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Chlorine in PDB 4jdp: Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound

Protein crystallography data

The structure of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound, PDB code: 4jdp was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, N.Al Obaidi, M.Stead, J.Love, K.N.Allen, D.Dunaway-Mariano, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.77 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.559, 64.733, 135.062, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 20.6

Other elements in 4jdp:

The structure of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound (pdb code 4jdp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound, PDB code: 4jdp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4jdp

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Chlorine binding site 1 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl302

b:31.1
occ:1.00
 OG A:SER44 3.0 23.6 1.0
O A:HOH429 3.0 37.4 1.0
O A:HOH503 3.1 37.4 1.0
O A:HOH412 3.1 25.9 1.0
ND2 A:ASN46 3.6 29.7 1.0
CB A:SER44 3.8 23.0 1.0
CB A:ASN46 3.9 26.5 1.0
CD1 A:LEU54 4.0 30.0 1.0
CD2 A:LEU54 4.2 28.8 1.0
CG A:ASN46 4.3 29.7 1.0
CB A:ILE12 4.3 22.8 1.0
CB A:ASP13 4.5 28.4 1.0
CD1 A:ILE12 4.6 24.6 1.0
CG2 A:ILE12 4.6 24.6 1.0
N A:ASP13 4.7 23.3 1.0
O A:HOH480 4.8 37.7 1.0
NH1 A:ARG57 4.8 30.0 1.0
CG A:LEU54 4.8 26.6 1.0
O A:HOH404 4.8 25.6 1.0
CG1 A:ILE12 4.9 23.2 1.0
CA A:ASN46 4.9 25.6 1.0
N A:ASN46 5.0 23.0 1.0

Chlorine binding site 2 out of 8 in 4jdp

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Chlorine binding site 2 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl303

b:46.2
occ:1.00
 ND2 A:ASN46 3.2 29.7 1.0
O A:HOH588 3.2 51.3 1.0
NH1 A:ARG57 3.4 30.0 1.0
NE A:ARG49 3.4 44.6 0.5
NH2 A:ARG57 3.7 33.4 1.0
NH1 A:ARG49 3.7 47.9 0.5
CG A:ARG49 3.8 34.9 0.5
CG A:ARG49 3.8 31.4 0.5
CZ A:ARG49 3.9 48.1 0.5
CZ A:ARG57 4.0 30.1 1.0
CD A:ARG49 4.2 40.4 0.5
NE A:ARG49 4.3 39.6 0.5
CG A:ASN46 4.3 29.7 1.0
OD1 A:ASN46 4.5 26.5 1.0
CD A:ARG49 4.6 35.2 0.5
O A:HOH503 4.9 37.4 1.0
OG1 A:THR48 5.0 30.1 1.0
CB A:ARG49 5.0 29.2 0.5
NH2 A:ARG49 5.0 48.5 0.5

Chlorine binding site 3 out of 8 in 4jdp

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Chlorine binding site 3 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl304

b:33.3
occ:1.00
 O A:HOH491 3.0 44.2 1.0
ND2 A:ASN148 3.1 23.1 1.0
N A:THR163 3.3 21.3 1.0
O A:HOH450 3.4 37.7 1.0
CA A:GLY162 3.5 23.6 1.0
OG1 A:THR163 3.6 24.8 1.0
C A:GLY162 3.9 23.4 1.0
CB A:ASP150 4.0 23.9 1.0
CG A:ASN148 4.1 22.7 1.0
CB A:THR163 4.2 22.0 1.0
CA A:THR163 4.3 21.3 1.0
OD1 A:ASN148 4.3 23.4 1.0
O A:ASP150 4.4 24.6 1.0
OD1 A:ASP150 4.6 25.4 1.0
CG A:ASP150 4.6 24.1 1.0
CB A:SER122 4.6 22.0 0.5
CB A:SER122 4.6 21.5 0.5
CD1 A:PHE153 4.7 54.0 1.0
OG A:SER122 4.7 22.5 0.5
CB A:PHE153 4.7 46.9 1.0
O A:HOH577 4.8 47.9 1.0
OG A:SER122 4.8 24.5 0.5
N A:GLY162 4.9 21.8 1.0
OG A:SER47 4.9 32.1 1.0
CA A:ASP150 5.0 24.7 1.0

Chlorine binding site 4 out of 8 in 4jdp

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Chlorine binding site 4 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl305

b:50.7
occ:1.00
 O A:HOH568 2.9 43.0 1.0
N A:GLU64 2.9 28.5 1.0
O A:HOH593 3.2 45.3 1.0
CD A:LYS34 3.6 42.5 1.0
CA A:LEU63 3.6 27.6 1.0
O A:GLU64 3.7 29.2 1.0
C A:LEU63 3.8 27.1 1.0
CB A:GLU64 3.8 36.9 1.0
CA A:GLU64 3.8 30.1 1.0
CD2 A:LEU63 4.0 29.3 1.0
CB A:LEU63 4.0 27.0 1.0
CG A:LYS31 4.0 36.0 1.0
C A:GLU64 4.2 30.2 1.0
CE A:LYS34 4.3 43.7 1.0
CA A:LYS31 4.5 28.5 1.0
O A:GLY62 4.6 28.7 1.0
CG A:LEU63 4.7 28.4 1.0
CB A:LYS34 4.7 33.8 1.0
CG A:LYS34 4.7 40.5 1.0
CB A:LYS31 4.8 32.1 1.0
N A:LEU63 4.9 26.2 1.0
CD A:LYS31 4.9 39.6 1.0
O A:LEU63 5.0 30.2 1.0

Chlorine binding site 5 out of 8 in 4jdp

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Chlorine binding site 5 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl302

b:30.0
occ:1.00
 OG B:SER44 3.0 22.9 1.0
O B:HOH423 3.1 35.4 1.0
O B:HOH491 3.1 31.6 1.0
O B:HOH411 3.2 24.7 1.0
ND2 B:ASN46 3.6 33.4 1.0
CB B:SER44 3.8 23.4 1.0
CB B:ASN46 3.8 28.4 1.0
CD1 B:LEU54 4.0 36.2 1.0
CB B:ILE12 4.2 24.7 1.0
CG B:ASN46 4.2 33.6 1.0
CD2 B:LEU54 4.4 36.7 1.0
CD1 B:ILE12 4.4 25.7 1.0
CG2 B:ILE12 4.5 26.5 1.0
CB B:ASP13 4.6 27.5 1.0
N B:ASP13 4.7 22.8 1.0
NH1 B:ARG57 4.7 34.5 1.0
O B:HOH468 4.7 35.0 1.0
O B:HOH406 4.8 26.7 1.0
CG1 B:ILE12 4.8 24.2 1.0
CG B:LEU54 4.8 34.0 1.0
N B:ASN46 4.9 25.1 1.0
CA B:ASN46 4.9 25.7 1.0
CA B:SER44 5.0 22.6 1.0

Chlorine binding site 6 out of 8 in 4jdp

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Chlorine binding site 6 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl303

b:46.4
occ:1.00
 O B:HOH530 3.1 52.0 1.0
ND2 B:ASN46 3.2 33.4 1.0
NH1 B:ARG57 3.3 34.5 1.0
NH2 B:ARG57 3.4 38.2 1.0
O B:HOH551 3.5 62.0 1.0
NE B:ARG49 3.6 45.6 0.5
CZ B:ARG49 3.6 45.3 0.5
CG B:ARG49 3.7 36.2 0.5
CG B:ARG49 3.7 36.0 0.5
NH1 B:ARG49 3.8 47.2 0.5
CZ B:ARG57 3.8 36.7 1.0
NE B:ARG49 3.8 42.8 0.5
NH2 B:ARG49 4.0 44.9 0.5
CD B:ARG49 4.2 40.8 0.5
CG B:ASN46 4.3 33.6 1.0
CZ B:ARG49 4.3 48.4 0.5
CD B:ARG49 4.4 39.6 0.5
NH2 B:ARG49 4.4 50.7 0.5
OD1 B:ASN46 4.5 31.9 1.0
O B:HOH501 4.6 59.7 1.0
O B:HOH491 4.8 31.6 1.0
OG1 B:THR48 4.8 28.1 1.0

Chlorine binding site 7 out of 8 in 4jdp

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Chlorine binding site 7 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl304

b:26.5
occ:1.00
 O B:HOH447 3.2 33.0 1.0
O B:HOH427 3.2 28.4 1.0
ND2 B:ASN148 3.2 22.8 1.0
N B:THR163 3.4 21.6 1.0
CA B:GLY162 3.5 21.2 1.0
OG1 B:THR163 3.7 21.2 1.0
O B:HOH492 3.7 38.1 1.0
C B:GLY162 3.9 20.5 1.0
CB B:ASP150 4.1 22.1 1.0
CD2 B:PHE153 4.2 35.4 1.0
CB B:PHE153 4.3 28.6 1.0
CG B:ASN148 4.3 20.5 1.0
CB B:THR163 4.4 22.1 1.0
CA B:THR163 4.5 21.3 1.0
O B:ASP150 4.5 23.7 1.0
OD1 B:ASN148 4.6 22.0 1.0
CB B:SER122 4.6 24.2 1.0
CG B:ASP150 4.7 21.1 1.0
CG B:PHE153 4.7 33.2 1.0
OD1 B:ASP150 4.7 21.5 1.0
N B:GLY162 4.7 20.8 1.0
OG B:SER122 4.8 29.1 1.0
OG B:SER47 5.0 25.9 1.0
O B:PRO161 5.0 24.8 1.0

Chlorine binding site 8 out of 8 in 4jdp

Go back to Chlorine Binding Sites List in 4jdp
Chlorine binding site 8 out of 8 in the Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of Probable P-Nitrophenyl Phosphatase (PHO2) (Target Efi-501307) From Archaeoglobus Fulgidus Dsm 4304 with Magnesium Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl305

b:50.5
occ:1.00
 O B:HOH586 2.8 43.0 1.0
O B:HOH591 2.9 46.5 1.0
N B:SER50 3.1 28.9 1.0
CG1 B:ILE53 3.4 36.3 1.0
CA B:GLY97 3.4 29.8 1.0
OG B:SER50 3.5 29.9 1.0
CA B:ARG49 3.7 31.7 0.5
CA B:ARG49 3.7 31.6 0.5
CB B:SER50 3.7 29.8 1.0
C B:ARG49 3.9 30.1 1.0
O B:THR48 3.9 32.5 1.0
CB B:ILE53 4.0 31.7 1.0
CD B:ARG49 4.0 39.6 0.5
O B:HOH558 4.0 41.7 1.0
CA B:SER50 4.0 29.1 1.0
N B:GLY97 4.1 27.7 1.0
CD B:ARG49 4.2 40.8 0.5
O B:HOH417 4.2 32.5 1.0
OE2 B:GLU100 4.3 42.8 1.0
CB B:ARG49 4.4 34.3 0.5
CB B:ARG49 4.4 34.1 0.5
CG2 B:ILE53 4.5 32.2 1.0
CD1 B:ILE53 4.6 37.1 1.0
N B:ARG49 4.7 29.4 1.0
NH2 B:ARG52 4.7 43.3 1.0
C B:GLY97 4.7 25.4 1.0
C B:THR48 4.7 31.9 1.0
CG B:ARG49 4.9 36.0 0.5
O B:GLY97 5.0 27.2 1.0
CG B:ARG49 5.0 36.2 0.5

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, N.F.Al Obaidi, M.Stead, J.Love, K.N.Allen, D.Dunaway-Mariano, J.A.Gerlt, S.C.Almo. Crystal Structure of Probable P-Nitrophenyl Phosphatase From Archaeoglobus Fulgidus. To Be Published.
Page generated: Sun Jul 21 17:22:44 2024

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