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Magnesium in PDB 5d1f: Crystal Structure of Maize Pdrp Bound with Amp and HG2+

Enzymatic activity of Crystal Structure of Maize Pdrp Bound with Amp and HG2+

All present enzymatic activity of Crystal Structure of Maize Pdrp Bound with Amp and HG2+:
2.7.11.32; 2.7.4.27;

Protein crystallography data

The structure of Crystal Structure of Maize Pdrp Bound with Amp and HG2+, PDB code: 5d1f was solved by L.Jiang, Z.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.68 / 3.40
Space group P 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 175.514, 175.514, 175.514, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 24.3

Other elements in 5d1f:

The structure of Crystal Structure of Maize Pdrp Bound with Amp and HG2+ also contains other interesting chemical elements:

Mercury (Hg) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Maize Pdrp Bound with Amp and HG2+ (pdb code 5d1f). 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 Maize Pdrp Bound with Amp and HG2+, PDB code: 5d1f:

Magnesium binding site 1 out of 1 in 5d1f

Go back to Magnesium Binding Sites List in 5d1f
Magnesium binding site 1 out of 1 in the Crystal Structure of Maize Pdrp Bound with Amp and HG2+


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 Maize Pdrp Bound with Amp and HG2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:53.8
occ:1.00
O3P A:AMP501 2.6 34.8 1.0
O5' A:AMP501 2.7 34.7 1.0
OG1 A:THR204 2.9 41.0 1.0
P A:AMP501 3.2 33.8 1.0
C A:GLY148 3.4 34.1 1.0
CA A:GLY148 3.4 34.3 1.0
N A:ALA151 3.4 32.3 1.0
CB A:SER144 3.6 36.6 1.0
OG A:SER144 3.6 38.0 1.0
O1P A:AMP501 3.6 33.3 1.0
O A:GLY148 3.6 33.0 1.0
N A:GLY148 3.7 34.2 1.0
N A:THR150 3.7 33.6 1.0
CB A:ALA151 3.7 33.0 1.0
CB A:THR150 3.7 30.9 1.0
CG2 A:THR204 3.8 40.3 1.0
N A:TRP149 3.8 35.6 1.0
C5' A:AMP501 3.9 35.9 1.0
CB A:THR204 3.9 39.8 1.0
CA A:THR150 4.1 32.0 1.0
CA A:ALA151 4.2 33.5 1.0
OG1 A:THR150 4.2 30.6 1.0
C A:THR150 4.3 31.6 1.0
O2P A:AMP501 4.5 33.1 1.0
C A:TRP149 4.6 35.1 1.0
C4' A:AMP501 4.6 36.9 1.0
CA A:TRP149 4.8 36.6 1.0
CA A:SER144 4.9 35.1 1.0
CG2 A:THR150 4.9 30.9 1.0
C3' A:AMP501 5.0 37.4 1.0
C A:THR147 5.0 33.9 1.0

Reference:

L.Jiang, Y.B.Chen, J.Zheng, Z.Chen, Y.Liu, Y.Tao, W.Wu, Z.Chen, B.C.Wang. Structural Basis of Reversible Phosphorylation By Maize Pyruvate Orthophosphate Dikinase Regulatory Protein Plant Physiol. V. 170 732 2016.
ISSN: ESSN 1532-2548
PubMed: 26620526
DOI: 10.1104/PP.15.01709
Page generated: Mon Dec 14 20:09:43 2020

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