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Chlorine in PDB 4gir: Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)

Protein crystallography data

The structure of Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212), PDB code: 4gir was solved by M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.23 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.836, 146.836, 169.524, 90.00, 90.00, 90.00
R / Rfree (%) 14.8 / 19.3

Other elements in 4gir:

The structure of Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) (pdb code 4gir). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212), PDB code: 4gir:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 4gir

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Chlorine binding site 1 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:52.9
occ:1.00
 O A:HOH696 3.3 32.7 1.0
CG A:ASP393 3.4 16.5 1.0
N A:ASP393 3.4 11.5 1.0
OD1 A:ASP393 3.5 17.0 1.0
OD2 A:ASP393 3.6 14.3 1.0
CB A:LEU391 3.7 9.8 1.0
CD A:PRO392 3.8 14.9 1.0
CB A:ASP393 3.8 11.1 1.0
N A:PRO392 3.8 13.9 1.0
CB A:PRO392 4.1 12.9 1.0
CA A:ASP393 4.2 14.7 1.0
CG A:PRO392 4.3 14.8 1.0
C A:LEU391 4.3 11.6 1.0
CA A:PRO392 4.3 12.4 1.0
C A:PRO392 4.3 13.6 1.0
O A:HOH703 4.6 23.1 1.0
CA A:LEU391 4.6 10.1 1.0
CD1 A:LEU391 4.7 12.2 1.0
CG A:LEU391 4.8 11.8 1.0

Chlorine binding site 2 out of 9 in 4gir

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Chlorine binding site 2 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:45.6
occ:1.00
 N A:HIS384 3.3 27.5 1.0
O A:HOH701 3.5 33.8 1.0
CA A:HIS384 3.6 20.1 1.0
N A:GLU385 3.8 13.5 1.0
CG A:PRO383 3.8 22.9 1.0
CD A:PRO383 3.9 19.5 1.0
C A:HIS384 4.2 15.9 1.0
NH2 A:ARG382 4.3 31.6 1.0
N A:PRO383 4.4 21.0 1.0
C A:PRO383 4.5 28.4 1.0
NE A:ARG382 4.7 28.5 1.0
CB A:PRO383 4.8 22.4 1.0
CA A:PRO383 4.8 21.7 1.0
CB A:ARG382 4.9 15.9 1.0
CB A:GLU385 4.9 21.8 1.0
CZ A:ARG382 4.9 28.5 1.0
CB A:HIS384 4.9 12.9 1.0
CA A:GLU385 4.9 15.1 1.0
CG A:GLU385 4.9 32.1 1.0

Chlorine binding site 3 out of 9 in 4gir

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Chlorine binding site 3 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:39.6
occ:1.00
 N B:HIS384 3.4 22.3 1.0
CA B:HIS384 3.7 15.3 1.0
CD B:PRO383 3.8 25.6 1.0
CL B:CL407 3.8 52.3 1.0
CG B:PRO383 3.8 22.3 1.0
NH2 B:ARG382 3.9 38.9 1.0
N B:GLU385 4.0 13.2 1.0
N B:PRO383 4.2 22.4 1.0
NE B:ARG382 4.3 29.7 1.0
C B:HIS384 4.4 17.0 1.0
C B:PRO383 4.5 24.7 1.0
CZ B:ARG382 4.6 33.2 1.0
CB B:ARG382 4.7 13.7 1.0
CA B:PRO383 4.8 24.6 1.0
CB B:PRO383 4.8 24.1 1.0
C B:ARG382 4.9 19.7 1.0
CG B:GLU385 5.0 34.7 1.0

Chlorine binding site 4 out of 9 in 4gir

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Chlorine binding site 4 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:57.1
occ:1.00
 CG B:ASP393 3.4 19.0 1.0
N B:ASP393 3.4 12.6 1.0
CD B:PRO392 3.5 13.8 1.0
OD1 B:ASP393 3.6 17.5 1.0
OD2 B:ASP393 3.7 19.0 1.0
N B:PRO392 3.7 12.1 1.0
CB B:LEU391 3.8 11.4 1.0
CB B:ASP393 3.8 13.6 1.0
OE1 D:GLN122 3.9 25.9 1.0
CD D:GLN122 3.9 20.3 1.0
NE2 D:GLN122 4.0 24.5 1.0
CB B:PRO392 4.1 12.6 1.0
CG B:PRO392 4.2 13.8 1.0
CA B:ASP393 4.3 12.8 1.0
CA B:PRO392 4.3 12.6 1.0
C B:PRO392 4.3 16.0 1.0
C B:LEU391 4.3 12.0 1.0
O B:HOH620 4.6 25.7 1.0
O D:HOH793 4.6 38.0 1.0
O B:HOH508 4.6 12.9 1.0
CD1 B:LEU391 4.6 10.8 1.0
CA B:LEU391 4.7 17.8 1.0
CG D:GLN122 4.8 14.3 1.0
O D:HOH706 4.8 29.9 1.0
O D:HOH734 4.8 27.4 1.0
CG B:LEU391 4.8 13.8 1.0

Chlorine binding site 5 out of 9 in 4gir

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Chlorine binding site 5 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:52.3
occ:1.00
 CD1 B:TRP386 3.3 14.6 1.0
N B:TRP386 3.3 13.8 1.0
N B:GLU385 3.5 13.2 1.0
CL B:CL404 3.8 39.6 1.0
CB B:TRP386 3.9 16.0 1.0
CG B:TRP386 4.0 12.3 1.0
C B:HIS384 4.0 17.0 1.0
CA B:GLU385 4.1 19.4 1.0
C B:GLU385 4.1 15.3 1.0
CA B:TRP386 4.2 17.5 1.0
CB B:GLU385 4.2 25.0 1.0
CA B:HIS384 4.3 15.3 1.0
NE1 B:TRP386 4.5 12.0 1.0
O B:HIS384 4.8 19.4 1.0
O3 B:SO4403 4.9 36.5 1.0

Chlorine binding site 6 out of 9 in 4gir

Go back to Chlorine Binding Sites List in 4gir
Chlorine binding site 6 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:53.4
occ:1.00
 N B:ALA340 3.3 18.6 1.0
CB B:LYS339 3.7 25.9 1.0
CA B:LYS339 3.8 24.3 1.0
CB B:ALA340 3.8 15.3 1.0
O B:HOH748 3.9 19.3 1.0
C B:LYS339 4.0 22.1 1.0
CA B:ALA340 4.2 17.4 1.0
CG B:LYS339 4.2 34.0 1.0
CD B:LYS339 5.0 38.4 1.0

Chlorine binding site 7 out of 9 in 4gir

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Chlorine binding site 7 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:45.5
occ:1.00
 N C:HIS384 3.3 27.7 1.0
CG C:PRO383 3.6 21.2 1.0
CA C:HIS384 3.6 20.4 1.0
O C:HOH557 3.7 20.9 1.0
N C:GLU385 3.7 15.8 1.0
CD C:PRO383 3.9 24.0 1.0
C C:HIS384 4.2 17.5 1.0
C C:PRO383 4.3 27.5 1.0
N C:PRO383 4.3 24.9 1.0
NH2 C:ARG382 4.5 31.3 1.0
CB C:PRO383 4.6 22.6 1.0
CG C:GLU385 4.7 33.0 1.0
CA C:PRO383 4.7 23.7 1.0
OE1 C:GLU385 4.7 53.9 1.0
CB C:GLU385 4.7 23.8 1.0
CA C:GLU385 4.8 17.4 1.0
NE C:ARG382 4.8 31.2 1.0
CB C:HIS384 5.0 17.7 1.0

Chlorine binding site 8 out of 9 in 4gir

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Chlorine binding site 8 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


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 An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:44.2
occ:1.00
 N D:HIS384 3.3 25.4 1.0
CA D:HIS384 3.7 17.1 1.0
CG D:PRO383 3.7 29.3 1.0
CD D:PRO383 3.8 27.7 1.0
O D:HOH838 3.8 27.6 1.0
NH2 D:ARG382 3.9 37.3 1.0
N D:GLU385 4.0 13.6 1.0
N D:PRO383 4.2 27.9 1.0
NE D:ARG382 4.3 31.5 1.0
C D:PRO383 4.4 32.2 1.0
C D:HIS384 4.4 17.6 1.0
CZ D:ARG382 4.5 33.3 1.0
CA D:PRO383 4.7 27.9 1.0
CB D:PRO383 4.7 30.2 1.0
CB D:ARG382 4.8 20.4 1.0
C D:ARG382 4.9 24.1 1.0
CB D:HIS384 5.0 16.6 1.0

Chlorine binding site 9 out of 9 in 4gir

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Chlorine binding site 9 out of 9 in the Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl405

b:51.8
occ:1.00
 N D:ALA340 2.9 20.2 1.0
CA D:LYS339 3.5 20.9 1.0
CB D:LYS339 3.6 25.8 1.0
CB D:ALA340 3.7 17.9 1.0
C D:LYS339 3.7 21.3 1.0
CA D:ALA340 3.9 17.6 1.0
CG D:LYS339 4.0 32.0 1.0
O D:HOH684 4.0 23.0 1.0
CD D:LYS339 4.8 35.7 1.0
N D:LYS339 4.8 21.5 1.0
O D:LYS339 4.9 21.9 1.0

Reference:

M.W.Vetting, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Enolase Family Member From Vibrio Harveyi (Efi-Target 501692) with Homology to Mannonate Dehydratase, with Mg, Ethylene Glycol and Sulfate Bound (Ordered Loops, Space Group P41212) To Be Published.
Page generated: Sun Jul 21 14:41:49 2024

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