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Zinc in PDB 1ei6: Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate

Enzymatic activity of Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate

All present enzymatic activity of Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate:
3.11.1.2;

Protein crystallography data

The structure of Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate, PDB code: 1ei6 was solved by H.M.Holden, M.M.Benning, D.Dunaway-Mariano, A.D.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.500, 129.540, 133.380, 90.00, 96.90, 90.00
R / Rfree (%) n/a / n/a

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate (pdb code 1ei6). 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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate, PDB code: 1ei6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1ei6

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Zinc binding site 1 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn408

b:24.5
occ:1.00
 OG1 A:THR64 1.6 15.8 1.0
OD1 A:ASP25 1.8 19.1 1.0
NE2 A:HIS242 1.8 13.6 1.0
OD1 A:ASP241 2.0 28.0 1.0
CG A:ASP25 2.6 14.0 1.0
CD2 A:HIS242 2.6 7.5 1.0
O4 A:PPF410 2.7 43.6 1.0
CG A:ASP241 2.9 34.0 1.0
CB A:THR64 2.9 24.0 1.0
CE1 A:HIS242 2.9 8.6 1.0
OD2 A:ASP25 3.0 30.2 1.0
OD2 A:ASP241 3.3 11.8 1.0
CA A:THR64 3.5 9.2 1.0
OD2 A:ASP202 3.6 5.5 1.0
CG2 A:THR64 3.7 4.6 1.0
C1 A:PPF410 3.7 0.0 1.0
CG A:HIS242 3.8 13.6 1.0
O2 A:PPF410 3.9 52.4 1.0
CB A:ASP25 3.9 18.4 1.0
ND1 A:HIS242 3.9 13.1 1.0
N A:THR64 4.0 17.9 1.0
N A:GLY26 4.1 9.5 1.0
CB A:ASP241 4.1 14.3 1.0
CG A:ASP202 4.2 33.1 1.0
CA A:ASP25 4.2 9.3 1.0
P1 A:PPF410 4.4 47.6 1.0
C A:ASP25 4.5 22.9 1.0
CE1 A:HIS368 4.5 12.5 1.0
O A:HOH470 4.6 35.2 1.0
ZN A:ZN409 4.6 23.8 1.0
O A:HOH436 4.6 21.6 1.0
CB A:ASP202 4.6 17.4 1.0
NE2 A:HIS368 4.7 6.1 1.0
O5 A:PPF410 4.7 36.0 1.0
C A:THR64 4.8 3.1 1.0
C A:PHE63 4.8 27.0 1.0
OD1 A:ASP202 4.8 13.9 1.0
CA A:GLY26 4.9 4.3 1.0
O3 A:PPF410 4.9 49.9 1.0

Zinc binding site 2 out of 8 in 1ei6

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Zinc binding site 2 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn409

b:23.8
occ:1.00
 O3 A:PPF410 1.8 49.9 1.0
OD2 A:ASP202 1.9 5.5 1.0
NE2 A:HIS368 2.2 6.1 1.0
NE2 A:HIS206 2.2 19.5 1.0
CG A:ASP202 2.8 33.1 1.0
CD2 A:HIS206 2.9 9.6 1.0
P1 A:PPF410 3.0 47.6 1.0
OD1 A:ASP202 3.1 13.9 1.0
CE1 A:HIS368 3.1 12.5 1.0
CD2 A:HIS368 3.2 4.6 1.0
O4 A:PPF410 3.4 43.6 1.0
CE1 A:HIS206 3.4 48.8 1.0
O2 A:PPF410 3.5 52.4 1.0
C1 A:PPF410 3.5 0.0 1.0
CB A:ASP202 4.1 17.4 1.0
CG A:HIS206 4.1 17.1 1.0
CE1 A:HIS242 4.2 8.6 1.0
O1 A:PPF410 4.3 0.0 1.0
NE2 A:HIS242 4.3 13.6 1.0
ND1 A:HIS368 4.3 18.0 1.0
CG A:HIS368 4.3 16.1 1.0
ND1 A:HIS206 4.3 13.8 1.0
CE A:MET244 4.5 6.2 1.0
ZN A:ZN408 4.6 24.5 1.0
O5 A:PPF410 4.6 36.0 1.0
OD1 A:ASP25 4.7 19.1 1.0
OG1 A:THR64 4.9 15.8 1.0

Zinc binding site 3 out of 8 in 1ei6

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Zinc binding site 3 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn408

b:16.7
occ:1.00
 OG1 B:THR64 1.7 21.6 1.0
OD1 B:ASP241 1.9 5.7 1.0
NE2 B:HIS242 2.0 12.7 1.0
OD1 B:ASP25 2.2 6.7 1.0
CG B:ASP25 2.8 7.1 1.0
CG B:ASP241 2.9 23.2 1.0
CB B:THR64 2.9 17.6 1.0
CD2 B:HIS242 2.9 30.4 1.0
CE1 B:HIS242 2.9 4.9 1.0
OD2 B:ASP25 3.1 24.7 1.0
CA B:THR64 3.3 14.5 1.0
OD2 B:ASP241 3.4 12.7 1.0
O3 B:TLA411 3.5 22.5 1.0
CG2 B:THR64 3.6 4.0 1.0
N B:THR64 3.8 15.7 1.0
OD2 B:ASP202 3.9 27.8 1.0
CB B:ASP25 4.0 11.4 1.0
CG B:HIS242 4.0 9.2 1.0
ND1 B:HIS242 4.0 19.4 1.0
CB B:ASP241 4.1 8.5 1.0
O B:HOH563 4.2 21.8 1.0
CG B:ASP202 4.3 9.2 1.0
CE1 B:HIS368 4.4 18.7 1.0
N B:GLY26 4.4 11.2 1.0
CA B:ASP25 4.5 22.2 1.0
ZN B:ZN409 4.5 20.1 1.0
NE2 B:HIS368 4.5 11.2 1.0
C B:PHE63 4.6 6.9 1.0
O11 B:TLA411 4.6 29.5 1.0
C B:THR64 4.7 13.2 1.0
C3 B:TLA411 4.7 15.8 1.0
OD1 B:ASP202 4.7 19.1 1.0
C B:ASP25 4.8 17.2 1.0
CB B:ASP202 4.8 17.0 1.0
O B:HOH657 4.9 19.9 1.0

Zinc binding site 4 out of 8 in 1ei6

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Zinc binding site 4 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn409

b:20.1
occ:1.00
 O41 B:TLA411 2.0 16.6 1.0
OD2 B:ASP202 2.1 27.8 1.0
NE2 B:HIS206 2.2 25.3 1.0
NE2 B:HIS368 2.2 11.2 1.0
O3 B:TLA411 2.3 22.5 1.0
CD2 B:HIS368 3.0 28.6 1.0
CD2 B:HIS206 3.0 10.3 1.0
C4 B:TLA411 3.0 25.2 1.0
CG B:ASP202 3.1 9.2 1.0
C3 B:TLA411 3.2 15.8 1.0
CE1 B:HIS206 3.3 19.4 1.0
OD1 B:ASP202 3.3 19.1 1.0
CE1 B:HIS368 3.4 18.7 1.0
O2 B:TLA411 3.4 31.9 1.0
C2 B:TLA411 3.6 36.8 1.0
O4 B:TLA411 4.1 24.3 1.0
CG B:HIS206 4.2 15.8 1.0
CE1 B:HIS242 4.2 4.9 1.0
CG B:HIS368 4.2 7.4 1.0
ND1 B:HIS285 4.3 21.5 1.0
ND1 B:HIS206 4.3 21.4 1.0
CD2 B:HIS286 4.3 23.4 1.0
OG1 B:THR64 4.4 21.6 1.0
ND1 B:HIS368 4.4 29.2 1.0
CB B:ASP202 4.4 17.0 1.0
NE2 B:HIS242 4.5 12.7 1.0
ZN B:ZN408 4.5 16.7 1.0
CE B:MET244 4.5 1.2 1.0
O11 B:TLA411 4.5 29.5 1.0
O B:HOH563 4.6 21.8 1.0
C1 B:TLA411 4.6 18.8 1.0
OD1 B:ASP25 4.7 6.7 1.0
NE2 B:HIS286 4.9 19.5 1.0
CB B:HIS285 5.0 18.4 1.0

Zinc binding site 5 out of 8 in 1ei6

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Zinc binding site 5 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn408

b:18.7
occ:1.00
 OG1 C:THR64 1.6 7.8 1.0
OD1 C:ASP241 1.7 8.1 1.0
OD1 C:ASP25 2.1 39.1 1.0
NE2 C:HIS242 2.3 2.8 1.0
CG C:ASP25 2.6 1.5 1.0
CG C:ASP241 2.6 16.0 1.0
OD2 C:ASP25 2.8 12.2 1.0
CB C:THR64 3.0 33.1 1.0
O3 C:PPF413 3.0 0.0 1.0
OD2 C:ASP241 3.0 9.1 1.0
CE1 C:HIS242 3.1 1.0 1.0
CD2 C:HIS242 3.2 32.5 1.0
CA C:THR64 3.6 1.0 1.0
CG2 C:THR64 3.7 10.0 1.0
OD2 C:ASP202 3.7 13.1 1.0
O5 C:PPF413 3.8 0.0 1.0
CB C:ASP25 3.9 10.8 1.0
CB C:ASP241 4.0 10.7 1.0
N C:THR64 4.1 30.4 1.0
N C:GLY26 4.1 6.2 1.0
CG C:ASP202 4.1 11.6 1.0
P1 C:PPF413 4.1 66.3 1.0
ND1 C:HIS242 4.2 33.8 1.0
O C:HOH696 4.2 33.0 1.0
CA C:ASP25 4.3 11.1 1.0
CG C:HIS242 4.3 11.2 1.0
C1 C:PPF413 4.4 47.4 1.0
CB C:ASP202 4.4 2.9 1.0
C C:ASP25 4.4 30.6 1.0
O C:HOH845 4.6 27.9 1.0
NE2 C:HIS368 4.6 3.6 1.0
OD1 C:ASP202 4.6 20.9 1.0
ZN C:ZN409 4.6 22.1 1.0
CE1 C:HIS368 4.7 23.8 1.0
O1 C:PPF413 4.7 51.4 1.0
C C:PHE63 4.8 1.2 1.0
C C:THR64 4.8 9.0 1.0
CA C:GLY26 4.9 1.0 1.0

Zinc binding site 6 out of 8 in 1ei6

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Zinc binding site 6 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn409

b:22.1
occ:1.00
 O1 C:PPF413 1.7 51.4 1.0
OD2 C:ASP202 1.7 13.1 1.0
NE2 C:HIS206 2.0 7.4 1.0
NE2 C:HIS368 2.3 3.6 1.0
CG C:ASP202 2.6 11.6 1.0
OD1 C:ASP202 2.9 20.9 1.0
CD2 C:HIS206 2.9 45.1 1.0
CD2 C:HIS368 2.9 5.9 1.0
P1 C:PPF413 2.9 66.3 1.0
CE1 C:HIS206 3.0 11.4 1.0
O3 C:PPF413 3.1 0.0 1.0
CE1 C:HIS368 3.5 23.8 1.0
CB C:ASP202 3.9 2.9 1.0
O2 C:PPF413 3.9 77.8 1.0
CG C:HIS206 4.1 19.1 1.0
C1 C:PPF413 4.1 47.4 1.0
ND1 C:HIS206 4.1 7.5 1.0
CG C:HIS368 4.2 22.5 1.0
O5 C:PPF413 4.3 0.0 1.0
ND1 C:HIS368 4.4 15.4 1.0
CE1 C:HIS242 4.5 1.0 1.0
CE C:MET244 4.6 11.8 1.0
ZN C:ZN408 4.6 18.7 1.0
OG1 C:THR64 4.7 7.8 1.0
NE2 C:HIS242 4.7 2.8 1.0
OD1 C:ASP25 4.8 39.1 1.0

Zinc binding site 7 out of 8 in 1ei6

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Zinc binding site 7 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn408

b:20.9
occ:1.00
 OG1 D:THR64 1.8 32.7 1.0
NE2 D:HIS242 1.9 14.6 1.0
OD1 D:ASP241 2.0 7.9 1.0
OD1 D:ASP25 2.1 13.0 1.0
CG D:ASP25 2.7 9.1 1.0
CE1 D:HIS242 2.8 6.1 1.0
OD2 D:ASP25 2.8 11.2 1.0
CD2 D:HIS242 2.9 16.5 1.0
CB D:THR64 2.9 3.2 1.0
CG D:ASP241 2.9 9.2 1.0
CG2 D:THR64 3.3 19.2 1.0
OD2 D:ASP241 3.4 12.9 1.0
CA D:THR64 3.4 13.2 1.0
N D:THR64 3.8 9.3 1.0
O2 D:PPF412 3.9 0.0 1.0
OD2 D:ASP202 3.9 28.3 1.0
ND1 D:HIS242 4.0 13.0 1.0
CG D:HIS242 4.0 1.0 1.0
O D:HOH879 4.1 30.2 1.0
O3 D:PPF412 4.1 23.0 1.0
CB D:ASP25 4.2 14.7 1.0
CG D:ASP202 4.2 8.0 1.0
CB D:ASP241 4.2 4.8 1.0
N D:GLY26 4.3 18.0 1.0
CE1 D:HIS368 4.5 15.7 1.0
OD1 D:ASP202 4.5 6.5 1.0
CA D:ASP25 4.5 26.3 1.0
P1 D:PPF412 4.5 48.3 1.0
O4 D:PPF412 4.6 24.6 1.0
ZN D:ZN409 4.6 21.7 1.0
NE2 D:HIS368 4.6 15.0 1.0
O D:HOH860 4.6 21.7 1.0
C D:PHE63 4.7 20.1 1.0
C D:ASP25 4.8 13.4 1.0
CB D:ASP202 4.8 18.9 1.0
C D:THR64 4.8 10.3 1.0
C1 D:PPF412 5.0 0.0 1.0

Zinc binding site 8 out of 8 in 1ei6

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Zinc binding site 8 out of 8 in the Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate


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 Phosphonoacetate Hydrolase Complexed with Phosphonoformate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn409

b:21.7
occ:1.00
 O3 D:PPF412 1.4 23.0 1.0
NE2 D:HIS206 2.0 20.0 1.0
OD2 D:ASP202 2.0 28.3 1.0
NE2 D:HIS368 2.2 15.0 1.0
P1 D:PPF412 2.8 48.3 1.0
CD2 D:HIS206 2.9 3.1 1.0
CG D:ASP202 2.9 8.0 1.0
CD2 D:HIS368 3.0 22.0 1.0
CE1 D:HIS206 3.1 12.7 1.0
OD1 D:ASP202 3.2 6.5 1.0
CE1 D:HIS368 3.2 15.7 1.0
O1 D:PPF412 3.5 32.8 1.0
C1 D:PPF412 3.6 0.0 1.0
O2 D:PPF412 3.8 0.0 1.0
CE1 D:HIS242 4.1 6.1 1.0
O5 D:PPF412 4.1 41.1 1.0
CG D:HIS206 4.1 3.8 1.0
ND1 D:HIS206 4.1 18.0 1.0
CG D:HIS368 4.2 6.3 1.0
CD2 D:HIS286 4.2 18.7 1.0
CB D:ASP202 4.2 18.9 1.0
CE D:MET244 4.3 9.2 1.0
ND1 D:HIS368 4.3 33.0 1.0
O4 D:PPF412 4.4 24.6 1.0
ND1 D:HIS285 4.4 43.2 1.0
NE2 D:HIS242 4.5 14.6 1.0
ZN D:ZN408 4.6 20.9 1.0
OG1 D:THR64 4.6 32.7 1.0
NE2 D:HIS286 4.7 35.6 1.0
CB D:HIS285 4.8 22.1 1.0
OD1 D:ASP25 4.9 13.0 1.0
O D:HOH879 5.0 30.2 1.0

Reference:

H.M.Holden, M.M.Benning, D.Dunaway-Mariano, A.D.Kim. Crystal Structure of Phosphonoacetate Hydrolase Complexed with Phosphonoformate To Be Published.
Page generated: Wed Dec 16 02:48:23 2020

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