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Cobalt 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:

Magnesium (Mg) 2 atoms
Potassium (K) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt 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 Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 3gah

Go back to Cobalt Binding Sites List in 3gah
Cobalt 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 Cobalt with other atoms in the Co 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:Co800

b:8.1
occ:0.50
 CO A:B12800 0.0 8.1 0.5
CO A:B12800 0.3 16.2 0.5
N22 A:B12800 1.8 19.8 0.5
N21 A:B12800 1.8 21.1 0.5
N24 A:B12800 1.9 8.4 0.5
N21 A:B12800 1.9 6.8 0.5
N22 A:B12800 1.9 6.0 0.5
N23 A:B12800 1.9 7.1 0.5
N24 A:B12800 1.9 18.6 0.5
N23 A:B12800 2.0 20.3 0.5
C19 A:B12800 2.8 20.0 0.5
C1 A:B12800 2.8 16.2 0.5
C9 A:B12800 2.8 6.5 0.5
C19 A:B12800 2.8 7.8 0.5
C9 A:B12800 2.9 16.6 0.5
C4 A:B12800 2.9 16.5 0.5
C11 A:B12800 2.9 8.2 0.5
C1 A:B12800 2.9 8.6 0.5
C14 A:B12800 2.9 13.4 0.5
C11 A:B12800 2.9 16.4 0.5
C4 A:B12800 2.9 7.3 0.5
C6 A:B12800 2.9 15.4 0.5
C16 A:B12800 3.0 10.0 0.5
C6 A:B12800 3.0 6.6 0.5
C14 A:B12800 3.0 12.3 0.5
C16 A:B12800 3.0 19.7 0.5
C10 A:B12800 3.3 8.2 0.5
C10 A:B12800 3.3 18.2 0.5
C5' A:ATP999 3.3 8.9 1.0
C5 A:B12800 3.3 7.0 0.5
C15 A:B12800 3.3 11.2 0.5
C5 A:B12800 3.3 17.7 0.5
C15 A:B12800 3.5 19.7 0.5
C20 A:B12800 3.5 11.0 0.5
C20 A:B12800 3.5 16.5 0.5
C4' A:ATP999 3.8 9.6 1.0
C2 A:B12800 4.0 15.7 0.5
C18 A:B12800 4.1 15.1 0.5
C8 A:B12800 4.1 7.4 0.5
C3 A:B12800 4.1 15.6 0.5
C13 A:B12800 4.2 17.0 0.5
C8 A:B12800 4.2 15.9 0.5
C2 A:B12800 4.2 8.6 0.5
C18 A:B12800 4.2 11.2 0.5
C12 A:B12800 4.2 10.9 0.5
C3 A:B12800 4.2 9.9 0.5
C7 A:B12800 4.2 14.9 0.5
C7 A:B12800 4.2 5.9 0.5
C12 A:B12800 4.2 15.3 0.5
C17 A:B12800 4.3 9.5 0.5
C13 A:B12800 4.3 18.7 0.5
C17 A:B12800 4.3 18.3 0.5
C26 A:B12800 4.4 13.6 0.5
O4' A:ATP999 4.6 9.0 1.0
C41 A:B12800 4.6 9.1 0.5
C26 A:B12800 4.6 10.8 0.5
O5' A:ATP999 4.7 8.4 1.0
C48 A:B12800 4.8 21.5 0.5
C35 A:B12800 4.8 7.0 0.5
C35 A:B12800 4.8 17.2 0.5
C53 A:B12800 4.9 9.9 0.5
C37 A:B12800 4.9 14.1 0.5
C37 A:B12800 4.9 7.5 0.5
C48 A:B12800 4.9 21.6 0.5
O3' A:ATP999 4.9 10.2 1.0
C41 A:B12800 4.9 14.8 0.5
C47 A:B12800 4.9 11.2 0.5
C53 A:B12800 5.0 17.9 0.5
C54 A:B12800 5.0 17.6 0.5

Cobalt binding site 2 out of 2 in 3gah

Go back to Cobalt Binding Sites List in 3gah
Cobalt 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 Cobalt with other atoms in the Co 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:Co800

b:16.2
occ:0.50
 CO A:B12800 0.0 16.2 0.5
CO A:B12800 0.3 8.1 0.5
N24 A:B12800 1.7 8.4 0.5
N24 A:B12800 1.8 18.6 0.5
N21 A:B12800 1.8 6.8 0.5
N21 A:B12800 1.9 21.1 0.5
N23 A:B12800 1.9 7.1 0.5
N23 A:B12800 1.9 20.3 0.5
N22 A:B12800 2.0 19.8 0.5
N22 A:B12800 2.0 6.0 0.5
C19 A:B12800 2.6 20.0 0.5
C19 A:B12800 2.7 7.8 0.5
C1 A:B12800 2.8 16.2 0.5
C16 A:B12800 2.8 10.0 0.5
C1 A:B12800 2.8 8.6 0.5
C16 A:B12800 2.9 19.7 0.5
C14 A:B12800 2.9 13.4 0.5
C4 A:B12800 2.9 16.5 0.5
C4 A:B12800 2.9 7.3 0.5
C11 A:B12800 2.9 8.2 0.5
C11 A:B12800 2.9 16.4 0.5
C14 A:B12800 2.9 12.3 0.5
C9 A:B12800 3.0 6.5 0.5
C9 A:B12800 3.0 16.6 0.5
C6 A:B12800 3.0 15.4 0.5
C6 A:B12800 3.1 6.6 0.5
C5' A:ATP999 3.1 8.9 1.0
C15 A:B12800 3.3 11.2 0.5
C15 A:B12800 3.3 19.7 0.5
C10 A:B12800 3.3 8.2 0.5
C10 A:B12800 3.4 18.2 0.5
C5 A:B12800 3.4 7.0 0.5
C5 A:B12800 3.4 17.7 0.5
C20 A:B12800 3.5 11.0 0.5
C4' A:ATP999 3.5 9.6 1.0
C20 A:B12800 3.6 16.5 0.5
C18 A:B12800 4.0 15.1 0.5
C2 A:B12800 4.0 15.7 0.5
C18 A:B12800 4.0 11.2 0.5
C17 A:B12800 4.1 9.5 0.5
C2 A:B12800 4.1 8.6 0.5
C17 A:B12800 4.1 18.3 0.5
C3 A:B12800 4.1 15.6 0.5
C13 A:B12800 4.2 17.0 0.5
C3 A:B12800 4.2 9.9 0.5
C13 A:B12800 4.2 18.7 0.5
C12 A:B12800 4.2 10.9 0.5
C12 A:B12800 4.2 15.3 0.5
C8 A:B12800 4.3 7.4 0.5
C26 A:B12800 4.3 13.6 0.5
C8 A:B12800 4.3 15.9 0.5
C7 A:B12800 4.3 14.9 0.5
C7 A:B12800 4.3 5.9 0.5
O4' A:ATP999 4.4 9.0 1.0
C26 A:B12800 4.5 10.8 0.5
O5' A:ATP999 4.5 8.4 1.0
O3' A:ATP999 4.6 10.2 1.0
C3' A:ATP999 4.7 9.0 1.0
C54 A:B12800 4.8 17.6 0.5
C53 A:B12800 4.8 9.9 0.5
C48 A:B12800 4.8 21.5 0.5
C53 A:B12800 4.8 17.9 0.5
C54 A:B12800 4.8 12.2 0.5
C41 A:B12800 4.9 9.1 0.5
C47 A:B12800 4.9 11.2 0.5
C35 A:B12800 4.9 7.0 0.5
C35 A:B12800 4.9 17.2 0.5
C37 A:B12800 4.9 14.1 0.5
C37 A:B12800 4.9 7.5 0.5
C47 A:B12800 4.9 21.3 0.5
O2A A:ATP999 5.0 10.1 1.0
C48 A:B12800 5.0 21.6 0.5

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: Tue Jul 30 15:59:09 2024

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