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Magnesium in PDB 3cb3: Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate

Protein crystallography data

The structure of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate, PDB code: 3cb3 was solved by A.A.Fedorov, E.V.Fedorov, W.S.Yew, S.K.Burley, J.A.Gerlt, S.C.Almo, Newyork Sgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.91 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 195.466, 84.739, 118.247, 90.00, 126.04, 90.00
R / Rfree (%) 21 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate (pdb code 3cb3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate, PDB code: 3cb3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3cb3

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Magnesium binding site 1 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:23.8
occ:1.00
 O A:HOH602 2.0 20.6 1.0
OE2 A:GLU237 2.0 21.9 1.0
O1A A:LGT601 2.1 32.2 1.0
O2 A:LGT601 2.1 33.6 1.0
OD2 A:ASP211 2.1 17.6 1.0
OE1 A:GLU263 2.1 22.5 1.0
C1 A:LGT601 2.8 35.1 1.0
C2 A:LGT601 2.9 36.2 1.0
CD A:GLU237 3.1 19.8 1.0
CD A:GLU263 3.1 21.1 1.0
CG A:ASP211 3.1 18.1 1.0
OE2 A:GLU263 3.3 23.2 1.0
OD1 A:ASP211 3.5 17.7 1.0
OE1 A:GLU237 3.9 21.9 1.0
CG A:GLU237 3.9 18.0 1.0
O A:HOH738 4.0 42.2 1.0
OD1 A:ASN213 4.0 23.1 1.0
O1B A:LGT601 4.0 35.4 1.0
NZ A:LYS180 4.1 23.9 1.0
C3 A:LGT601 4.2 38.5 1.0
OE1 A:GLU238 4.2 26.2 1.0
O A:HOH629 4.4 24.8 1.0
O3 A:LGT601 4.4 39.1 1.0
CB A:ASP211 4.4 15.2 1.0
CG A:GLU263 4.5 19.1 1.0
CE A:LYS180 4.7 21.1 1.0
CD2 A:HIS313 4.7 25.6 1.0
CG A:ASN213 4.8 22.1 1.0
CG A:GLU238 4.9 20.7 1.0
O A:HOH741 4.9 41.7 1.0
CD A:GLU238 5.0 25.7 1.0

Magnesium binding site 2 out of 8 in 3cb3

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Magnesium binding site 2 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:21.1
occ:1.00
 O A:HOH671 1.9 24.9 1.0
O A:HOH612 2.0 14.2 1.0
O A:ALA252 2.0 19.1 1.0
O A:HOH680 2.1 19.6 1.0
O A:PHE255 2.1 21.9 1.0
O A:HOH632 2.2 20.9 1.0
C A:ALA252 3.2 20.8 1.0
C A:PHE255 3.4 21.8 1.0
CA A:ALA252 3.8 20.0 1.0
O A:ASP256 4.1 20.9 1.0
OD1 A:ASP281 4.1 24.9 1.0
OD2 A:ASP281 4.1 20.6 1.0
N A:ASP256 4.2 19.9 1.0
N A:LEU253 4.3 21.5 1.0
CA A:ASP256 4.3 20.2 1.0
C A:ASP256 4.3 20.7 1.0
O A:THR257 4.3 15.7 1.0
N A:PHE255 4.3 22.2 1.0
CA A:PHE255 4.3 23.2 1.0
O A:HOH625 4.4 19.4 1.0
O A:LEU253 4.5 27.8 1.0
CB A:ALA252 4.5 19.9 1.0
C A:LEU253 4.5 26.4 1.0
CG A:ASP281 4.5 23.4 1.0
CA A:LEU253 4.5 24.5 1.0
O A:HOH698 4.7 27.9 1.0
O A:LEU251 4.8 19.8 1.0
OE1 B:GLN222 4.9 44.6 1.0
C A:THR257 5.0 17.9 1.0

Magnesium binding site 3 out of 8 in 3cb3

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Magnesium binding site 3 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:31.1
occ:1.00
 OE2 B:GLU237 2.0 24.3 1.0
OD2 B:ASP211 2.1 22.1 1.0
OE1 B:GLU263 2.1 31.5 1.0
O B:HOH602 2.1 29.6 1.0
O2 B:LGT601 2.1 37.9 1.0
O1A B:LGT601 2.2 39.1 1.0
CD B:GLU263 3.0 31.4 1.0
C1 B:LGT601 3.0 40.8 1.0
C2 B:LGT601 3.1 40.5 1.0
CD B:GLU237 3.1 23.4 1.0
CG B:ASP211 3.1 22.5 1.0
OE2 B:GLU263 3.2 30.8 1.0
OD1 B:ASP211 3.5 19.6 1.0
OE1 B:GLU237 3.9 23.9 1.0
CG B:GLU237 3.9 22.8 1.0
NZ B:LYS180 4.0 30.7 1.0
OD1 B:ASN213 4.0 30.9 1.0
O1B B:LGT601 4.2 43.1 1.0
OE1 B:GLU238 4.3 28.2 1.0
C3 B:LGT601 4.3 42.3 1.0
O B:HOH658 4.3 29.4 1.0
O3 B:LGT601 4.3 40.0 1.0
CG B:GLU263 4.3 29.1 1.0
CB B:ASP211 4.4 21.6 1.0
CD2 B:HIS313 4.7 26.4 1.0
NZ B:LYS182 4.7 41.4 1.0
CE B:LYS180 4.7 26.5 1.0
CG B:GLU238 4.9 23.4 1.0
CB B:GLU237 4.9 19.7 1.0
CD B:GLU238 5.0 27.8 1.0
NE2 B:HIS313 5.0 26.4 1.0

Magnesium binding site 4 out of 8 in 3cb3

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Magnesium binding site 4 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:28.7
occ:1.00
 O B:ALA252 2.0 19.9 1.0
O B:HOH701 2.1 24.3 1.0
O B:HOH608 2.1 17.1 1.0
O B:PHE255 2.2 26.0 1.0
O B:HOH702 2.2 31.4 1.0
O B:HOH723 2.3 28.5 1.0
C B:ALA252 3.1 21.5 1.0
C B:PHE255 3.4 25.1 1.0
CA B:ALA252 3.8 19.4 1.0
OD1 B:ASP281 4.0 25.1 1.0
OD2 B:ASP281 4.2 19.8 1.0
N B:LEU253 4.2 22.1 1.0
O B:ASP256 4.2 24.0 1.0
O B:HOH641 4.3 23.8 1.0
N B:ASP256 4.3 24.5 1.0
CA B:ASP256 4.3 26.2 1.0
N B:PHE255 4.3 28.3 1.0
CB B:ALA252 4.4 20.7 1.0
C B:ASP256 4.4 24.5 1.0
CA B:PHE255 4.4 26.4 1.0
O B:LEU253 4.4 28.4 1.0
O B:THR257 4.5 21.6 1.0
C B:LEU253 4.5 26.8 1.0
CG B:ASP281 4.5 22.4 1.0
CA B:LEU253 4.5 25.1 1.0
O B:HOH720 4.6 35.3 1.0
O B:LEU251 4.9 20.9 1.0

Magnesium binding site 5 out of 8 in 3cb3

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Magnesium binding site 5 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:36.5
occ:1.00
 O C:HOH602 1.9 30.1 1.0
O2 C:LGT601 2.0 34.5 1.0
OE2 C:GLU237 2.1 29.6 1.0
OE1 C:GLU263 2.1 29.9 1.0
O1A C:LGT601 2.1 35.5 1.0
OD2 C:ASP211 2.2 25.2 1.0
C1 C:LGT601 2.9 38.4 1.0
CD C:GLU263 2.9 30.6 1.0
C2 C:LGT601 2.9 38.2 1.0
CG C:ASP211 3.1 24.0 1.0
CD C:GLU237 3.1 27.1 1.0
OE2 C:GLU263 3.2 31.8 1.0
OD1 C:ASP211 3.3 26.2 1.0
CG C:GLU237 3.8 23.8 1.0
OD1 C:ASN213 3.9 36.0 1.0
OE1 C:GLU238 4.0 29.8 1.0
OE1 C:GLU237 4.0 25.5 1.0
NZ C:LYS180 4.1 29.8 1.0
O1B C:LGT601 4.1 41.2 1.0
O C:HOH612 4.2 20.9 1.0
C3 C:LGT601 4.2 40.8 1.0
CG C:GLU263 4.2 26.9 1.0
O3 C:LGT601 4.4 38.3 1.0
CB C:ASP211 4.5 24.5 1.0
CD C:GLU238 4.8 30.1 1.0
CD2 C:HIS313 4.8 29.1 1.0
NZ C:LYS182 4.8 48.6 1.0
CE C:LYS180 4.8 29.2 1.0
CG C:GLU238 4.8 25.5 1.0
CG C:ASN213 4.8 34.3 1.0
CB C:GLU237 4.9 23.1 1.0

Magnesium binding site 6 out of 8 in 3cb3

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Magnesium binding site 6 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg502

b:32.2
occ:1.00
 O C:HOH623 2.0 31.4 1.0
O C:ALA252 2.1 24.5 1.0
O C:HOH622 2.1 21.6 1.0
O C:PHE255 2.2 27.8 1.0
O C:HOH707 2.2 28.2 1.0
O C:HOH611 2.2 19.7 1.0
C C:ALA252 3.1 24.0 1.0
C C:PHE255 3.4 26.4 1.0
CA C:ALA252 3.7 21.5 1.0
O C:ASP256 4.1 24.7 1.0
OD1 C:ASP281 4.1 26.4 1.0
OD2 C:ASP281 4.2 21.1 1.0
C C:ASP256 4.2 24.6 1.0
CA C:ASP256 4.2 25.0 1.0
N C:LEU253 4.3 25.7 1.0
N C:PHE255 4.3 29.4 1.0
N C:ASP256 4.3 25.8 1.0
CB C:ALA252 4.3 20.1 1.0
O C:THR257 4.4 20.0 1.0
CA C:PHE255 4.4 27.3 1.0
O C:HOH669 4.5 28.1 1.0
CG C:ASP281 4.5 23.6 1.0
O C:HOH680 4.6 28.9 1.0
C C:LEU253 4.6 29.8 1.0
CA C:LEU253 4.6 28.3 1.0
O C:LEU253 4.7 30.5 1.0
O C:LEU251 4.9 21.0 1.0
C C:THR257 4.9 21.1 1.0
N C:THR257 5.0 22.9 1.0

Magnesium binding site 7 out of 8 in 3cb3

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Magnesium binding site 7 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg502

b:29.8
occ:1.00
 O D:HOH602 2.0 19.9 1.0
OE2 D:GLU237 2.0 22.5 1.0
OE1 D:GLU263 2.1 27.3 1.0
O2 D:LGT601 2.1 29.6 1.0
O1A D:LGT601 2.1 35.0 1.0
OD2 D:ASP211 2.2 20.6 1.0
C1 D:LGT601 2.9 36.0 1.0
CD D:GLU263 3.0 23.8 1.0
C2 D:LGT601 3.0 36.0 1.0
CD D:GLU237 3.1 20.9 1.0
OE2 D:GLU263 3.2 23.7 1.0
CG D:ASP211 3.2 20.3 1.0
OD1 D:ASP211 3.6 23.1 1.0
CG D:GLU237 3.9 18.8 1.0
NZ D:LYS180 4.0 29.6 1.0
OE1 D:GLU238 4.0 28.6 1.0
OD1 D:ASN213 4.0 24.9 1.0
OE1 D:GLU237 4.1 20.1 1.0
O1B D:LGT601 4.1 38.3 1.0
C3 D:LGT601 4.3 37.8 1.0
O D:HOH617 4.3 31.3 1.0
O3 D:LGT601 4.4 38.7 1.0
CG D:GLU263 4.4 24.3 1.0
O D:HOH726 4.4 45.1 1.0
CB D:ASP211 4.5 17.4 1.0
CD2 D:HIS313 4.5 24.8 1.0
CE D:LYS180 4.8 25.9 1.0
NE2 D:HIS313 4.8 25.2 1.0
CG D:ASN213 4.9 25.4 1.0
CD D:GLU238 4.9 28.3 1.0

Magnesium binding site 8 out of 8 in 3cb3

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Magnesium binding site 8 out of 8 in the Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg503

b:21.3
occ:1.00
 O D:ALA252 2.0 21.4 1.0
O D:HOH607 2.1 15.5 1.0
O D:PHE255 2.1 19.8 1.0
O D:HOH618 2.2 18.1 1.0
O D:HOH619 2.2 17.6 1.0
O D:HOH620 2.2 25.5 1.0
C D:ALA252 3.1 20.7 1.0
C D:PHE255 3.3 20.4 1.0
CA D:ALA252 3.8 19.9 1.0
O D:ASP256 4.1 20.4 1.0
OD1 D:ASP281 4.1 25.5 1.0
OD2 D:ASP281 4.1 19.2 1.0
N D:PHE255 4.2 22.7 1.0
N D:ASP256 4.2 20.0 1.0
O D:THR257 4.2 19.2 1.0
C D:ASP256 4.2 20.9 1.0
N D:LEU253 4.3 20.5 1.0
CA D:ASP256 4.3 20.5 1.0
CA D:PHE255 4.3 21.8 1.0
O D:HOH625 4.4 21.0 1.0
CB D:ALA252 4.4 19.1 1.0
O D:LEU253 4.5 23.9 1.0
C D:LEU253 4.5 23.2 1.0
CG D:ASP281 4.5 22.8 1.0
CD1 D:ILE259 4.6 31.7 1.0
CA D:LEU253 4.6 20.8 1.0
O D:LEU251 4.7 17.7 1.0
C D:THR257 4.9 21.2 1.0
CB D:PHE255 5.0 19.3 1.0

Reference:

A.A.Fedorov, E.V.Fedorov, W.S.Yew, S.K.Burley, J.A.Gerlt, S.C.Almo. Crystal Structure of L-Talarate Dehydratase From Polaromonas Sp. JS666 Complexed with Mg and L-Glucarate. To Be Published.
Page generated: Wed Aug 14 09:33:12 2024

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