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Magnesium in PDB 4afy: Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg

Enzymatic activity of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg

All present enzymatic activity of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg:
3.1.4.52;

Protein crystallography data

The structure of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg, PDB code: 4afy was solved by J.Robert-Paganin, S.Nonin-Lecomte, S.Rety, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.209 / 2.01
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 104.330, 104.330, 154.240, 90.00, 90.00, 90.00
R / Rfree (%) 20.85 / 23.9

Other elements in 4afy:

The structure of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg (pdb code 4afy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg, PDB code: 4afy:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4afy

Go back to Magnesium Binding Sites List in 4afy
Magnesium binding site 1 out of 3 in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg


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 the Fimx Eal Domain in Complex with Reaction Product Pgpg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:40.5
occ:1.00
OE1 A:GLU475 2.6 26.0 1.0
O A:HOH2134 2.7 33.3 1.0
O5' C:G1 2.8 33.0 1.0
OE1 A:GLN461 2.9 25.9 1.0
OE1 A:GLN671 3.4 25.5 1.0
OP2 C:G1 3.4 64.8 1.0
OP1 C:G2 3.4 69.2 1.0
P C:G1 3.5 64.0 1.0
CD A:GLU475 3.6 34.0 1.0
C5' C:G1 3.6 61.1 1.0
CD A:GLN671 3.8 26.5 1.0
NE2 A:GLN671 3.8 24.5 1.0
OE2 A:GLU475 3.9 26.2 1.0
CD A:GLN461 4.0 25.4 1.0
O A:HOH2017 4.0 27.4 1.0
NZ A:LYS616 4.0 31.2 1.0
CD2 A:LEU477 4.3 33.9 1.0
OP1 C:G1 4.3 28.6 1.0
CD1 A:LEU477 4.3 28.9 1.0
P C:G2 4.4 85.3 1.0
O C:HOH2003 4.4 44.2 1.0
OP2 C:G2 4.5 56.2 1.0
C4' C:G1 4.6 41.9 1.0
CB A:GLN461 4.7 24.0 1.0
O3' C:G1 4.7 63.3 1.0
CG A:LEU477 4.8 30.1 1.0
CG A:GLN461 4.8 24.4 1.0
CG A:GLU475 4.8 26.1 1.0
NE2 A:GLN461 4.8 24.5 1.0
O C:HOH2001 4.9 48.4 1.0
CG A:GLN671 4.9 25.2 1.0

Magnesium binding site 2 out of 3 in 4afy

Go back to Magnesium Binding Sites List in 4afy
Magnesium binding site 2 out of 3 in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg


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 the Fimx Eal Domain in Complex with Reaction Product Pgpg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:51.2
occ:1.00
O A:HOH2135 2.1 48.5 1.0
OD2 A:ASP442 2.7 41.1 1.0
O A:HOH2010 2.8 57.1 1.0
OD1 A:ASP442 3.2 33.6 1.0
CG A:ASP442 3.3 35.6 1.0
O A:HOH2136 3.6 52.2 1.0
N A:ALA445 3.8 35.8 1.0
CB A:ILE444 3.8 30.7 1.0
CG2 A:ILE444 3.9 43.7 1.0
O A:HOH2008 4.0 40.2 1.0
CB A:ALA445 4.0 38.1 1.0
CB B:SER655 4.1 33.8 1.0
C A:ILE444 4.3 37.6 1.0
CA A:ALA445 4.3 36.3 1.0
CA A:ILE444 4.6 30.9 1.0
OE1 A:GLN448 4.7 59.2 1.0
OG B:SER655 4.8 29.8 1.0
CB A:ASP442 4.8 30.9 1.0
OG B:SER657 4.9 47.9 1.0
CG1 A:ILE444 5.0 33.6 1.0

Magnesium binding site 3 out of 3 in 4afy

Go back to Magnesium Binding Sites List in 4afy
Magnesium binding site 3 out of 3 in the Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Fimx Eal Domain in Complex with Reaction Product Pgpg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg801

b:35.3
occ:1.00
OE1 B:GLU475 2.7 23.5 1.0
O B:HOH2125 2.7 31.5 1.0
OE1 B:GLN461 2.9 25.2 1.0
O5' D:G1 2.9 30.1 1.0
OP2 D:G1 3.4 64.4 1.0
OP2 D:G2 3.5 65.0 1.0
OE1 B:GLN671 3.6 26.5 1.0
CD B:GLU475 3.6 30.2 1.0
P D:G1 3.6 61.7 1.0
C5' D:G1 3.7 59.4 1.0
NE2 B:GLN671 3.8 23.3 1.0
CD B:GLN671 3.9 25.1 1.0
O A:HOH2043 3.9 25.5 1.0
CD B:GLN461 4.0 26.3 1.0
OE2 B:GLU475 4.1 24.9 1.0
CD1 B:LEU477 4.1 31.4 1.0
CD2 B:LEU477 4.1 32.8 1.0
NZ B:LYS616 4.2 30.8 1.0
OP1 D:G1 4.4 24.8 1.0
O D:HOH2002 4.5 41.4 1.0
CB B:GLN461 4.6 23.5 1.0
CG B:LEU477 4.7 26.1 1.0
O D:HOH2001 4.7 39.5 1.0
P D:G2 4.7 72.8 1.0
C4' D:G1 4.8 37.8 1.0
CG B:GLU475 4.8 26.7 1.0
CG B:GLN461 4.8 21.2 1.0
NE2 B:GLN461 4.9 26.0 1.0
O B:HOH2033 4.9 41.8 1.0

Reference:

J.Robert-Paganin, S.Nonin-Lecomte, S.Rety. Crystal Structure of An Eal Domain in Complex with Reaction Product 5'-Pgpg Plos One V. 7 52424 2012.
ISSN: ISSN 1932-6203
PubMed: 23285035
DOI: 10.1371/JOURNAL.PONE.0052424
Page generated: Mon Dec 14 09:07:44 2020

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