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Magnesium in PDB 3r5f: Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp

Enzymatic activity of Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp

All present enzymatic activity of Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp:
6.3.2.4;

Protein crystallography data

The structure of Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp, PDB code: 3r5f was solved by T.T.N.Doan, J.K.Kim, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.95 / 2.07
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.225, 83.225, 97.143, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp (pdb code 3r5f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp, PDB code: 3r5f:

Magnesium binding site 1 out of 1 in 3r5f

Go back to Magnesium Binding Sites List in 3r5f
Magnesium binding site 1 out of 1 in the Crystal Structure of D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp


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 D-Alanine-D-Alnine Ligase From Xanthomonas Oryzae Pv. Oryzae with Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg369

b:45.0
occ:1.00
 O A:HOH480 2.6 52.4 1.0
OD2 A:ASP302 2.6 30.4 1.0
O1A A:ATP368 2.8 66.5 1.0
O3G A:ATP368 2.9 75.1 1.0
OE2 A:GLU315 3.1 44.6 1.0
ND2 A:ASN314 3.2 39.4 1.0
CD A:GLU315 3.5 39.6 1.0
O A:HOH476 3.6 57.9 1.0
CG A:ASP302 3.6 29.8 1.0
CB A:GLU315 3.8 30.8 1.0
CB A:ASP302 3.9 27.0 1.0
O1B A:ATP368 3.9 73.8 1.0
OE1 A:GLU315 4.0 48.2 1.0
PA A:ATP368 4.1 63.9 1.0
CG A:GLU315 4.3 38.4 1.0
PG A:ATP368 4.4 77.7 1.0
NH2 A:ARG300 4.4 30.5 1.0
CG A:ASN314 4.4 33.2 1.0
O A:HOH394 4.5 49.5 1.0
O3' A:ATP368 4.6 52.0 1.0
O2A A:ATP368 4.6 63.6 1.0
OD1 A:ASP302 4.7 31.9 1.0
PB A:ATP368 4.9 73.9 1.0
O3B A:ATP368 5.0 73.4 1.0

Reference:

T.T.N.Doan, J.K.Kim, L.W.Kang. Crystal Structure of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae with Atp To Be Published.
Page generated: Mon Dec 14 08:44:05 2020

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