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Sodium in PDB 4h83: Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)

Protein crystallography data

The structure of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127), PDB code: 4h83 was solved by J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.13 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.983, 102.950, 234.431, 90.00, 90.00, 90.00
R / Rfree (%) 14.7 / 20.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) (pdb code 4h83). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127), PDB code: 4h83:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4h83

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Sodium binding site 1 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:26.9
occ:1.00
 O D:HOH631 2.1 38.4 1.0
O F:HOH626 2.2 27.5 1.0
O D:HOH621 2.3 30.2 1.0
O A:TYR258 2.3 25.7 1.0
O D:TYR258 2.5 20.9 1.0
O F:TYR258 2.5 19.4 1.0
O A:HOH622 3.5 28.1 1.0
C A:TYR258 3.6 22.6 1.0
C F:TYR258 3.7 20.6 1.0
C D:TYR258 3.7 20.2 1.0
O F:HOH579 3.8 37.3 1.0
O D:HOH546 3.8 29.8 1.0
O F:HOH655 3.9 29.4 1.0
CA A:TYR258 4.4 17.8 1.0
N A:GLN259 4.5 18.0 1.0
CA A:GLN259 4.5 18.0 1.0
CA D:GLN259 4.5 17.3 1.0
O A:GLY260 4.5 22.2 1.0
CA F:TYR258 4.6 19.7 1.0
N D:GLN259 4.6 18.2 1.0
O D:GLY260 4.6 20.4 1.0
CA D:TYR258 4.6 21.5 1.0
N F:GLN259 4.7 19.6 1.0
CA F:GLN259 4.7 18.1 1.0
C A:GLN259 4.8 22.0 1.0
C D:GLN259 4.8 23.1 1.0
O F:GLY260 4.8 25.2 1.0
O D:GLN259 4.8 21.3 1.0
O A:GLN259 4.9 19.4 1.0
CB A:TYR258 5.0 16.5 1.0
C F:GLN259 5.0 17.5 1.0

Sodium binding site 2 out of 8 in 4h83

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Sodium binding site 2 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:38.6
occ:1.00
 OD2 A:ASP215 2.3 27.6 1.0
OE2 A:GLU241 2.4 23.3 1.0
OE1 A:GLN268 2.4 29.5 1.0
O A:HOH625 2.6 40.2 1.0
CG A:ASP215 3.0 30.0 1.0
CD A:GLN268 3.3 30.7 1.0
OD1 A:ASP215 3.3 25.2 1.0
CD A:GLU241 3.4 29.1 1.0
NE2 A:GLN268 3.6 28.2 1.0
ND2 A:ASN217 3.6 35.9 1.0
NZ A:LYS184 3.8 29.3 1.0
CG A:GLU241 3.8 18.2 1.0
CD2 A:HIS318 4.2 34.2 1.0
OE2 A:GLU242 4.3 36.0 1.0
CB A:ASP215 4.3 19.0 1.0
OE1 A:GLU241 4.5 29.8 1.0
NZ A:LYS186 4.6 45.0 1.0
CG A:GLN268 4.6 24.0 1.0
CD A:LYS184 4.6 30.7 1.0
ND2 A:ASN289 4.6 16.7 1.0
NE2 A:HIS318 4.6 40.7 1.0
CG A:ASN217 4.7 34.3 1.0
CE A:LYS184 4.7 25.5 1.0
CB A:GLU241 4.7 19.0 1.0

Sodium binding site 3 out of 8 in 4h83

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Sodium binding site 3 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na401

b:23.2
occ:1.00
 O B:TYR258 2.2 21.2 1.0
O B:HOH608 2.2 30.2 1.0
O C:TYR258 2.2 21.1 1.0
O E:TYR258 2.4 19.2 1.0
O E:HOH615 2.5 27.4 1.0
O B:HOH596 2.6 24.8 1.0
C B:TYR258 3.4 22.9 1.0
C C:TYR258 3.4 17.9 1.0
C E:TYR258 3.6 16.3 1.0
O C:HOH578 3.7 42.9 1.0
N B:GLN259 4.3 19.7 1.0
CA C:TYR258 4.3 15.1 1.0
CA B:TYR258 4.3 16.8 1.0
N C:GLN259 4.4 19.3 1.0
CA C:GLN259 4.4 17.0 1.0
CA B:GLN259 4.4 22.0 1.0
O E:HOH530 4.5 33.5 1.0
N E:GLN259 4.5 16.4 1.0
CA E:TYR258 4.5 16.3 1.0
O C:GLY260 4.5 23.7 1.0
CA E:GLN259 4.5 18.8 1.0
O B:HOH545 4.5 36.7 1.0
C C:GLN259 4.6 22.6 1.0
O B:GLY260 4.7 23.4 1.0
C B:GLN259 4.7 24.5 1.0
O C:GLN259 4.7 15.6 1.0
O B:GLN259 4.7 22.6 1.0
C E:GLN259 4.8 22.8 1.0
O E:GLY260 4.8 21.1 1.0
O E:GLN259 4.8 24.7 1.0
CB B:TYR258 4.8 16.5 1.0
O C:HOH637 4.9 38.4 1.0
CB C:TYR258 4.9 17.1 1.0

Sodium binding site 4 out of 8 in 4h83

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Sodium binding site 4 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:41.7
occ:1.00
 O B:HOH617 2.3 47.1 1.0
OD2 B:ASP215 2.3 31.8 1.0
O B:HOH607 2.4 35.7 1.0
OE2 B:GLU241 2.4 28.6 1.0
OE1 B:GLN268 2.7 39.1 1.0
CG B:ASP215 3.1 30.4 1.0
O B:HOH624 3.3 48.9 1.0
OD1 B:ASP215 3.3 29.5 1.0
CD B:GLU241 3.4 25.1 1.0
CD B:GLN268 3.6 36.8 1.0
ND2 B:ASN217 3.7 33.2 1.0
NZ B:LYS184 3.8 25.3 1.0
NE2 B:GLN268 3.9 31.2 1.0
CD2 B:HIS318 3.9 37.0 1.0
CG B:GLU241 4.0 23.4 1.0
NE2 B:HIS318 4.3 35.0 1.0
CB B:ASP215 4.4 20.7 1.0
OE1 B:GLU241 4.4 27.9 1.0
CD B:LYS184 4.5 27.1 1.0
NZ B:LYS186 4.5 46.6 1.0
OE2 B:GLU242 4.7 41.2 1.0
ND2 B:ASN289 4.7 19.6 1.0
CE B:LYS184 4.7 25.3 1.0
CG B:ASN217 4.8 34.7 1.0
CB B:GLU241 4.9 21.3 1.0
CG B:GLN268 4.9 26.2 1.0

Sodium binding site 5 out of 8 in 4h83

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Sodium binding site 5 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:37.8
occ:1.00
 OE2 C:GLU241 2.2 21.3 1.0
OE1 C:GLN268 2.4 34.7 1.0
O C:HOH644 2.4 38.5 1.0
OD2 C:ASP215 2.7 29.9 1.0
O C:HOH623 3.0 39.0 1.0
CG C:ASP215 3.2 27.2 1.0
OD1 C:ASP215 3.2 23.2 1.0
CD C:GLU241 3.3 23.7 1.0
CD C:GLN268 3.3 36.6 1.0
NE2 C:GLN268 3.5 27.6 1.0
OE2 C:GLU242 3.7 37.0 1.0
NZ C:LYS184 3.8 31.8 1.0
CG C:GLU241 3.8 21.8 1.0
ND1 C:HIS318 3.8 41.4 1.0
ND2 C:ASN217 4.2 39.8 1.0
ND2 C:ASN289 4.2 23.4 1.0
CE1 C:HIS318 4.2 42.9 1.0
OE1 C:GLU241 4.3 29.1 1.0
CB C:ASP215 4.5 22.3 1.0
CD C:LYS184 4.5 35.2 1.0
CD C:GLU242 4.7 37.8 1.0
CG C:GLN268 4.7 32.8 1.0
NZ C:LYS186 4.7 44.0 1.0
CE C:LYS184 4.7 25.5 1.0
CB C:GLU241 4.8 20.0 1.0
CG C:GLU242 4.9 26.7 1.0

Sodium binding site 6 out of 8 in 4h83

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Sodium binding site 6 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:40.0
occ:1.00
 O D:HOH637 2.2 34.5 1.0
OE2 D:GLU241 2.2 24.7 1.0
OD2 D:ASP215 2.3 34.1 1.0
O D:HOH638 2.5 35.1 1.0
OE1 D:GLN268 2.5 42.5 1.0
CG D:ASP215 3.1 33.4 1.0
O D:HOH632 3.2 42.6 1.0
OD1 D:ASP215 3.3 26.8 1.0
CD D:GLU241 3.4 25.4 1.0
CD D:GLN268 3.5 35.2 1.0
ND2 D:ASN217 3.7 36.5 1.0
NZ D:LYS184 3.8 28.4 1.0
CD2 D:HIS318 3.8 35.8 1.0
NE2 D:GLN268 3.9 30.6 1.0
CG D:GLU241 3.9 21.7 1.0
NE2 D:HIS318 4.1 45.0 1.0
CB D:ASP215 4.4 25.7 1.0
OE2 D:GLU242 4.4 39.6 1.0
OE1 D:GLU241 4.4 27.9 1.0
CD D:LYS184 4.5 29.4 1.0
NZ D:LYS186 4.6 43.4 1.0
O D:HOH627 4.6 37.1 1.0
ND2 D:ASN289 4.7 15.2 1.0
CE D:LYS184 4.7 21.4 1.0
CB D:GLU241 4.8 15.3 1.0
CG D:GLN268 4.8 26.8 1.0
CG D:ASN217 4.9 37.2 1.0

Sodium binding site 7 out of 8 in 4h83

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Sodium binding site 7 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na401

b:31.3
occ:1.00
 O E:HOH656 2.0 28.0 1.0
OE2 E:GLU241 2.2 20.9 1.0
OE1 E:GLN268 2.4 35.0 1.0
OD2 E:ASP215 2.4 24.6 1.0
O E:HOH629 2.6 32.9 1.0
CG E:ASP215 3.1 24.8 1.0
CD E:GLU241 3.3 19.3 1.0
CD E:GLN268 3.3 33.7 1.0
OD1 E:ASP215 3.4 19.1 1.0
NZ E:LYS184 3.6 34.1 1.0
NE2 E:GLN268 3.7 27.8 1.0
CG E:GLU241 3.8 24.3 1.0
CD2 E:HIS318 4.1 34.1 1.0
ND2 E:ASN217 4.1 35.6 1.0
OE1 E:GLU242 4.3 27.4 1.0
OE1 E:GLU241 4.4 22.6 1.0
CB E:ASP215 4.4 19.3 1.0
ND2 E:ASN289 4.4 18.1 1.0
NE2 E:HIS318 4.4 44.4 1.0
NZ E:LYS186 4.5 40.5 1.0
CE E:LYS184 4.6 24.8 1.0
CD E:LYS184 4.6 27.2 1.0
CB E:GLU241 4.6 18.7 1.0
CG E:GLN268 4.7 28.6 1.0
O E:HOH623 4.7 41.8 1.0
CG E:GLU242 4.8 32.1 1.0
CG E:ASN217 4.8 31.9 1.0
CD E:GLU242 4.9 33.2 1.0

Sodium binding site 8 out of 8 in 4h83

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Sodium binding site 8 out of 8 in the Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme (Efi Target:502127) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na402

b:33.5
occ:1.00
 O F:HOH627 2.3 28.9 1.0
OE1 F:GLU241 2.3 22.9 1.0
OE1 F:GLN268 2.4 29.2 1.0
OD2 F:ASP215 2.4 29.0 1.0
O F:HOH634 2.5 28.3 1.0
O F:HOH621 2.6 41.0 1.0
CG F:ASP215 3.3 26.7 1.0
CD F:GLN268 3.3 31.0 1.0
CD F:GLU241 3.4 20.2 1.0
OD1 F:ASP215 3.5 20.2 1.0
NE2 F:GLN268 3.6 26.2 1.0
NZ F:LYS184 3.7 28.5 1.0
ND2 F:ASN217 3.7 29.5 1.0
CD2 F:HIS318 3.9 33.4 1.0
CG F:GLU241 3.9 18.2 1.0
O F:HOH638 4.1 40.6 1.0
NZ F:LYS186 4.3 39.5 1.0
NE2 F:HIS318 4.4 43.2 1.0
OE2 F:GLU242 4.4 26.2 1.0
ND2 F:ASN289 4.4 18.1 1.0
CD F:LYS184 4.4 28.2 1.0
OE2 F:GLU241 4.5 21.6 1.0
CB F:ASP215 4.5 15.9 1.0
CE F:LYS184 4.6 28.0 1.0
CG F:ASN217 4.6 24.1 1.0
CG F:GLN268 4.6 22.9 1.0
OD1 F:ASN217 4.9 28.4 1.0
CG F:HIS318 4.9 29.7 1.0
CB F:GLU241 4.9 15.9 1.0

Reference:

J.Kim, R.Toro, R.Bhosle, N.F.Al Obaidi, L.L.Morisco, S.R.Wasserman, S.Sojitra, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, M.Stead, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of Mandelate Racemase/Muconate Lactonizing Enzyme To Be Published.
Page generated: Mon Oct 7 15:45:02 2024

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