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Sodium in PDB 2bdr: Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49

Enzymatic activity of Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49

All present enzymatic activity of Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49:
3.5.3.19;

Protein crystallography data

The structure of Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49, PDB code: 2bdr was solved by F.Forouhar, M.Abashidze, S.Jayaraman, C.K.Ho, K.Conover, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomicsconsortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.13 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.027, 55.268, 81.843, 90.00, 93.98, 90.00
R / Rfree (%) 19.8 / 21.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49 (pdb code 2bdr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49, PDB code: 2bdr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2bdr

Go back to Sodium Binding Sites List in 2bdr
Sodium binding site 1 out of 3 in the Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49


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 Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:47.4
occ:1.00
 O A:MSE66 2.4 16.4 1.0
CD A:PRO67 2.9 16.7 1.0
C A:MSE66 3.0 15.5 1.0
N A:PRO67 3.2 15.1 1.0
CA A:MSE66 4.3 16.1 1.0
CG A:PRO67 4.4 16.6 1.0
CB A:MSE66 4.4 18.9 1.0
CA A:PRO67 4.5 15.1 1.0
N A:MSE66 4.8 14.6 1.0
CB A:PRO67 4.9 14.7 1.0

Sodium binding site 2 out of 3 in 2bdr

Go back to Sodium Binding Sites List in 2bdr
Sodium binding site 2 out of 3 in the Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49


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 Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:22.4
occ:1.00
 NE2 A:GLN81 2.6 10.6 1.0
O A:HOH473 2.6 30.2 1.0
NE2 A:HIS76 2.8 23.1 1.0
OE2 A:GLU74 2.8 29.7 1.0
O A:HOH487 2.8 34.2 1.0
CE1 A:HIS126 3.2 24.8 1.0
CD A:GLU74 3.3 24.1 1.0
CE1 A:HIS76 3.4 21.7 1.0
CD A:GLN81 3.5 10.3 1.0
ND1 A:HIS126 3.6 25.6 1.0
CD2 A:HIS76 3.7 21.3 1.0
CG A:GLU74 3.7 19.0 1.0
OE1 A:GLN81 3.7 14.2 1.0
OE1 A:GLU74 4.0 26.7 1.0
NE2 A:HIS126 4.2 25.5 1.0
ND1 A:HIS76 4.4 19.2 1.0
O A:HOH441 4.6 16.2 1.0
CG A:HIS76 4.6 17.0 1.0
O A:HOH566 4.6 37.8 1.0
CG A:HIS126 4.7 19.2 1.0
CG A:GLN81 4.9 8.6 1.0
O A:HOH461 4.9 17.5 1.0
CE1 A:PHE83 5.0 11.8 1.0
CD2 A:HIS126 5.0 22.2 1.0

Sodium binding site 3 out of 3 in 2bdr

Go back to Sodium Binding Sites List in 2bdr
Sodium binding site 3 out of 3 in the Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49


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 Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:48.3
occ:1.00
 O A:HOH452 2.7 33.1 1.0
ND2 A:ASN148 2.8 19.6 1.0
CG A:ASN148 3.0 17.1 1.0
OD1 A:ASN148 3.3 21.8 1.0
OD1 A:ASP151 3.6 16.9 1.0
CB A:ASN148 3.7 15.1 1.0
O A:CYS150 4.6 14.5 1.0
O A:HOH448 4.8 22.8 1.0
CG A:ASP151 4.9 15.7 1.0
O A:HOH482 4.9 29.3 1.0

Reference:

F.Forouhar, M.Abashidze, S.Jayaraman, C.K.Ho, K.Conover, T.B.Acton, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of the Putative Ureidoglycolate Hydrolase PP4288 From Pseudomonas Putida, Northeast Structural Genomics Target PPR49 To Be Published.
Page generated: Sun Aug 17 10:10:06 2025

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