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Sodium in PDB 5ydb: Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution

Enzymatic activity of Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution

All present enzymatic activity of Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution:
4.2.1.10;

Protein crystallography data

The structure of Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution, PDB code: 5ydb was solved by N.Iqbal, P.Kaur, S.Sharma, T.P.Singh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.56 / 1.76
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 139.117, 139.117, 79.587, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 24.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution (pdb code 5ydb). 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 the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution, PDB code: 5ydb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5ydb

Go back to Sodium Binding Sites List in 5ydb
Sodium binding site 1 out of 4 in the Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution


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 the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:48.7
occ:1.00
 SG A:CYS127 2.6 50.7 1.0
NE2 A:HIS107 3.3 56.3 1.0
CB A:CYS127 3.4 42.3 1.0
CD2 A:HIS107 3.6 56.4 1.0
CG1 A:VAL125 3.9 35.1 1.0
NA B:NA201 4.3 40.6 1.0
CG2 A:VAL106 4.4 43.1 1.0
N A:CYS127 4.4 33.4 1.0
CB B:VAL125 4.5 33.9 1.0
CE1 A:HIS107 4.5 61.2 1.0
CA A:CYS127 4.5 34.2 1.0
CB A:VAL125 4.8 32.6 1.0
CG A:HIS107 4.9 53.5 1.0
O B:VAL125 4.9 32.9 1.0
CG1 B:VAL125 5.0 36.8 1.0

Sodium binding site 2 out of 4 in 5ydb

Go back to Sodium Binding Sites List in 5ydb
Sodium binding site 2 out of 4 in the Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution


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 the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:40.6
occ:1.00
 SG B:CYS127 2.6 50.3 1.0
CB B:CYS127 3.3 36.1 1.0
NE2 B:HIS107 3.5 66.7 1.0
CD2 B:HIS107 3.6 61.0 1.0
O B:HOH334 4.1 70.7 1.0
O B:HOH339 4.2 56.2 1.0
CG1 B:VAL125 4.2 36.8 1.0
NA A:NA201 4.3 48.7 1.0
CA B:CYS127 4.5 32.9 1.0
CB A:VAL125 4.6 32.6 1.0
N B:CYS127 4.6 31.8 1.0
CE1 B:HIS107 4.8 67.5 1.0
CG1 B:VAL106 4.8 49.1 1.0
CG B:HIS107 4.9 57.4 1.0
CG2 A:VAL125 4.9 36.1 1.0

Sodium binding site 3 out of 4 in 5ydb

Go back to Sodium Binding Sites List in 5ydb
Sodium binding site 3 out of 4 in the Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution


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 the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na201

b:43.1
occ:1.00
 SG C:CYS127 2.6 53.1 1.0
NE2 C:HIS107 2.7 67.7 1.0
CD2 C:HIS107 3.4 63.1 1.0
CB C:CYS127 3.6 39.8 1.0
CG2 C:VAL106 3.8 48.2 1.0
CE1 C:HIS107 3.8 62.7 1.0
CG1 C:VAL125 3.9 37.4 1.0
NA D:NA201 4.3 42.7 1.0
N C:CYS127 4.6 34.1 1.0
CB D:VAL125 4.6 38.4 1.0
CG C:HIS107 4.6 57.7 1.0
CA C:CYS127 4.6 35.5 1.0
ND1 C:HIS107 4.8 58.8 1.0
CB C:VAL125 4.8 38.1 1.0
NE2 D:HIS107 4.9 58.7 1.0
CG2 D:VAL125 5.0 41.0 1.0

Sodium binding site 4 out of 4 in 5ydb

Go back to Sodium Binding Sites List in 5ydb
Sodium binding site 4 out of 4 in the Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution


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 the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na201

b:42.7
occ:1.00
 SG D:CYS127 2.4 51.4 1.0
NE2 D:HIS107 3.2 58.7 1.0
CB D:CYS127 3.4 38.6 1.0
CD2 D:HIS107 3.4 54.2 1.0
CG2 D:VAL106 3.9 48.1 1.0
CG1 D:VAL125 4.3 41.3 1.0
NA C:NA201 4.3 43.1 1.0
CB C:VAL125 4.3 38.1 1.0
CE1 D:HIS107 4.4 57.8 1.0
CA D:CYS127 4.5 37.3 1.0
N D:CYS127 4.5 36.8 1.0
CG D:HIS107 4.7 50.3 1.0
CG1 C:VAL125 4.8 37.4 1.0
O C:VAL125 4.9 37.9 1.0
CG2 C:VAL125 4.9 40.2 1.0

Reference:

N.Iqbal, P.Kaur, S.Sharma, T.P.Singh. Crystal Structure of the Complex of Type II Dehydroquinate Dehydratase From Acinetobacter Baumannii with Dehydroquinic Acid at 1.76 Angstrom Resolution To Be Published.
Page generated: Tue Oct 8 01:22:23 2024

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