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Sodium in PDB 4g8t: Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop

Enzymatic activity of Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop

All present enzymatic activity of Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop:
4.2.1.40;

Protein crystallography data

The structure of Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop, PDB code: 4g8t was solved by M.W.Vetting, 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, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, 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) 28.48 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 110.837, 124.854, 139.093, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 17.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop (pdb code 4g8t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop, PDB code: 4g8t:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4g8t

Go back to Sodium Binding Sites List in 4g8t
Sodium binding site 1 out of 4 in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop


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 A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:23.0
occ:1.00
 OD1 A:ASN285 2.3 25.4 1.0
OD1 A:ASP231 2.4 15.6 1.0
OD2 A:ASP257 2.5 14.3 1.0
OD2 A:ASP231 2.8 20.1 1.0
CG A:ASP231 2.9 14.8 1.0
OE2 A:GLU256 3.0 20.0 1.0
ND2 A:ASN233 3.3 17.4 1.0
CG A:ASP257 3.4 13.1 1.0
CB A:ASP257 3.5 11.6 1.0
CG A:ASN285 3.6 17.6 1.0
O A:HOH697 3.6 20.9 1.0
CG A:GLU256 3.6 13.1 1.0
CD A:GLU256 3.6 18.4 1.0
O A:HOH654 3.8 20.4 1.0
CG A:ASN233 3.9 14.0 1.0
CA A:ASN233 4.1 13.1 1.0
SD A:MET286 4.2 13.5 1.0
ND2 A:ASN285 4.4 19.6 1.0
CB A:ASP231 4.4 13.1 1.0
CG A:MET286 4.4 10.2 1.0
N A:ASN233 4.4 11.6 1.0
OD1 A:ASN233 4.4 15.7 1.0
N A:ASN285 4.4 12.1 1.0
OD1 A:ASP257 4.5 13.8 1.0
CB A:ASN233 4.6 11.9 1.0
CB A:ASN285 4.6 14.1 1.0
OE1 A:GLU256 4.7 19.5 1.0
CA A:ASP257 4.8 9.5 1.0
N A:ASP257 4.8 11.7 1.0
NZ A:LYS203 4.8 15.9 1.0
CB A:GLU256 4.8 10.5 1.0
C A:GLU256 4.8 13.5 1.0
O A:GLU256 4.9 14.2 1.0

Sodium binding site 2 out of 4 in 4g8t

Go back to Sodium Binding Sites List in 4g8t
Sodium binding site 2 out of 4 in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop


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 A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:26.4
occ:1.00
 OD1 B:ASN285 2.3 31.6 1.0
OD1 B:ASP231 2.5 17.7 1.0
OD2 B:ASP257 2.5 15.1 1.0
OE2 B:GLU256 2.5 22.3 1.0
OD2 B:ASP231 2.7 20.4 1.0
CG B:ASP231 2.9 17.9 1.0
CD B:GLU256 3.3 20.2 1.0
ND2 B:ASN233 3.4 15.7 1.0
CG B:GLU256 3.4 16.1 1.0
CG B:ASP257 3.4 12.9 1.0
O B:HOH640 3.5 21.7 1.0
CG B:ASN285 3.5 21.6 1.0
O B:HOH685 3.6 23.0 1.0
CB B:ASP257 3.6 15.0 1.0
CG B:ASN233 4.0 16.0 1.0
N B:ASN285 4.3 12.0 1.0
CB B:ASP231 4.3 13.8 1.0
CA B:ASN233 4.3 16.2 1.0
ND2 B:ASN285 4.4 19.3 1.0
OE1 B:GLU256 4.4 23.1 1.0
SD B:MET286 4.5 14.9 1.0
CG B:MET286 4.5 15.2 1.0
CB B:ASN285 4.5 14.5 1.0
OD1 B:ASN233 4.5 15.3 1.0
N B:ASN233 4.6 14.7 1.0
OD1 B:ASP257 4.6 14.0 1.0
CB B:GLU256 4.7 15.1 1.0
N B:ASP257 4.8 14.4 1.0
CB B:ASN233 4.8 14.5 1.0
C B:GLU256 4.8 14.5 1.0
NZ B:LYS203 4.8 17.0 1.0
CA B:ASP257 4.8 13.5 1.0
O B:GLU256 4.9 16.6 1.0
CA B:ASN285 4.9 15.9 1.0

Sodium binding site 3 out of 4 in 4g8t

Go back to Sodium Binding Sites List in 4g8t
Sodium binding site 3 out of 4 in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop


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 A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:33.7
occ:1.00
 OE2 C:GLU256 2.1 22.4 1.0
O C:HOH746 2.1 23.6 1.0
O C:HOH1044 2.1 16.4 1.0
OD1 C:ASN285 2.2 35.5 1.0
OD2 C:ASP231 2.2 17.8 1.0
O C:HOH728 2.4 22.9 1.0
CG C:ASP231 3.1 16.7 1.0
CD C:GLU256 3.1 18.7 1.0
CG C:ASN285 3.1 24.2 1.0
ND2 C:ASN285 3.4 17.9 1.0
OD1 C:ASP231 3.4 16.1 1.0
ND2 C:ASN233 3.8 16.3 1.0
CG C:GLU256 3.9 16.1 1.0
NZ C:LYS203 3.9 18.9 1.0
OE1 C:GLU256 4.0 20.3 1.0
NZ C:LYS201 4.0 18.3 1.0
CD2 C:HIS335 4.1 18.5 1.0
OD2 C:ASP257 4.2 17.6 1.0
CB C:ASP231 4.3 15.7 1.0
O C:HOH684 4.5 18.9 1.0
OH C:TYR146 4.5 24.2 1.0
CB C:ASN285 4.5 16.6 1.0
CG C:ASN233 4.6 18.4 1.0
OD1 C:ASN233 4.7 19.2 1.0
NE2 C:HIS335 4.8 19.5 1.0
O C:HOH713 4.8 22.9 1.0
CD1 C:LEU307 4.8 19.4 1.0
N C:ASN285 4.9 17.6 1.0
CE C:LYS203 5.0 25.3 1.0

Sodium binding site 4 out of 4 in 4g8t

Go back to Sodium Binding Sites List in 4g8t
Sodium binding site 4 out of 4 in the Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop


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 A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:40.8
occ:1.00
 O D:HOH1072 2.1 15.9 1.0
OD2 D:ASP231 2.2 15.9 1.0
OD1 D:ASN285 2.2 42.3 1.0
OE2 D:GLU256 2.2 19.8 1.0
O D:HOH753 2.2 30.3 1.0
O D:HOH715 2.3 23.4 1.0
CG D:ASP231 3.0 16.2 1.0
CG D:ASN285 3.2 27.5 1.0
OD1 D:ASP231 3.2 14.3 1.0
CD D:GLU256 3.2 18.1 1.0
ND2 D:ASN233 3.6 20.3 1.0
ND2 D:ASN285 3.7 23.7 1.0
NZ D:LYS203 3.8 18.5 1.0
CG D:GLU256 3.9 11.5 1.0
NZ D:LYS201 4.0 30.4 1.0
OE1 D:GLU256 4.1 20.9 1.0
OD2 D:ASP257 4.2 15.7 1.0
CB D:ASP231 4.2 11.9 1.0
CD2 D:HIS335 4.3 22.9 1.0
CG D:ASN233 4.4 23.5 1.0
CB D:ASN285 4.4 15.9 1.0
O D:HOH626 4.6 18.7 1.0
OH D:TYR146 4.6 21.4 1.0
OD1 D:ASN233 4.6 17.9 1.0
CE D:LYS201 4.7 24.1 1.0
CE D:LYS203 4.9 22.7 1.0
N D:ASN285 4.9 14.9 1.0
NE2 D:HIS335 4.9 20.2 1.0

Reference:

M.W.Vetting, 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, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Glucarate Dehydratase Related Protein, From Actinobacillus Succinogenes, Target Efi-502312, with Sodium and Sulfate Bound, Ordered Loop To Be Published.
Page generated: Mon Oct 7 15:31:55 2024

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