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Sodium in PDB 3ci3: Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi

Enzymatic activity of Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi

All present enzymatic activity of Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi:
2.5.1.17;

Protein crystallography data

The structure of Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi, PDB code: 3ci3 was solved by M.St.Maurice, P.E.Mera, J.C.Escalante-Semerena, I.Rayment, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.11
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 67.965, 67.965, 110.941, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 18

Other elements in 3ci3:

The structure of Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi (pdb code 3ci3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi, PDB code: 3ci3:

Sodium binding site 1 out of 1 in 3ci3

Go back to Sodium Binding Sites List in 3ci3
Sodium binding site 1 out of 1 in the Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Partial Adenosylcobalamin and Pppi within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na189

b:15.9
occ:1.00
 O1G A:3PO901 2.5 9.9 0.9
O1A A:3PO901 2.5 7.3 0.9
O A:ILE3 2.6 13.4 1.0
O2A A:3PO901 2.7 9.7 0.9
PA A:3PO901 3.1 8.1 0.9
O3G A:3PO901 3.3 8.1 0.9
PG A:3PO901 3.3 7.9 0.9
C A:ILE3 3.6 12.2 1.0
C35 A:B12800 3.6 10.3 1.0
O A:HOH911 3.7 8.6 1.0
MG A:MG190 3.8 7.0 1.0
O3A A:3PO901 3.8 10.0 0.9
O A:HOH906 3.9 10.3 1.0
CA A:TYR4 3.9 11.2 1.0
O28 A:B12800 4.0 13.5 1.0
N A:TYR4 4.2 12.6 1.0
O3B A:3PO901 4.2 8.1 0.9
N A:THR5 4.4 11.1 1.0
O5' A:3PO901 4.5 8.6 0.9
C5 A:B12800 4.6 9.6 1.0
PB A:3PO901 4.6 8.0 0.9
O2G A:3PO901 4.6 10.2 0.9
C37 A:B12800 4.7 8.3 1.0
CA A:ILE3 4.8 13.2 1.0
C A:TYR4 4.8 11.4 1.0
O1B A:3PO901 4.8 7.9 0.9
CB A:TYR4 4.8 11.6 1.0
CB A:ILE3 4.9 13.0 1.0

Reference:

M.St Maurice, P.Mera, K.Park, T.C.Brunold, J.C.Escalante-Semerena, I.Rayment. Structural Characterization of A Human-Type Corrinoid Adenosyltransferase Confirms That Coenzyme B12 Is Synthesized Through A Four-Coordinate Intermediate. Biochemistry V. 47 5755 2008.
ISSN: ISSN 0006-2960
PubMed: 18452306
DOI: 10.1021/BI800132D
Page generated: Mon Oct 7 07:09:03 2024

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