Atomistry » Sodium » PDB 4gxj-4hfc » 4h83
Atomistry »
  Sodium »
    PDB 4gxj-4hfc »
      4h83 »

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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Go back to Sodium Binding Sites List in 4h83
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy