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Magnesium in PDB 4hut: Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp

Enzymatic activity of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp

All present enzymatic activity of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp:
2.5.1.17;

Protein crystallography data

The structure of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp, PDB code: 4hut was solved by T.C.Moore, S.A.Newmister, I.Rayment, J.C.Escalante-Semerena, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.862, 74.223, 92.396, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 23.2

Other elements in 4hut:

The structure of Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp also contains other interesting chemical elements:

Cobalt (Co) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp (pdb code 4hut). 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 Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp, PDB code: 4hut:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4hut

Go back to Magnesium Binding Sites List in 4hut
Magnesium binding site 1 out of 2 in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin 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 Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:27.6
occ:1.00
 O2A A:ATP202 2.0 28.6 1.0
OE2 A:GLU128 2.0 24.4 1.0
O A:HOH302 2.1 25.7 1.0
O2B A:ATP202 2.1 25.7 1.0
OG1 A:THR42 2.1 27.0 1.0
O A:HOH301 2.2 22.1 1.0
CD A:GLU128 3.0 29.2 1.0
CB A:THR42 3.1 24.2 1.0
PA A:ATP202 3.3 29.1 1.0
PB A:ATP202 3.3 25.2 1.0
OE1 A:GLU128 3.4 30.3 1.0
O3A A:ATP202 3.6 27.8 1.0
O A:HOH304 3.9 35.9 1.0
O5' A:ATP202 3.9 29.7 1.0
N A:THR42 4.0 24.9 1.0
O1G A:ATP202 4.0 27.8 1.0
OD2 A:ASP127 4.1 24.1 1.0
CA A:THR42 4.1 26.3 1.0
CG2 A:THR42 4.1 25.5 1.0
O3B A:ATP202 4.1 27.5 1.0
O A:HOH367 4.3 32.7 1.0
CG A:GLU128 4.4 25.2 1.0
OG1 A:THR159 4.5 23.6 1.0
O1B A:ATP202 4.5 23.4 1.0
O1A A:ATP202 4.6 28.3 1.0
C47 A:B12203 4.7 31.0 1.0
PG A:ATP202 4.7 26.2 1.0
CG A:ASP127 4.8 27.6 1.0
OD1 A:ASP127 4.8 29.4 1.0
CE A:LYS41 4.9 26.5 1.0
CB A:LYS41 4.9 23.3 1.0
C5' A:ATP202 5.0 28.1 1.0

Magnesium binding site 2 out of 2 in 4hut

Go back to Magnesium Binding Sites List in 4hut
Magnesium binding site 2 out of 2 in the Structure of Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin 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 Atp:Co(I)Rrinoid Adenosyltransferase (Coba) From Salmonella Enterica in Complex with Four and Five-Coordinate Cob(II) Alamin and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg201

b:25.2
occ:1.00
 OE2 B:GLU128 1.9 24.7 1.0
O2A B:ATP202 2.0 27.5 1.0
O2B B:ATP202 2.1 26.7 1.0
OG1 B:THR42 2.1 22.5 1.0
O B:HOH303 2.2 21.8 1.0
O B:HOH301 2.2 24.0 1.0
CD B:GLU128 2.9 26.6 1.0
PA B:ATP202 3.2 28.4 1.0
CB B:THR42 3.2 21.7 1.0
OE1 B:GLU128 3.2 27.7 1.0
PB B:ATP202 3.3 23.6 1.0
O3A B:ATP202 3.6 25.0 1.0
O5' B:ATP202 3.6 35.9 1.0
NZ B:LYS66 3.6 20.8 1.0
N B:THR42 4.0 22.7 1.0
O1G B:ATP202 4.0 26.8 1.0
OD2 B:ASP127 4.0 24.8 1.0
O B:HOH302 4.0 22.7 1.0
CA B:THR42 4.2 22.2 1.0
O3B B:ATP202 4.2 25.9 1.0
C47 B:B12203 4.3 27.1 1.0
CG2 B:THR42 4.3 18.7 1.0
CG B:GLU128 4.3 27.1 1.0
CE B:LYS66 4.3 23.2 1.0
OG1 B:THR159 4.4 22.5 1.0
O1A B:ATP202 4.5 31.8 1.0
O1B B:ATP202 4.6 24.1 1.0
PG B:ATP202 4.7 24.6 1.0
OD1 B:ASP127 4.7 25.3 1.0
CE B:LYS41 4.7 22.6 1.0
CG B:ASP127 4.8 26.1 1.0
CB B:LYS41 4.8 24.6 1.0
C5' B:ATP202 5.0 38.8 1.0

Reference:

T.C.Moore, S.A.Newmister, I.Rayment, J.C.Escalante-Semerena. Structural Insights Into the Mechanism of Four-Coordinate Cob(II)Alamin Formation in the Active Site of the Salmonella Enterica Atp:Co(I)Rrinoid Adenosyltransferase Enzyme: Critical Role of Residues PHE91 and TRP93. Biochemistry V. 51 9647 2012.
ISSN: ISSN 0006-2960
PubMed: 23148601
DOI: 10.1021/BI301378D
Page generated: Fri Aug 16 16:25:42 2024

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