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Barium in PDB 2qde: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1, PDB code: 2qde was solved by R.Agarwal, S.K.Burley, S.Swaminathan, New York Sgx Research Center Forstructural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 119.063, 114.588, 146.229, 90.00, 101.45, 90.00
R / Rfree (%) 19.7 / 22.5

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 (pdb code 2qde). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 8 binding sites of Barium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1, PDB code: 2qde:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Barium binding site 1 out of 8 in 2qde

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Barium binding site 1 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ba401

b:50.2
occ:1.00
OD2 A:ASP246 2.7 20.0 1.0
OD2 A:ASP195 2.7 21.7 1.0
OE2 A:GLU221 2.8 18.7 1.0
OD1 A:ASN197 2.8 23.6 1.0
OD1 A:ASP195 3.1 18.8 1.0
CG A:ASP195 3.3 19.6 1.0
OE1 A:GLU247 3.4 20.7 1.0
OE2 A:GLU247 3.5 23.2 1.0
CG A:ASP246 3.7 19.9 1.0
CD A:GLU221 3.8 20.9 1.0
CD A:GLU247 3.8 21.8 1.0
CG A:ASN197 3.9 25.1 1.0
CB A:ASP246 4.0 18.3 1.0
CG A:GLU221 4.4 16.7 1.0
CA A:ASN197 4.4 22.6 1.0
CE1 A:TYR57 4.5 16.5 1.0
NZ A:LYS165 4.6 21.9 1.0
NZ A:LYS270 4.7 29.8 1.0
OE1 A:GLU221 4.7 20.6 1.0
N A:ASN197 4.8 20.6 1.0
CB A:ASN197 4.8 22.7 1.0
OD1 A:ASP246 4.8 19.4 1.0
CB A:ASP195 4.8 18.6 1.0
ND2 A:ASN197 4.8 26.3 1.0
CD1 A:TYR57 4.9 17.4 1.0

Barium binding site 2 out of 8 in 2qde

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Barium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba401

b:47.3
occ:1.00
OD2 B:ASP246 2.8 18.0 1.0
OD2 B:ASP195 2.8 26.2 1.0
OE2 B:GLU221 2.9 26.7 1.0
OD1 B:ASN197 2.9 27.9 1.0
O B:HOH481 3.1 36.4 1.0
OD1 B:ASP195 3.1 25.0 1.0
CG B:ASP195 3.4 25.8 1.0
OE1 B:GLU247 3.5 26.0 1.0
OE2 B:GLU247 3.5 27.0 1.0
CG B:ASP246 3.7 19.1 1.0
CD B:GLU221 3.8 26.1 1.0
CD B:GLU247 3.8 26.0 1.0
CB B:ASP246 4.0 17.3 1.0
CG B:ASN197 4.0 27.7 1.0
CG B:GLU221 4.3 24.1 1.0
CA B:ASN197 4.4 23.3 1.0
CE1 B:TYR57 4.6 17.8 1.0
NZ B:LYS270 4.7 29.4 1.0
N B:ASN197 4.7 22.3 1.0
OE1 B:GLU221 4.8 26.5 1.0
CB B:ASN197 4.8 24.7 1.0
OD1 B:ASP246 4.8 18.4 1.0
CB B:ASP195 4.9 24.1 1.0
NZ B:LYS165 4.9 28.4 1.0
CD1 B:TYR57 5.0 18.5 1.0

Barium binding site 3 out of 8 in 2qde

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Barium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba401

b:66.5
occ:1.00
OD2 C:ASP195 2.8 24.8 1.0
OE2 C:GLU221 2.8 20.5 1.0
OD2 C:ASP246 2.8 16.7 1.0
OD1 C:ASN197 2.9 26.3 1.0
OD1 C:ASP195 3.1 21.5 1.0
CG C:ASP195 3.3 23.3 1.0
OE1 C:GLU247 3.5 19.0 1.0
OE2 C:GLU247 3.5 23.9 1.0
CG C:ASP246 3.6 18.4 1.0
CD C:GLU247 3.8 21.2 1.0
CD C:GLU221 3.8 22.1 1.0
CB C:ASP246 3.9 17.2 1.0
CG C:ASN197 4.0 26.0 1.0
O C:HOH553 4.4 40.6 1.0
CA C:ASN197 4.5 23.8 1.0
CG C:GLU221 4.6 19.7 1.0
CE1 C:TYR57 4.6 18.5 1.0
OD1 C:ASP246 4.6 18.2 1.0
OE1 C:GLU221 4.7 24.2 1.0
N C:ASN197 4.8 19.4 1.0
CB C:ASN197 4.8 24.2 1.0
CB C:ASP195 4.8 22.9 1.0
NZ C:LYS270 4.8 26.8 1.0
NZ C:LYS165 4.8 24.5 1.0
ND2 C:ASN197 5.0 28.1 1.0

Barium binding site 4 out of 8 in 2qde

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Barium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ba401

b:38.4
occ:1.00
OD1 D:ASN197 2.8 21.6 1.0
OD2 D:ASP195 2.8 17.3 1.0
OD2 D:ASP246 2.9 15.9 1.0
OE2 D:GLU221 2.9 18.8 1.0
O D:HOH512 3.0 30.7 1.0
OD1 D:ASP195 3.1 13.4 1.0
OE2 D:GLU247 3.3 21.9 1.0
CG D:ASP195 3.3 16.0 1.0
OE1 D:GLU247 3.4 19.1 1.0
CD D:GLU247 3.7 19.5 1.0
CG D:ASP246 3.7 17.8 1.0
CD D:GLU221 3.8 18.2 1.0
CG D:ASN197 3.9 24.1 1.0
CB D:ASP246 4.0 14.8 1.0
CA D:ASN197 4.4 20.8 1.0
CE1 D:TYR57 4.4 16.2 1.0
CG D:GLU221 4.5 15.1 1.0
O D:HOH587 4.6 36.6 1.0
OE1 D:GLU221 4.7 19.1 1.0
CB D:ASN197 4.7 22.4 1.0
N D:ASN197 4.7 16.8 1.0
ND2 D:ASN197 4.7 26.8 1.0
NZ D:LYS165 4.7 25.7 1.0
OD1 D:ASP246 4.8 16.3 1.0
CD1 D:TYR57 4.8 15.9 1.0
CB D:ASP195 4.8 16.0 1.0
NZ D:LYS270 4.9 28.3 1.0

Barium binding site 5 out of 8 in 2qde

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Barium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ba401

b:42.4
occ:1.00
OE2 E:GLU221 2.7 16.6 1.0
OD2 E:ASP246 2.7 13.9 1.0
OD2 E:ASP195 2.8 20.0 1.0
OD1 E:ASN197 2.8 22.8 1.0
OD1 E:ASP195 3.1 17.7 1.0
CG E:ASP195 3.3 16.7 1.0
OE1 E:GLU247 3.4 19.2 1.0
OE2 E:GLU247 3.4 23.4 1.0
CG E:ASP246 3.7 15.6 1.0
CD E:GLU247 3.8 23.2 1.0
CD E:GLU221 3.8 18.9 1.0
CG E:ASN197 3.9 21.0 1.0
CB E:ASP246 4.0 13.7 1.0
O E:HOH527 4.3 38.3 1.0
CA E:ASN197 4.4 17.7 1.0
CE1 E:TYR57 4.4 13.5 1.0
CG E:GLU221 4.5 16.6 1.0
OE1 E:GLU221 4.6 19.9 1.0
N E:ASN197 4.7 15.7 1.0
CB E:ASN197 4.7 18.7 1.0
NZ E:LYS270 4.7 26.2 1.0
OD1 E:ASP246 4.8 16.6 1.0
CB E:ASP195 4.8 16.3 1.0
NZ E:LYS165 4.9 24.3 1.0
CD1 E:TYR57 4.9 13.0 1.0
ND2 E:ASN197 4.9 23.9 1.0

Barium binding site 6 out of 8 in 2qde

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Barium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ba401

b:39.9
occ:1.00
OD2 F:ASP195 2.7 16.0 1.0
OD2 F:ASP246 2.7 11.6 1.0
OE2 F:GLU221 2.8 15.9 1.0
OD1 F:ASN197 3.0 22.0 1.0
OD1 F:ASP195 3.2 15.2 1.0
OE2 F:GLU247 3.3 20.4 1.0
CG F:ASP195 3.3 14.8 1.0
OE1 F:GLU247 3.3 16.9 1.0
CD F:GLU247 3.7 18.9 1.0
CG F:ASP246 3.7 13.9 1.0
O F:HOH640 3.8 44.0 1.0
CD F:GLU221 3.8 17.5 1.0
CB F:ASP246 4.0 12.1 1.0
CG F:ASN197 4.1 21.7 1.0
CA F:ASN197 4.4 19.1 1.0
CG F:GLU221 4.4 15.3 1.0
CE1 F:TYR57 4.5 13.9 1.0
NZ F:LYS270 4.7 23.3 1.0
N F:ASN197 4.7 15.2 1.0
CB F:ASN197 4.7 18.1 1.0
OE1 F:GLU221 4.7 16.2 1.0
NZ F:LYS165 4.8 20.8 1.0
OD1 F:ASP246 4.8 12.8 1.0
CB F:ASP195 4.8 14.9 1.0
CD1 F:TYR57 4.9 14.7 1.0

Barium binding site 7 out of 8 in 2qde

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Barium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ba401

b:47.3
occ:1.00
OD2 G:ASP195 2.7 18.9 1.0
OD2 G:ASP246 2.8 15.9 1.0
OE2 G:GLU221 2.8 19.4 1.0
OD1 G:ASN197 2.9 21.7 1.0
OD1 G:ASP195 3.2 16.3 1.0
CG G:ASP195 3.3 17.9 1.0
OE2 G:GLU247 3.4 22.5 1.0
OE1 G:GLU247 3.5 19.3 1.0
CG G:ASP246 3.7 18.1 1.0
CD G:GLU247 3.8 21.1 1.0
CD G:GLU221 3.8 18.3 1.0
CB G:ASP246 4.0 15.0 1.0
CG G:ASN197 4.1 22.3 1.0
O G:HOH594 4.3 37.7 1.0
CE1 G:TYR57 4.5 16.2 1.0
CA G:ASN197 4.5 18.5 1.0
CG G:GLU221 4.5 16.6 1.0
OE1 G:GLU221 4.6 18.9 1.0
OD1 G:ASP246 4.7 17.7 1.0
NZ G:LYS270 4.8 25.2 1.0
N G:ASN197 4.8 16.1 1.0
NZ G:LYS165 4.8 24.5 1.0
CB G:ASN197 4.8 19.5 1.0
CB G:ASP195 4.8 14.6 1.0
CD1 G:TYR57 4.9 16.8 1.0

Barium binding site 8 out of 8 in 2qde

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Barium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Family Protein From Azoarcus Sp. EBN1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ba401

b:47.8
occ:1.00
OD2 H:ASP195 2.7 23.0 1.0
OD2 H:ASP246 2.7 20.2 1.0
OE2 H:GLU221 2.8 21.4 1.0
OD1 H:ASN197 2.9 24.6 1.0
OD1 H:ASP195 3.0 22.2 1.0
CG H:ASP195 3.2 21.6 1.0
OE2 H:GLU247 3.4 26.0 1.0
OE1 H:GLU247 3.5 24.4 1.0
CG H:ASP246 3.6 19.8 1.0
CD H:GLU247 3.8 25.4 1.0
CD H:GLU221 3.8 20.8 1.0
CB H:ASP246 3.9 17.0 1.0
CG H:ASN197 4.1 25.7 1.0
CA H:ASN197 4.4 21.9 1.0
CG H:GLU221 4.5 19.9 1.0
CE1 H:TYR57 4.5 19.9 1.0
NZ H:LYS270 4.6 29.5 1.0
CB H:ASP195 4.7 21.8 1.0
N H:ASN197 4.7 20.5 1.0
OD1 H:ASP246 4.7 18.5 1.0
OE1 H:GLU221 4.7 21.8 1.0
CB H:ASN197 4.7 23.0 1.0
NZ H:LYS165 4.7 27.8 1.0
O H:HOH547 4.8 35.1 1.0
CD1 H:TYR57 5.0 19.1 1.0

Reference:

R.Agarwal, S.K.Burley, S.Swaminathan. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme Family Protein From Azoarcus Sp. EBN1. To Be Published.
Page generated: Sat Dec 12 01:55:26 2020

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