CB A:HIS109 3.4 44.2 1.0
OE1 A:GLU139 3.4 59.4 1.0
CA A:HIS109 3.5 40.9 1.0
CD2 A:HIS112 3.6 56.1 1.0
NE2 A:HIS109 4.0 57.0 1.0
CD2 A:HIS109 4.0 53.9 1.0
ND1 A:HIS112 4.1 56.2 1.0
O A:HIS109 4.2 38.8 1.0
NH2 A:ARG140 4.3 91.3 1.0
CG A:GLU139 4.3 67.7 1.0
C A:HIS109 4.3 40.4 1.0
CG A:HIS112 4.5 52.3 1.0
N A:HIS109 4.5 38.7 1.0
CZ A:ARG140 4.8 89.6 1.0
NH1 A:ARG140 4.9 84.9 1.0

Zinc binding site 3 out of 8 in 6igs

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Zinc binding site 3 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:17.3
occ:1.00
 NE2 B:HIS112 1.9 13.8 1.0
ND1 B:HIS109 1.9 21.7 1.0
OE2 B:GLU139 2.1 17.8 1.0
CE1 B:HIS109 2.7 22.5 1.0
CD B:GLU139 2.8 18.8 1.0
CD2 B:HIS112 2.8 13.5 1.0
OE1 B:GLU139 2.9 18.2 1.0
CE1 B:HIS112 3.0 14.3 1.0
CG B:HIS109 3.1 20.0 1.0
CA B:HIS109 3.6 16.7 1.0
CB B:HIS109 3.6 18.1 1.0
NH1 B:ARG140 3.7 19.7 1.0
NE2 B:HIS109 4.0 21.9 1.0
CG B:HIS112 4.0 13.6 1.0
ND1 B:HIS112 4.1 14.0 1.0
CD2 B:HIS109 4.1 21.4 1.0
O B:HIS109 4.2 16.7 1.0
CG B:GLU139 4.2 19.6 1.0
C B:HIS109 4.4 16.6 1.0
N B:HIS109 4.6 15.3 1.0
CZ B:ARG140 4.8 21.1 1.0
O B:GLY108 4.9 14.7 1.0
CE B:LYS113 4.9 20.7 1.0

Zinc binding site 4 out of 8 in 6igs

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Zinc binding site 4 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:37.9
occ:1.00
 OD1 B:ASP103 2.2 24.7 1.0
O B:HOH322 2.2 23.2 1.0
OE2 B:GLU102 2.2 22.6 1.0
O B:HOH344 2.3 34.4 1.0
O B:HOH335 2.5 32.0 1.0
O B:HOH346 2.6 34.5 1.0
CD B:GLU102 2.9 22.0 1.0
CG B:ASP103 3.0 20.7 1.0
OE1 B:GLU102 3.1 23.2 1.0
OD2 B:ASP103 3.3 24.0 1.0
N B:ASP103 4.0 15.8 1.0
CG B:GLU102 4.0 22.3 1.0
OG B:SER46 4.2 13.0 0.5
CB B:ASP103 4.3 18.7 1.0
N B:ILE104 4.4 15.7 1.0
CG1 B:VAL42 4.4 11.5 1.0
O B:ILE104 4.5 17.3 1.0
O B:VAL42 4.6 11.3 1.0
CA B:ASP103 4.6 16.8 1.0
O B:HOH317 4.8 23.1 1.0
CB B:VAL42 4.8 11.4 1.0
CA B:GLU102 4.9 16.3 1.0
C B:GLU102 4.9 15.3 1.0
CG2 B:ILE104 5.0 20.1 1.0

Zinc binding site 5 out of 8 in 6igs

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Zinc binding site 5 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn203

b:35.5
occ:1.00
 OE1 C:GLU102 1.9 39.7 1.0
O C:HOH302 2.0 36.9 1.0
O C:HOH301 2.3 23.7 1.0
OD1 C:ASP103 2.3 25.8 1.0
O C:HOH322 2.3 35.7 1.0
O C:HOH328 2.4 36.5 1.0
CD C:GLU102 2.8 35.3 1.0
CG C:ASP103 3.2 23.5 1.0
OE2 C:GLU102 3.3 36.1 1.0
OD2 C:ASP103 3.5 26.8 1.0
O3 C:SO4202 3.6 45.4 1.0
CG C:GLU102 3.8 32.1 1.0
N C:ASP103 4.1 20.5 1.0
OG C:SER46 4.2 19.0 0.5
O C:ILE104 4.3 23.2 1.0
N C:ILE104 4.4 19.8 1.0
CG1 C:VAL42 4.4 23.9 1.0
CB C:ASP103 4.5 21.4 1.0
O C:VAL42 4.6 26.0 1.0
CG2 C:ILE104 4.7 24.2 1.0
CA C:ASP103 4.8 20.7 1.0
O C:HOH319 4.8 26.7 1.0
CB C:GLU102 4.9 28.2 1.0
S C:SO4202 5.0 54.1 1.0
CB C:VAL42 5.0 24.9 1.0
CA C:GLU102 5.0 24.1 1.0

Zinc binding site 6 out of 8 in 6igs

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Zinc binding site 6 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn204

b:36.0
occ:1.00
 NE2 C:HIS112 2.0 32.8 1.0
OE2 C:GLU139 2.1 31.6 1.0
ND1 C:HIS109 2.1 42.3 1.0
CD C:GLU139 2.8 29.3 1.0
CE1 C:HIS109 2.9 44.0 1.0
CE1 C:HIS112 3.0 35.3 1.0
CG C:HIS109 3.0 37.1 1.0
OE1 C:GLU139 3.0 31.7 1.0
CD2 C:HIS112 3.0 34.1 1.0
CB C:HIS109 3.4 33.2 1.0
CA C:HIS109 3.5 30.5 1.0
NH2 C:ARG140 3.5 46.9 1.0
NE2 C:HIS109 4.0 42.1 1.0
CD2 C:HIS109 4.0 40.9 1.0
ND1 C:HIS112 4.1 34.8 1.0
CG C:HIS112 4.1 33.9 1.0
CG C:GLU139 4.2 28.5 1.0
C C:HIS109 4.4 31.7 1.0
CZ C:ARG140 4.4 47.5 1.0
N C:HIS109 4.5 28.5 1.0
O C:HIS109 4.5 32.1 1.0
NE C:ARG140 4.6 44.4 1.0

Zinc binding site 7 out of 8 in 6igs

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Zinc binding site 7 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn203

b:36.3
occ:1.00
 OD1 D:ASP103 2.2 30.8 1.0
OE1 D:GLU102 2.2 34.6 1.0
O D:HOH309 2.3 25.2 1.0
O D:HOH313 2.5 40.4 1.0
O D:HOH330 2.5 32.0 1.0
O D:HOH334 2.6 39.2 1.0
CD D:GLU102 2.9 30.9 1.0
CG D:ASP103 3.1 28.5 1.0
OE2 D:GLU102 3.2 31.5 1.0
OD2 D:ASP103 3.5 30.5 1.0
O2 D:SO4202 3.9 57.8 1.0
CG D:GLU102 4.1 29.7 1.0
N D:ASP103 4.1 22.6 1.0
CB D:ASP103 4.4 26.3 1.0
O D:ILE104 4.5 23.9 1.0
N D:ILE104 4.5 21.9 1.0
CG1 D:VAL42 4.5 21.6 1.0
O D:VAL42 4.5 18.7 1.0
CA D:ASP103 4.7 23.5 1.0
CG2 D:ILE104 4.9 25.3 1.0
CB D:VAL42 4.9 20.4 1.0
CA D:GLU102 5.0 24.0 1.0

Zinc binding site 8 out of 8 in 6igs

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Zinc binding site 8 out of 8 in the Crystal Structure of Hprt From F. Tularensis with Zinc


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 Hprt From F. Tularensis with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn204

b:30.8
occ:1.00
 OE1 D:GLU139 1.8 29.8 1.0
ND1 D:HIS109 1.9 32.0 1.0
NE2 D:HIS112 2.0 29.9 1.0
CE1 D:HIS109 2.8 32.5 1.0
CD D:GLU139 2.8 31.9 1.0
CD2 D:HIS112 3.0 28.8 1.0
CG D:HIS109 3.0 29.8 1.0
CE1 D:HIS112 3.1 30.5 1.0
OE2 D:GLU139 3.3 31.9 1.0
CB D:HIS109 3.5 27.3 1.0
CA D:HIS109 3.5 26.7 1.0
NE2 D:HIS109 4.0 32.4 1.0
CD2 D:HIS109 4.1 30.6 1.0
CG D:HIS112 4.2 28.5 1.0
ND1 D:HIS112 4.2 30.1 1.0
CG D:GLU139 4.2 32.1 1.0
O D:HIS109 4.3 29.0 1.0
C D:HIS109 4.4 27.4 1.0
N D:HIS109 4.6 26.3 1.0
NH2 D:ARG140 4.8 44.9 1.0

Reference:

G.C.Pavithra, U.A.Ramagopal. Crystal Structure of Hypoxanthine Phosphoribosyltransferase From Francisella Tularensis To Be Published.
Page generated: Mon Oct 28 23:49:58 2024

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