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Magnesium in PDB 3gah: Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp

Enzymatic activity of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp

All present enzymatic activity of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp:
2.5.1.17;

Protein crystallography data

The structure of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp, PDB code: 3gah 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 / 1.17
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 80.814, 80.814, 89.492, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 18.2

Other elements in 3gah:

The structure of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp also contains other interesting chemical elements:

Cobalt (Co) 2 atoms
Potassium (K) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp (pdb code 3gah). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp, PDB code: 3gah:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3gah

Go back to Magnesium Binding Sites List in 3gah
Magnesium binding site 1 out of 2 in the Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg189

b:8.5
occ:1.00
 O1A A:ATP999 2.0 8.7 1.0
O2G A:ATP999 2.0 8.8 1.0
O A:HOH193 2.0 8.9 1.0
O1B A:ATP999 2.1 9.1 1.0
O A:HOH192 2.1 9.3 1.0
PB A:ATP999 3.2 8.8 1.0
PA A:ATP999 3.2 8.6 1.0
PG A:ATP999 3.3 9.1 1.0
O3A A:ATP999 3.5 9.2 1.0
O3B A:ATP999 3.5 9.7 1.0
NZ A:LYS23 3.8 10.4 1.0
K A:K191 4.0 10.2 1.0
O3G A:ATP999 4.0 10.2 1.0
O2A A:ATP999 4.2 10.1 1.0
O A:HOH194 4.2 11.5 1.0
O5' A:ATP999 4.3 8.4 1.0
O1G A:ATP999 4.5 10.7 1.0
N7 A:ATP999 4.5 8.2 1.0
O2B A:ATP999 4.5 9.9 1.0
C8 A:ATP999 4.7 9.1 1.0
CE A:LYS23 4.8 9.2 1.0

Magnesium binding site 2 out of 2 in 3gah

Go back to Magnesium Binding Sites List in 3gah
Magnesium binding site 2 out of 2 in the Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A F112H Variant Pduo-Type Atp:Corrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Cobalamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:12.2
occ:1.00
 O A:HIS82 2.6 16.0 1.0
O A:HOH300 2.7 21.1 1.0
O A:ASP79 2.7 14.5 1.0
O A:PRO76 2.8 14.3 1.0
O A:HOH297 2.8 23.9 1.0
O A:ALA77 2.9 19.0 1.0
C A:ALA77 3.4 16.8 1.0
C A:ASP79 3.5 15.6 1.0
CA A:ALA77 3.7 16.0 1.0
C A:HIS82 3.7 14.2 1.0
C A:PRO76 3.8 13.0 1.0
N A:ASP79 4.0 17.0 1.0
CG2 A:THR75 4.0 13.7 1.0
N A:ALA77 4.2 13.5 1.0
N A:GLU80 4.3 15.1 1.0
CA A:ASP79 4.3 14.8 1.0
N A:ASP78 4.4 16.7 1.0
CA A:GLU80 4.4 16.1 1.0
O A:HOH365 4.4 37.1 1.0
O A:HOH368 4.5 34.8 1.0
CA A:SER83 4.6 14.6 0.5
CA A:HIS82 4.6 13.5 1.0
N A:HIS82 4.6 13.4 1.0
N A:SER83 4.6 14.7 0.5
C A:ASP78 4.6 18.9 1.0
O A:HOH294 4.7 23.7 1.0
N A:SER83 4.7 14.1 0.5
O A:HOH333 4.8 30.2 1.0
CB A:HIS82 4.8 13.7 1.0
CA A:SER83 4.9 12.8 0.5
CB A:ASP79 4.9 16.0 1.0
C A:GLU80 5.0 15.0 1.0
CA A:ASP78 5.0 18.2 1.0

Reference:

P.E.Mera, M.St Maurice, I.Rayment, J.C.Escalante-Semerena. Residue PHE112 of the Human-Type Corrinoid Adenosyltransferase (Pduo) Enzyme of Lactobacillus Reuteri Is Critical to the Formation of the Four-Coordinate Co(II) Corrinoid Substrate and to the Activity of the Enzyme. Biochemistry V. 48 3138 2009.
ISSN: ISSN 0006-2960
PubMed: 19236001
DOI: 10.1021/BI9000134
Page generated: Wed Aug 14 14:41:55 2024

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