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Chlorine in PDB 4mmw: Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate

Protein crystallography data

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate, PDB code: 4mmw was solved by A.A.Fedorov, E.V.Fedorov, A.Sakai, J.A.Gerlt, S.C.Almo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.10 / 1.65
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 118.099, 118.099, 133.278, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.4

Other elements in 4mmw:

The structure of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate (pdb code 4mmw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate, PDB code: 4mmw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 4mmw

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Chlorine binding site 1 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:22.6
occ:1.00
 O A:HOH838 3.2 30.8 1.0
NH2 A:ARG163 3.3 22.0 1.0
N A:MET353 3.3 18.6 1.0
NH2 A:ARG330 3.4 17.7 1.0
CD1 A:LEU349 3.5 29.7 1.0
OD1 A:ASP340 3.6 40.8 1.0
CA A:PRO352 3.7 17.6 1.0
CG A:ASP340 3.7 38.0 1.0
O A:MET353 3.8 21.2 1.0
C A:PRO352 4.0 18.4 1.0
OD2 A:ASP340 4.1 32.9 1.0
CB A:PRO352 4.2 18.1 1.0
CB A:ASP340 4.2 30.5 1.0
CA A:MET353 4.3 16.3 1.0
CZ A:ARG330 4.4 16.6 1.0
C A:MET353 4.5 18.8 1.0
CZ A:ARG163 4.6 24.2 1.0
CB A:MET353 4.7 17.3 1.0
NH1 A:ARG330 4.7 19.3 1.0
O A:HOH822 4.9 29.4 1.0
CA A:ASP340 4.9 23.8 1.0
O A:ASP351 4.9 19.8 1.0
N A:PRO352 4.9 18.0 1.0
CG A:LEU349 5.0 25.0 1.0

Chlorine binding site 2 out of 10 in 4mmw

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Chlorine binding site 2 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:28.4
occ:1.00
 O A:HOH545 3.1 19.1 1.0
O A:HOH627 3.2 27.0 1.0
O A:HOH571 3.2 27.5 1.0
O A:HOH867 3.3 38.3 1.0
N A:LEU132 3.5 16.1 1.0
CA A:VAL131 3.7 14.5 1.0
NH1 A:ARG128 3.7 17.4 1.0
CG2 A:VAL131 3.7 20.1 1.0
C A:VAL131 4.1 16.9 1.0
CB A:VAL131 4.2 19.5 1.0
CG A:LEU132 4.2 23.8 1.0
CE2 A:PHE358 4.2 23.2 1.0
O A:LYS130 4.3 17.6 1.0
CD A:ARG128 4.3 17.5 1.0
CB A:LEU132 4.4 16.8 1.0
O A:HOH730 4.5 24.1 1.0
CA A:LEU132 4.6 15.1 1.0
O A:ARG326 4.6 15.6 1.0
CD1 A:LEU132 4.7 25.8 1.0
CZ A:ARG128 4.7 17.2 1.0
N A:VAL131 4.7 16.3 1.0
CD2 A:PHE358 4.8 21.7 1.0
O A:HOH748 4.8 23.8 1.0
C A:LYS130 4.9 16.1 1.0
NE A:ARG128 5.0 14.9 1.0

Chlorine binding site 3 out of 10 in 4mmw

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Chlorine binding site 3 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:31.1
occ:1.00
 NZ A:LYS347 3.2 35.5 1.0
N A:PHE373 3.2 23.5 1.0
CE A:LYS347 3.5 35.0 1.0
N A:THR374 3.6 22.9 1.0
OG1 A:THR374 3.6 33.7 1.0
CB A:PHE373 3.8 23.6 1.0
CA A:PHE373 3.9 23.9 1.0
O A:ILE371 4.0 20.8 1.0
C A:ASP372 4.0 26.7 1.0
OD1 A:ASP372 4.1 28.9 1.0
CD1 A:PHE373 4.1 27.6 1.0
CA A:ASP372 4.2 20.2 1.0
C A:PHE373 4.2 24.9 1.0
CB A:THR374 4.3 28.1 1.0
CG A:PHE373 4.4 27.4 1.0
O A:HOH790 4.5 45.1 1.0
CA A:THR374 4.5 25.4 1.0
CG A:ASP372 4.9 28.2 1.0
C A:ILE371 5.0 21.7 1.0

Chlorine binding site 4 out of 10 in 4mmw

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Chlorine binding site 4 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:31.0
occ:1.00
 N A:MET1 3.3 20.6 1.0
CA A:MET1 3.4 22.5 1.0
CG A:ASP74 3.4 22.6 1.0
C A:MET1 3.4 22.6 1.0
OD2 A:ASP74 3.7 21.2 1.0
CB A:ASP74 3.7 22.5 1.0
OD1 A:ASP74 3.7 17.7 1.0
N A:ILE2 3.7 22.4 1.0
CD1 A:ILE2 3.8 32.4 1.0
O A:MET1 3.9 21.1 1.0
CA A:ASP74 3.9 18.3 1.0
O A:HOH650 4.0 30.0 1.0
CG1 A:ILE2 4.2 20.4 1.0
NH1 A:ARG76 4.4 18.7 1.0
CA A:ILE2 4.5 22.2 1.0
OE2 A:GLU43 4.8 34.9 1.0
N A:ASP74 4.8 18.2 1.0
CB A:MET1 4.9 28.4 1.0

Chlorine binding site 5 out of 10 in 4mmw

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Chlorine binding site 5 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:41.1
occ:1.00
 N A:MET1 3.2 20.6 1.0
CG A:MET1 3.4 37.3 1.0
NE A:ARG76 3.5 20.7 1.0
CZ A:ARG76 3.5 24.5 1.0
O A:HOH808 3.5 36.1 1.0
NH2 A:ARG76 3.6 22.1 1.0
CD A:ARG76 3.6 17.7 1.0
CE1 A:HIS75 3.9 22.0 1.0
CA A:MET1 4.0 22.5 1.0
NH1 A:ARG76 4.2 18.7 1.0
CB A:MET1 4.2 28.4 1.0
CG A:ARG76 4.5 17.9 1.0
ND1 A:HIS75 4.5 19.8 1.0
SD A:MET1 4.7 62.7 1.0
NE2 A:HIS75 4.9 18.2 1.0
OD1 A:ASP74 4.9 17.7 1.0

Chlorine binding site 6 out of 10 in 4mmw

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Chlorine binding site 6 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:21.7
occ:1.00
 N B:MET353 3.3 17.9 1.0
NH2 B:ARG163 3.3 20.1 1.0
O B:HOH838 3.3 37.5 1.0
NH2 B:ARG330 3.4 18.8 1.0
CD1 B:LEU349 3.5 32.3 1.0
CA B:PRO352 3.7 19.0 1.0
CG B:ASP340 3.8 37.1 1.0
O B:MET353 3.8 21.3 1.0
OD1 B:ASP340 3.9 35.9 1.0
C B:PRO352 4.0 18.7 1.0
OD2 B:ASP340 4.0 34.1 1.0
CB B:ASP340 4.1 29.9 1.0
CB B:PRO352 4.2 18.1 1.0
CA B:MET353 4.3 19.1 1.0
CZ B:ARG330 4.4 17.4 1.0
C B:MET353 4.5 19.2 1.0
CZ B:ARG163 4.6 22.0 1.0
CB B:MET353 4.7 16.2 1.0
NH1 B:ARG330 4.7 18.4 1.0
CA B:ASP340 4.9 24.7 1.0
O B:ASP351 5.0 19.5 1.0
N B:PRO352 5.0 19.6 1.0
CG B:LEU349 5.0 27.1 1.0
O B:HOH816 5.0 31.3 1.0

Chlorine binding site 7 out of 10 in 4mmw

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Chlorine binding site 7 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:24.5
occ:1.00
 O A:HOH676 2.8 36.8 1.0
O B:HOH841 3.0 29.9 1.0
N B:HIS60 3.3 18.4 1.0
CD B:PRO59 3.6 17.5 1.0
CB B:HIS60 3.8 23.1 1.0
N B:PRO59 3.8 17.0 1.0
CG B:ARG58 3.8 16.4 1.0
CB B:PRO59 3.9 21.3 1.0
CD B:ARG58 4.0 18.6 1.0
CB B:ARG58 4.0 17.4 1.0
CA B:HIS60 4.1 22.3 1.0
CG B:PRO59 4.1 23.4 1.0
C B:PRO59 4.2 21.7 1.0
CA B:PRO59 4.2 17.3 1.0
NE B:ARG58 4.3 16.6 1.0
C B:ARG58 4.4 17.1 1.0
CA B:ARG58 4.8 16.1 1.0
OE1 A:GLU55 4.8 29.4 1.0
O B:HOH658 4.8 38.4 1.0
O B:HOH845 4.9 39.8 1.0
OE2 A:GLU55 4.9 22.2 1.0

Chlorine binding site 8 out of 10 in 4mmw

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Chlorine binding site 8 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:29.3
occ:1.00
 O B:HOH544 3.1 20.6 1.0
O B:HOH628 3.2 26.1 1.0
O B:HOH586 3.2 26.9 1.0
N B:LEU132 3.5 15.1 1.0
NH1 B:ARG128 3.7 17.5 1.0
CA B:VAL131 3.7 14.0 1.0
CG2 B:VAL131 3.7 18.0 1.0
C B:VAL131 4.1 18.5 1.0
CB B:VAL131 4.2 21.7 1.0
CE2 B:PHE358 4.2 21.3 1.0
CG B:LEU132 4.2 22.4 1.0
O B:LYS130 4.3 18.4 1.0
CD B:ARG128 4.3 15.7 1.0
CB B:LEU132 4.4 17.6 1.0
O B:HOH725 4.5 21.7 1.0
CA B:LEU132 4.5 16.4 1.0
O B:ARG326 4.6 16.3 1.0
CZ B:ARG128 4.7 15.6 1.0
CD1 B:LEU132 4.7 23.8 1.0
N B:VAL131 4.7 16.4 1.0
CD2 B:PHE358 4.7 20.1 1.0
O B:HOH736 4.9 25.6 1.0
C B:LYS130 4.9 16.9 1.0
NE B:ARG128 4.9 15.6 1.0

Chlorine binding site 9 out of 10 in 4mmw

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Chlorine binding site 9 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


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 D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl409

b:30.5
occ:1.00
 N B:MET1 3.3 20.1 1.0
CA B:MET1 3.4 21.8 1.0
CG B:ASP74 3.4 22.9 1.0
C B:MET1 3.5 23.0 1.0
OD2 B:ASP74 3.6 22.1 1.0
CB B:ASP74 3.7 23.8 1.0
OD1 B:ASP74 3.7 18.1 1.0
CD1 B:ILE2 3.8 29.1 1.0
N B:ILE2 3.8 21.8 1.0
O B:HOH652 3.9 29.6 1.0
O B:MET1 3.9 21.8 1.0
CA B:ASP74 3.9 19.2 1.0
CG1 B:ILE2 4.1 21.5 1.0
NH1 B:ARG76 4.3 18.0 1.0
CA B:ILE2 4.5 20.7 1.0
N B:ASP74 4.8 19.8 1.0
OE2 B:GLU43 4.8 31.8 1.0
CB B:MET1 4.9 25.8 1.0

Chlorine binding site 10 out of 10 in 4mmw

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Chlorine binding site 10 out of 10 in the Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L- Lyxarohydroxamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl410

b:42.3
occ:1.00
 N B:MET1 3.2 20.1 1.0
CG B:MET1 3.4 37.6 1.0
NE B:ARG76 3.5 19.0 1.0
CZ B:ARG76 3.5 23.1 1.0
O B:HOH678 3.5 32.7 1.0
NH2 B:ARG76 3.6 20.1 1.0
CD B:ARG76 3.6 17.7 1.0
CE1 B:HIS75 3.9 19.6 1.0
CA B:MET1 4.0 21.8 1.0
NH1 B:ARG76 4.1 18.0 1.0
CB B:MET1 4.2 25.8 1.0
CG B:ARG76 4.5 18.8 1.0
ND1 B:HIS75 4.5 19.6 1.0
SD B:MET1 4.7 54.6 1.0
NE2 B:HIS75 4.9 18.2 1.0
OD1 B:ASP74 4.9 18.1 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, A.Sakai, J.A.Gerlt, S.C.Almo. Crystal Structure of D-Glucarate Dehydratase From Agrobacterium Tumefaciens Complexed with Magnesium, L-Xylarohydroxamate and L-Lyxarohydroxamate To Be Published.
Page generated: Sun Jul 21 20:02:30 2024

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