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Magnesium in PDB 2r6x: Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp

Enzymatic activity of Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp

All present enzymatic activity of Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp:
2.5.1.17;

Protein crystallography data

The structure of Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp, PDB code: 2r6x 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 / 2.61
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 64.772, 64.772, 169.438, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp (pdb code 2r6x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp, PDB code: 2r6x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2r6x

Go back to Magnesium Binding Sites List in 2r6x
Magnesium binding site 1 out of 4 in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with 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 D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg189

b:13.8
occ:1.00
 OD2 A:ASP160 2.6 24.2 1.0
OD1 A:ASP160 2.9 23.2 1.0
CG A:ASP160 3.1 24.7 1.0
O A:HOH1008 4.0 32.1 1.0
MG A:MG190 4.2 26.3 1.0
CB A:ASP160 4.6 26.3 1.0

Magnesium binding site 2 out of 4 in 2r6x

Go back to Magnesium Binding Sites List in 2r6x
Magnesium binding site 2 out of 4 in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with 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 D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg190

b:26.3
occ:1.00
 OD1 A:ASN156 2.1 28.2 1.0
CG A:ASN156 3.3 28.1 1.0
O A:ASN156 3.8 28.2 1.0
O A:HOH1008 4.1 32.1 1.0
ND2 A:ASN156 4.1 29.0 1.0
MG A:MG189 4.2 13.8 1.0
OE1 A:GLU135 4.3 28.5 1.0
OG A:SER159 4.4 25.3 1.0
CB A:ASN156 4.4 27.8 1.0
C A:ASN156 4.5 27.7 1.0
CA A:ASN156 4.5 27.8 1.0
OE2 A:GLU135 4.6 26.2 1.0
OD1 A:ASP160 4.6 23.2 1.0
CD A:GLU135 4.9 26.9 1.0
NH2 A:ARG132 4.9 31.6 1.0
O A:HOH1055 4.9 33.6 1.0
OD2 A:ASP160 5.0 24.2 1.0

Magnesium binding site 3 out of 4 in 2r6x

Go back to Magnesium Binding Sites List in 2r6x
Magnesium binding site 3 out of 4 in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg189

b:31.0
occ:1.00
 OD1 B:ASN156 2.1 31.4 1.0
O B:HOH999 2.2 26.3 1.0
CG B:ASN156 3.2 31.0 1.0
ND2 B:ASN156 3.8 32.0 1.0
O B:ASN156 4.1 31.0 1.0
NH2 B:ARG132 4.1 23.8 0.8
OE1 B:GLU135 4.2 29.4 1.0
OE2 B:GLU135 4.3 28.3 1.0
O B:HOH1023 4.3 26.0 1.0
CB B:ASN156 4.5 30.6 1.0
OG B:SER159 4.6 27.3 1.0
CA B:ASN156 4.6 30.6 1.0
CD B:GLU135 4.7 28.9 1.0
C B:ASN156 4.7 30.4 1.0
OD1 B:ASP160 4.8 29.7 1.0
O B:HOH1011 4.9 25.0 1.0
NE B:ARG132 5.0 21.7 0.8
CZ B:ARG132 5.0 22.2 0.8

Magnesium binding site 4 out of 4 in 2r6x

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Magnesium binding site 4 out of 4 in the Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A D35N Variant Pduo-Type Atp:Co(I)Rrinoid Adenosyltransferase From Lactobacillus Reuteri Complexed with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg190

b:25.0
occ:1.00
 O3G B:ATP995 2.5 33.2 1.0
O2A B:ATP995 2.8 33.3 1.0
O B:ILE3 3.0 49.5 1.0
O1G B:ATP995 3.2 32.1 1.0
PG B:ATP995 3.3 33.0 1.0
O B:HOH1039 3.4 30.9 1.0
O1A B:ATP995 3.5 33.2 1.0
PA B:ATP995 3.6 32.1 1.0
C B:ILE3 3.9 49.5 1.0
O3B B:ATP995 4.0 31.0 1.0
CA B:TYR4 4.0 49.2 1.0
N B:TYR4 4.4 49.1 1.0
O3A B:ATP995 4.6 31.9 1.0
N B:THR5 4.7 49.0 1.0
O2G B:ATP995 4.7 28.2 1.0
CB B:TYR4 4.7 49.0 1.0
PB B:ATP995 4.9 31.0 1.0
O5' B:ATP995 4.9 31.1 1.0
C B:TYR4 4.9 49.3 1.0

Reference:

P.E.Mera, M.St Maurice, I.Rayment, J.C.Escalante-Semerena. Structural and Functional Analyses of the Human-Type Corrinoid Adenosyltransferase (Pduo) From Lactobacillus Reuteri. Biochemistry V. 46 13829 2007.
ISSN: ISSN 0006-2960
PubMed: 17988155
DOI: 10.1021/BI701622J
Page generated: Wed Aug 14 03:16:44 2024

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