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Cobalt in PDB 1r8k: Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium]

Enzymatic activity of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium]

All present enzymatic activity of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium]:
1.1.1.262;

Protein crystallography data

The structure of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium], PDB code: 1r8k was solved by J.Osipiuk, P.Quartey, S.Moy, F.Collart, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.54 / 2.10
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 119.954, 119.954, 55.541, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.4

Other elements in 1r8k:

The structure of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium] also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium] (pdb code 1r8k). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium], PDB code: 1r8k:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 1r8k

Go back to Cobalt Binding Sites List in 1r8k
Cobalt binding site 1 out of 2 in the Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium]


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co902

b:24.2
occ:1.00
O A:HOH995 2.1 17.8 1.0
NE2 A:HIS266 2.2 23.9 1.0
O B:HOH1006 2.2 31.4 1.0
NE2 B:HIS211 2.3 30.1 1.0
O A:HOH1015 2.3 22.9 1.0
NE2 A:HIS166 2.3 25.2 1.0
CE1 B:HIS211 2.9 31.9 1.0
CD2 A:HIS166 2.9 24.1 1.0
CD2 A:HIS266 3.2 23.3 1.0
CE1 A:HIS266 3.2 21.9 1.0
CD2 B:HIS211 3.4 30.7 1.0
CE1 A:HIS166 3.5 24.8 1.0
ND1 B:HIS211 4.1 31.2 1.0
O A:HOH1065 4.2 33.1 1.0
CG A:HIS166 4.2 24.6 1.0
ND1 A:HIS266 4.3 23.3 1.0
CG A:HIS266 4.3 21.6 1.0
CD1 A:LEU270 4.3 17.0 1.0
CG B:HIS211 4.4 28.7 1.0
ND1 A:HIS166 4.4 25.4 1.0
OD2 B:ASP247 4.4 23.3 1.0

Cobalt binding site 2 out of 2 in 1r8k

Go back to Cobalt Binding Sites List in 1r8k
Cobalt binding site 2 out of 2 in the Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium]


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Pdxa Protein; Nad-Dependent Dehydrogenase/Carboxylase; Subunit of Pyridoxine Phosphate Biosynthetic Protein Pdxj- Pdxa [Salmonella Typhimurium] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co901

b:28.0
occ:1.00
NE2 A:HIS211 2.2 28.5 1.0
O B:HOH999 2.3 20.0 1.0
O A:HOH1003 2.3 23.6 1.0
NE2 B:HIS166 2.3 31.4 1.0
NE2 B:HIS266 2.4 26.5 1.0
O B:HOH1008 2.5 29.7 1.0
CE1 A:HIS211 2.9 28.6 1.0
CD2 B:HIS166 3.0 30.7 1.0
CD2 B:HIS266 3.2 27.3 1.0
CD2 A:HIS211 3.3 28.3 1.0
CE1 B:HIS166 3.5 31.5 1.0
CE1 B:HIS266 3.5 25.7 1.0
ND1 A:HIS211 4.1 28.5 1.0
CG B:HIS166 4.2 33.2 1.0
CG A:HIS211 4.3 27.4 1.0
OD2 B:ASP296 4.4 40.5 1.0
CD1 B:LEU270 4.4 22.6 1.0
ND1 B:HIS166 4.5 32.2 1.0
CG B:HIS266 4.5 26.7 1.0
ND1 B:HIS266 4.6 25.4 1.0
OD2 A:ASP247 4.6 29.8 1.0
OD1 B:ASP296 4.6 39.0 1.0
CG B:ASP296 4.9 39.7 1.0

Reference:

J.Osipiuk, P.Quartey, S.Moy, F.Collart, A.Joachimiak. Crystal Structure of Nad-Dependent Dehydrogenase/Carboxylase of Salmonella Typhimurium To Be Published.
Page generated: Sun Dec 13 10:35:51 2020

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