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Chlorine in PDB 4dwd: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium, PDB code: 4dwd was solved by V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, 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) 19.94 / 1.50
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 136.598, 136.598, 80.603, 90.00, 90.00, 90.00
R / Rfree (%) 14.2 / 17.2

Other elements in 4dwd:

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium (pdb code 4dwd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium, PDB code: 4dwd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 4dwd

Go back to Chlorine Binding Sites List in 4dwd
Chlorine binding site 1 out of 5 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium


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 Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:12.6
occ:1.00
 OE2 A:GLU224 2.9 12.8 0.5
N A:GLY248 3.2 9.2 1.0
OG1 A:THR251 3.2 8.6 1.0
O A:HOH665 3.3 11.2 1.0
N A:GLN250 3.3 9.7 1.0
C A:GLN250 3.5 9.2 1.0
CA A:GLY248 3.6 10.0 1.0
CA A:GLN250 3.7 10.1 1.0
C A:GLY248 3.7 9.7 1.0
CB A:GLN250 3.7 10.7 1.0
OE2 A:GLU224 3.7 17.7 0.5
N A:THR251 3.8 8.4 1.0
CD A:GLU224 3.8 13.7 0.5
N A:GLU249 3.8 9.3 1.0
O A:GLN250 3.8 9.8 1.0
OE1 A:GLU224 3.9 14.3 0.5
OE1 A:GLU224 3.9 17.0 0.5
CB A:HIS228 4.0 9.8 1.0
CD A:GLU224 4.0 15.8 0.5
CB A:ALA247 4.2 9.5 1.0
O A:HOH677 4.2 11.2 1.0
O A:GLY248 4.3 9.8 1.0
C A:ALA247 4.3 9.1 1.0
CB A:THR251 4.3 9.0 1.0
C A:GLU249 4.4 10.6 1.0
CA A:THR251 4.5 8.9 1.0
CA A:ALA247 4.6 9.6 1.0
CG A:HIS228 4.7 10.2 1.0
CA A:GLU249 4.7 10.4 1.0
CD2 A:HIS228 4.7 10.5 1.0
CG A:GLN250 4.7 11.6 1.0
CD2 A:LEU260 4.8 9.8 1.0
CA A:HIS228 4.8 10.0 1.0
CG A:GLU249 5.0 16.0 1.0

Chlorine binding site 2 out of 5 in 4dwd

Go back to Chlorine Binding Sites List in 4dwd
Chlorine binding site 2 out of 5 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium


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 Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:17.9
occ:1.00
 O A:HOH611 2.8 12.4 1.0
NZ B:LYS258 3.1 13.8 1.0
N A:ALA233 3.1 9.1 1.0
N A:GLY232 3.2 9.3 1.0
CA A:GLY232 3.5 10.2 1.0
CA A:HIS230 3.6 9.6 1.0
C A:HIS230 3.6 9.0 1.0
CB A:HIS230 3.7 9.7 1.0
O B:HOH662 3.7 13.1 1.0
C A:GLY232 3.8 9.2 1.0
O B:HOH708 3.8 20.8 1.0
N A:VAL231 3.8 8.4 1.0
CE B:LYS258 4.0 11.9 1.0
CB A:ALA233 4.0 9.7 1.0
O A:HIS230 4.0 8.9 1.0
CA A:ALA233 4.2 9.3 1.0
C A:VAL231 4.2 9.2 1.0
ND1 A:HIS230 4.4 10.6 1.0
CG A:HIS230 4.5 9.0 1.0
CA A:VAL231 4.7 9.1 1.0
N A:HIS230 5.0 9.2 1.0
O A:GLY232 5.0 9.4 1.0

Chlorine binding site 3 out of 5 in 4dwd

Go back to Chlorine Binding Sites List in 4dwd
Chlorine binding site 3 out of 5 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium


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 Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:21.1
occ:1.00
 NZ B:LYS106 3.2 17.4 1.0
O B:HOH892 3.2 28.8 1.0
CE B:LYS106 3.5 16.2 1.0
O B:LEU117 3.6 12.7 1.0
CB B:LEU117 3.9 11.5 1.0
CD2 B:LEU117 4.1 11.9 1.0
C B:LEU117 4.3 11.6 1.0
CA B:LEU117 4.3 11.7 1.0
CG B:LEU117 4.4 11.2 1.0
CH2 B:TRP103 4.6 13.6 1.0
CZ3 B:TRP103 4.8 12.8 1.0
CD1 B:LEU117 4.8 13.3 1.0

Chlorine binding site 4 out of 5 in 4dwd

Go back to Chlorine Binding Sites List in 4dwd
Chlorine binding site 4 out of 5 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium


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 Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl503

b:12.5
occ:1.00
 OE2 B:GLU224 2.9 14.9 0.5
N B:GLY248 3.2 9.6 1.0
OG1 B:THR251 3.2 9.2 1.0
O B:HOH649 3.3 12.6 1.0
N B:GLN250 3.3 9.8 1.0
CA B:GLY248 3.6 10.2 1.0
C B:GLN250 3.6 8.4 1.0
OE2 B:GLU224 3.6 21.2 0.5
CA B:GLN250 3.7 8.9 1.0
C B:GLY248 3.7 9.7 1.0
CB B:GLN250 3.8 9.9 1.0
N B:THR251 3.8 8.4 1.0
CD B:GLU224 3.8 17.0 0.5
N B:GLU249 3.8 9.6 1.0
O B:GLN250 3.9 9.4 1.0
OE1 B:GLU224 3.9 14.6 0.5
OE1 B:GLU224 3.9 15.9 0.5
CD B:GLU224 3.9 17.3 0.5
CB B:HIS228 4.0 10.4 1.0
CB B:ALA247 4.2 9.4 1.0
O B:HOH638 4.3 11.4 1.0
C B:ALA247 4.3 9.6 1.0
CB B:THR251 4.3 8.8 1.0
O B:GLY248 4.4 9.6 1.0
C B:GLU249 4.5 10.3 1.0
CA B:THR251 4.6 9.0 1.0
CA B:ALA247 4.6 9.9 1.0
CG B:HIS228 4.7 10.6 1.0
CD2 B:HIS228 4.7 10.7 1.0
CA B:GLU249 4.7 10.1 0.5
CA B:GLU249 4.7 10.1 0.5
CG B:GLN250 4.7 11.4 1.0
CA B:HIS228 4.8 9.7 1.0
CD2 B:LEU260 4.8 9.4 1.0
O B:HIS228 5.0 10.9 1.0

Chlorine binding site 5 out of 5 in 4dwd

Go back to Chlorine Binding Sites List in 4dwd
Chlorine binding site 5 out of 5 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium


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 Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl504

b:17.3
occ:1.00
 O B:HOH615 2.8 11.9 1.0
N B:ALA233 3.1 8.4 1.0
NZ A:LYS258 3.2 13.9 1.0
N B:GLY232 3.3 8.8 1.0
CA B:HIS230 3.5 9.5 1.0
CA B:GLY232 3.6 10.3 1.0
C B:HIS230 3.6 8.5 1.0
CB B:HIS230 3.6 9.5 1.0
O A:HOH682 3.7 12.5 1.0
N B:VAL231 3.8 8.3 1.0
C B:GLY232 3.8 8.9 1.0
O A:HOH760 3.9 20.6 1.0
CB B:ALA233 4.0 9.5 1.0
CE A:LYS258 4.0 11.7 1.0
O B:HIS230 4.0 8.9 1.0
CA B:ALA233 4.1 8.7 1.0
C B:VAL231 4.3 8.7 1.0
CG B:HIS230 4.4 9.2 1.0
ND1 B:HIS230 4.4 10.9 1.0
CA B:VAL231 4.7 8.8 1.0
N B:HIS230 4.9 9.4 1.0

Reference:

V.N.Malashkevich, R.Toro, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium To Be Published.
Page generated: Fri Jul 11 14:32:16 2025

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