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Zinc in PDB 2e18: Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3

Enzymatic activity of Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3

All present enzymatic activity of Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3:
6.3.1.5;

Protein crystallography data

The structure of Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3, PDB code: 2e18 was solved by K.Shimizu, Riken Structural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.58 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 84.919, 84.919, 113.576, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3 (pdb code 2e18). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3, PDB code: 2e18:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2e18

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Zinc binding site 1 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:27.9
occ:1.00
 OE1 A:GLU95 2.0 21.7 1.0
N1 A:IMD1300 2.1 30.0 1.0
N1 A:IMD1301 2.1 34.5 1.0
CD A:GLU95 2.7 23.2 1.0
OE2 A:GLU95 2.8 25.0 1.0
C5 A:IMD1301 2.9 34.8 1.0
C5 A:IMD1300 3.0 30.5 1.0
C2 A:IMD1300 3.0 30.0 1.0
C2 A:IMD1301 3.1 32.6 1.0
CE B:LYS79 3.6 25.8 1.0
C4 A:IMD1301 4.1 33.6 1.0
N3 A:IMD1300 4.1 31.6 1.0
C4 A:IMD1300 4.2 30.7 1.0
N3 A:IMD1301 4.2 32.9 1.0
CG A:GLU95 4.2 23.3 1.0
NZ B:LYS79 4.4 26.3 1.0
O A:HOH1379 4.5 41.6 1.0
CG B:LYS79 4.6 22.4 1.0
CD B:LYS79 4.7 24.6 1.0
CB A:GLU95 4.8 20.9 1.0

Zinc binding site 2 out of 6 in 2e18

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Zinc binding site 2 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1304

b:53.1
occ:1.00
 N1 A:IMD1302 1.9 48.6 1.0
N A:MET1 1.9 38.5 1.0
OE2 A:GLU202 1.9 42.8 1.0
CD A:GLU202 2.7 38.2 1.0
C2 A:IMD1302 2.8 48.6 1.0
C5 A:IMD1302 2.9 48.8 1.0
OE1 A:GLU202 3.0 36.9 1.0
CA A:MET1 3.1 39.8 1.0
CB A:MET1 3.4 38.0 1.0
O A:HOH1521 3.9 51.8 1.0
N3 A:IMD1302 3.9 51.2 1.0
C4 A:IMD1302 4.0 50.4 1.0
CG A:GLU202 4.1 38.3 1.0
C A:MET1 4.3 39.5 1.0
O A:MET1 4.5 39.9 1.0
CG A:MET1 4.9 38.7 1.0
CZ3 A:TRP205 5.0 32.7 1.0

Zinc binding site 3 out of 6 in 2e18

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Zinc binding site 3 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1305

b:63.3
occ:1.00
 OE2 A:GLU134 2.2 30.9 1.0
OD2 A:ASP34 2.4 31.5 1.0
O A:HOH1542 2.5 50.8 1.0
CD A:GLU134 2.9 29.8 1.0
OE1 A:GLU134 2.9 31.0 1.0
O A:HOH1545 2.9 61.6 1.0
O A:HOH1543 3.2 49.6 1.0
CG A:ASP34 3.4 28.3 1.0
CB A:ASP34 3.7 24.0 1.0
O A:HOH1345 3.9 37.8 1.0
O A:THR129 3.9 24.5 1.0
O A:HOH1326 3.9 28.7 1.0
ND2 A:ASN131 4.2 21.9 1.0
O A:HOH1544 4.2 63.4 1.0
CG A:GLU134 4.3 27.9 1.0
O A:HOH1546 4.5 58.0 1.0
OD1 A:ASP34 4.5 33.2 1.0
CA A:SER130 4.6 26.2 1.0
O A:HOH1318 4.6 22.2 1.0
C A:THR129 4.7 25.9 1.0
NZ A:LYS158 4.9 32.3 1.0
OG1 A:THR129 5.0 27.8 1.0
N A:ASN131 5.0 23.9 1.0

Zinc binding site 4 out of 6 in 2e18

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Zinc binding site 4 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1306

b:56.0
occ:1.00
 OE2 A:GLU190 2.1 43.1 1.0
O A:HOH1539 2.5 24.2 1.0
O A:HOH1540 2.8 50.4 1.0
CD A:GLU190 2.8 42.9 1.0
OE1 A:GLU190 2.9 43.7 1.0
O A:HOH1538 3.3 51.5 1.0
CB A:SER196 4.0 36.2 1.0
CG A:GLU190 4.3 41.5 1.0
N A:TYR197 4.3 34.8 1.0
CH2 A:TRP162 4.3 33.1 1.0
CA A:SER196 4.5 36.3 1.0
CZ3 A:TRP162 4.8 34.1 1.0
C A:SER196 4.9 35.1 1.0

Zinc binding site 5 out of 6 in 2e18

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Zinc binding site 5 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1307

b:77.1
occ:1.00
 OE2 B:GLU134 2.1 37.0 1.0
O B:HOH1503 2.4 58.2 1.0
OD2 B:ASP34 2.6 35.6 1.0
O B:HOH1505 2.7 56.2 1.0
OE1 B:GLU134 2.7 38.2 1.0
CD B:GLU134 2.7 35.5 1.0
O B:HOH1502 3.1 56.3 1.0
O B:HOH1501 3.2 56.6 1.0
CG B:ASP34 3.6 33.4 1.0
O B:THR129 3.7 24.9 1.0
CB B:ASP34 3.8 29.8 1.0
CG B:GLU134 4.2 33.5 1.0
O B:HOH1416 4.2 44.7 1.0
ND2 B:ASN131 4.3 28.4 1.0
O B:HOH1394 4.3 47.7 1.0
O B:HOH1466 4.4 52.2 1.0
CA B:SER130 4.4 27.9 1.0
C B:THR129 4.6 24.8 1.0
OD1 B:ASP34 4.7 37.1 1.0
NZ B:LYS158 4.8 37.8 1.0
O B:HOH1327 4.8 25.0 1.0
N B:SER130 4.9 25.3 1.0
N B:ASN131 4.9 28.3 1.0
OG1 B:THR129 4.9 24.7 1.0
O B:HOH1504 5.0 58.9 1.0

Zinc binding site 6 out of 6 in 2e18

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Zinc binding site 6 out of 6 in the Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3


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 Project PH0182 From Pyrococcus Horikoshii OT3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1308

b:63.0
occ:1.00
 OE2 B:GLU190 1.7 58.2 1.0
O B:HOH1499 2.5 30.6 1.0
CD B:GLU190 2.7 57.0 1.0
O B:HOH1500 2.8 55.1 1.0
OE1 B:GLU190 3.0 58.4 1.0
O B:HOH1498 3.1 58.1 1.0
CH2 B:TRP162 4.0 39.7 1.0
CG B:GLU190 4.0 56.5 1.0
CB B:SER196 4.2 49.3 1.0
N B:TYR197 4.4 45.5 1.0
CZ3 B:TRP162 4.6 38.9 1.0
CA B:SER196 4.7 49.4 1.0
OD1 B:ASN198 4.8 52.6 1.0
CZ2 B:TRP162 4.8 39.0 1.0

Reference:

K.Shimizu, N.Kunishima. Crystal Structure of Project PH0182 From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Wed Oct 16 22:55:39 2024

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