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Zinc in PDB 3pfo: Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution

Enzymatic activity of Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution

All present enzymatic activity of Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution:
3.5.1.16;

Protein crystallography data

The structure of Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution, PDB code: 3pfo was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 87.074, 48.823, 111.879, 90.00, 111.02, 90.00
R / Rfree (%) 17.1 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution (pdb code 3pfo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution, PDB code: 3pfo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3pfo

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Zinc binding site 1 out of 4 in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution


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 A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn450

b:27.9
occ:0.75
 OD1 A:ASP143 2.0 27.8 1.0
O A:HOH510 2.1 29.8 1.0
OE1 A:GLU201 2.1 28.1 1.0
NE2 A:HIS110 2.1 21.2 1.0
OE2 A:GLU201 2.5 25.8 1.0
CD A:GLU201 2.7 26.8 1.0
CG A:ASP143 3.0 28.2 1.0
CE1 A:HIS110 3.1 24.0 1.0
CD2 A:HIS110 3.1 24.0 1.0
OD2 A:ASP143 3.4 30.9 1.0
ZN A:ZN451 3.5 37.4 0.8
OE1 A:GLU177 3.6 27.1 1.0
OE2 A:GLU178 3.9 28.2 1.0
CD A:GLU177 4.0 28.1 1.0
OE2 A:GLU177 4.2 26.9 1.0
CG A:GLU201 4.2 24.1 1.0
ND1 A:HIS110 4.2 25.1 1.0
CB A:MSE144 4.2 23.7 1.0
CG A:HIS110 4.3 23.3 1.0
CG A:MSE144 4.3 21.6 1.0
CB A:ASP143 4.3 25.6 1.0
SE A:MSE144 4.5 19.6 0.8
CD A:GLU178 4.5 25.4 1.0
C A:ASP143 4.5 24.8 1.0
CA A:ASP143 4.6 25.6 1.0
O A:HOH788 4.7 37.7 1.0
CD A:PRO202 4.8 24.1 1.0
N A:MSE144 4.8 24.3 1.0
OE1 A:GLU178 4.8 25.2 1.0
O A:ASP143 4.8 24.9 1.0
CB A:GLU201 4.9 23.2 1.0
CG A:GLU177 5.0 24.5 1.0

Zinc binding site 2 out of 4 in 3pfo

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Zinc binding site 2 out of 4 in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution


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 A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn451

b:37.4
occ:0.75
 OD2 A:ASP143 2.1 30.9 1.0
O A:HOH510 2.2 29.8 1.0
OE2 A:GLU178 2.2 28.2 1.0
NE2 A:HIS401 2.3 24.7 1.0
OE1 A:GLU178 2.4 25.2 1.0
CD A:GLU178 2.7 25.4 1.0
CG A:ASP143 3.1 28.2 1.0
CE1 A:HIS401 3.2 25.4 1.0
CD2 A:HIS401 3.3 25.2 1.0
OD1 A:ASP143 3.4 27.8 1.0
ZN A:ZN450 3.5 27.9 0.8
O A:HOH788 3.7 37.7 1.0
NE2 B:HIS227 4.2 52.4 1.0
CG A:GLU178 4.2 23.7 1.0
OE1 A:GLU177 4.2 27.1 1.0
O A:HOH584 4.3 25.8 1.0
ND1 A:HIS401 4.3 26.7 1.0
CD2 B:HIS227 4.4 50.7 1.0
CG A:HIS401 4.4 25.7 1.0
CB A:ASP143 4.4 25.6 1.0
O A:HOH554 4.6 24.2 1.0
NE2 A:HIS110 4.6 21.2 1.0
CE1 A:HIS110 4.7 24.0 1.0
CG1 A:VAL114 4.7 21.1 1.0

Zinc binding site 3 out of 4 in 3pfo

Go back to Zinc Binding Sites List in 3pfo
Zinc binding site 3 out of 4 in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution


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 A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn450

b:53.9
occ:0.75
 O B:HOH511 2.2 47.9 1.0
OD2 B:ASP143 2.3 38.9 1.0
OE2 B:GLU178 2.3 33.0 1.0
NE2 B:HIS401 2.3 31.8 1.0
OE1 B:GLU178 2.4 28.5 1.0
CD B:GLU178 2.7 31.4 1.0
CG B:ASP143 3.1 37.7 1.0
OD1 B:ASP143 3.2 40.6 1.0
CE1 B:HIS401 3.3 33.3 1.0
CD2 B:HIS401 3.3 34.0 1.0
ZN B:ZN451 3.4 40.4 0.8
O B:HOH1147 3.9 48.5 1.0
OE1 B:GLU177 4.1 29.6 1.0
NE2 A:HIS227 4.1 39.2 0.5
CG B:GLU178 4.1 28.8 1.0
O B:HOH967 4.4 29.1 1.0
ND1 B:HIS401 4.4 31.6 1.0
CG B:HIS401 4.4 32.1 1.0
CD2 A:HIS227 4.4 39.1 0.5
CB B:ASP143 4.5 34.7 1.0
NE2 B:HIS110 4.6 29.5 1.0
CE1 B:HIS110 4.6 30.6 1.0
O B:HOH987 4.6 29.7 1.0
CG1 B:VAL114 4.7 28.2 1.0

Zinc binding site 4 out of 4 in 3pfo

Go back to Zinc Binding Sites List in 3pfo
Zinc binding site 4 out of 4 in the Crystal Structure of A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution


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 A Putative Acetylornithine Deacetylase (RPA2325) From Rhodopseudomonas Palustris CGA009 at 1.90 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn451

b:40.4
occ:0.75
 OD1 B:ASP143 2.0 40.6 1.0
NE2 B:HIS110 2.1 29.5 1.0
O B:HOH511 2.1 47.9 1.0
OE1 B:GLU201 2.2 37.2 1.0
OE2 B:GLU201 2.7 34.1 1.0
CD B:GLU201 2.8 33.4 1.0
CE1 B:HIS110 3.0 30.6 1.0
CG B:ASP143 3.2 37.7 1.0
CD2 B:HIS110 3.2 31.3 1.0
ZN B:ZN450 3.4 53.9 0.8
OE1 B:GLU177 3.5 29.6 1.0
OD2 B:ASP143 3.7 38.9 1.0
OE2 B:GLU178 4.0 33.0 1.0
CD B:GLU177 4.0 31.6 1.0
CB B:MSE144 4.1 34.2 1.0
ND1 B:HIS110 4.1 29.1 1.0
CG B:HIS110 4.3 29.5 1.0
CG B:GLU201 4.3 33.3 1.0
CG B:MSE144 4.3 34.0 1.0
OE2 B:GLU177 4.3 34.2 1.0
CB B:ASP143 4.4 34.7 1.0
SE B:MSE144 4.5 30.6 0.8
CD B:GLU178 4.5 31.4 1.0
C B:ASP143 4.6 33.6 1.0
CA B:ASP143 4.6 35.3 1.0
N B:MSE144 4.7 33.5 1.0
CD B:PRO202 4.8 37.1 1.0
OE1 B:GLU178 4.8 28.5 1.0
O B:ASP143 4.9 33.2 1.0
CB B:GLU201 4.9 34.8 1.0
CG B:GLU177 5.0 32.1 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
Page generated: Sat Oct 26 11:25:06 2024

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