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Magnesium 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:

Chlorine (Cl) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Protein From Paracoccus Denitrificans PD1222 Complexed with Magnesium, PDB code: 4dwd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4dwd

Go back to Magnesium Binding Sites List in 4dwd
Magnesium binding site 1 out of 3 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 Magnesium with other atoms in the Mg 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:Mg500

b:11.5
occ:1.00
O B:HOH857 2.0 13.0 1.0
O A:HOH641 2.1 12.3 1.0
O A:HOH870 2.1 14.5 1.0
O B:HOH856 2.1 12.3 1.0
O B:HOH855 2.1 12.7 1.0
O A:HOH871 2.1 11.9 1.0
O B:HOH627 4.2 16.0 1.0
O A:HOH613 4.2 15.9 1.0
O A:HOH635 4.3 11.1 1.0
O B:HOH706 4.3 15.7 1.0
O B:HOH621 4.3 10.8 1.0
OD2 A:ASP259 4.3 12.7 1.0
O A:HOH659 4.3 17.4 1.0
OD2 B:ASP259 4.4 13.7 1.0
O A:HOH632 4.4 12.2 1.0
O B:HOH666 4.4 12.3 1.0
O B:HOH632 4.4 12.8 1.0
O A:HOH643 4.4 13.2 1.0
CB A:ALA256 4.8 9.4 1.0
CB B:ALA256 4.8 10.4 1.0

Magnesium binding site 2 out of 3 in 4dwd

Go back to Magnesium Binding Sites List in 4dwd
Magnesium binding site 2 out of 3 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 Magnesium with other atoms in the Mg 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:Mg501

b:6.7
occ:0.25
O A:HOH700 2.1 21.5 1.0
O A:HOH680 4.3 16.4 1.0
O A:HOH602 4.4 10.1 1.0
O A:HOH869 4.4 12.8 1.0
NH2 A:ARG212 4.7 10.2 1.0

Magnesium binding site 3 out of 3 in 4dwd

Go back to Magnesium Binding Sites List in 4dwd
Magnesium binding site 3 out of 3 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 Magnesium with other atoms in the Mg 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:Mg501

b:6.3
occ:0.25
O B:HOH923 2.0 25.0 1.0
O B:HOH636 4.2 15.8 1.0
O B:HOH609 4.3 9.2 1.0
O B:HOH854 4.4 11.3 1.0
NH2 B:ARG212 4.7 8.3 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: Mon Dec 14 13:19:05 2020

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