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Magnesium in PDB 4njk: Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+

Enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+

All present enzymatic activity of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+:
4.3.99.3;

Protein crystallography data

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+, PDB code: 4njk was solved by D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.18 / 1.91
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 118.790, 118.790, 102.664, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.3

Other elements in 4njk:

The structure of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+ also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+ (pdb code 4njk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+, PDB code: 4njk:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4njk

Go back to Magnesium Binding Sites List in 4njk
Magnesium binding site 1 out of 2 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:32.9
occ:1.00
 O7B A:2KA303 2.4 34.2 1.0
O A:HOH441 2.8 39.5 1.0
O A:HOH601 2.8 52.1 1.0
O6 A:2KA303 2.9 33.0 1.0
OG1 A:THR51 2.9 45.3 1.0
O A:HOH414 3.0 36.7 1.0
C7A A:2KA303 3.4 31.3 1.0
NH2 A:ARG27 3.6 33.2 1.0
C6 A:2KA303 3.6 30.1 1.0
OD1 A:ASP50 3.7 42.3 1.0
C7 A:2KA303 3.9 29.2 1.0
C5 A:2KA303 3.9 27.8 1.0
NH1 A:ARG27 4.0 33.4 1.0
O A:HOH516 4.1 47.4 1.0
CZ A:ARG27 4.1 34.8 1.0
CB A:THR51 4.2 43.3 1.0
CE A:SAM302 4.3 28.8 1.0
CG A:ASP50 4.3 40.3 1.0
OD2 A:ASP50 4.4 37.0 1.0
O7A A:2KA303 4.5 30.5 1.0
CG2 A:THR51 4.5 37.6 1.0
NE2 A:HIS204 4.7 29.9 1.0
N1 A:2KA303 4.8 29.5 1.0
O A:HOH438 4.9 42.6 1.0
CA A:THR51 5.0 40.4 1.0

Magnesium binding site 2 out of 2 in 4njk

Go back to Magnesium Binding Sites List in 4njk
Magnesium binding site 2 out of 2 in the Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Quee From Burkholderia Multivorans in Complex with Adomet, 7-Carboxy-7-Deazaguanine, and MG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:34.8
occ:1.00
 O7A B:2KA303 2.3 31.5 1.0
O B:HOH442 2.6 39.0 1.0
O6 B:2KA303 2.9 30.8 1.0
OG1 B:THR51 2.9 44.3 1.0
O B:HOH413 3.0 33.5 1.0
O B:HOH477 3.1 41.9 1.0
C7A B:2KA303 3.3 30.4 1.0
NH2 B:ARG27 3.6 35.5 1.0
C6 B:2KA303 3.7 30.4 1.0
OD1 B:ASP50 3.7 41.0 0.8
C7 B:2KA303 3.8 28.4 1.0
C5 B:2KA303 3.9 28.2 1.0
NH1 B:ARG27 4.0 32.3 1.0
CZ B:ARG27 4.1 35.2 1.0
O B:HOH462 4.3 46.4 1.0
OD2 B:ASP50 4.3 40.2 0.8
CB B:THR51 4.3 43.9 1.0
CG B:ASP50 4.3 40.2 0.8
O7B B:2KA303 4.4 28.4 1.0
CE B:SAM302 4.4 36.9 1.0
CG2 B:THR51 4.5 42.5 1.0
NE2 B:HIS204 4.8 25.5 1.0
N1 B:2KA303 4.8 28.4 1.0

Reference:

D.P.Dowling, N.A.Bruender, A.P.Young, R.M.Mccarty, V.Bandarian, C.L.Drennan. Radical Sam Enzyme Quee Defines A New Minimal Core Fold and Metal-Dependent Mechanism. Nat.Chem.Biol. V. 10 106 2014.
ISSN: ISSN 1552-4450
PubMed: 24362703
DOI: 10.1038/NCHEMBIO.1426
Page generated: Mon Aug 19 23:35:57 2024

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