Magnesium in PDB 4kb0: Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc )

The structure of Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ), PDB code: 4kb0 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.80 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.257, 81.944, 73.444, 90.00, 105.46, 90.00
R / Rfree (%)	18.9 / 21.1

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ) (pdb code 4kb0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ), PDB code: 4kb0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc )


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 Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:27.4 occ:1.00 OP1 C:DC18 2.1 20.2 1.0 OD2 A:ASP186 2.2 34.5 1.0 OE1 A:GLU25 2.3 36.4 1.0 OD1 A:ASP23 2.9 26.2 1.0 MG C:MG101 3.2 29.9 1.0 OD2 A:ASP23 3.2 30.3 1.0 CG A:ASP186 3.3 25.6 1.0 CD A:GLU25 3.3 34.1 1.0 CG A:ASP23 3.4 24.5 1.0 O A:HOH548 3.4 31.5 1.0 OE2 A:GLU25 3.5 27.5 1.0 P C:DC18 3.6 19.6 1.0 CB A:ASP186 3.7 16.7 1.0 O A:HOH529 3.7 23.7 1.0 CA A:HIS181 4.3 33.3 1.0 O A:VAL24 4.3 24.6 1.0 C A:HIS181 4.3 35.1 1.0 OD1 A:ASP186 4.3 29.1 1.0 O A:SER182 4.4 30.2 1.0 O3' C:DC17 4.4 15.0 1.0 N A:SER182 4.4 38.6 1.0 O5' C:DC18 4.4 18.2 1.0 C A:SER182 4.4 33.1 1.0 OP2 C:DC18 4.5 19.4 1.0 O A:HOH402 4.5 19.1 1.0 C5' C:DC18 4.5 14.3 1.0 CG A:GLU25 4.6 26.8 1.0 N A:ALA183 4.7 24.4 1.0 CA A:ALA183 4.8 28.1 1.0 O C:HOH202 4.8 16.3 1.0 O A:HIS181 4.8 35.9 1.0 CB A:ASP23 4.9 15.7 1.0 N A:HIS181 4.9 38.2 1.0 CA A:SER182 4.9 29.8 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc )


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 Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:31.2 occ:1.00 OP1 D:DC18 2.0 19.8 1.0 OE1 B:GLU25 2.2 36.4 1.0 OD2 B:ASP186 2.3 32.8 1.0 CD B:GLU25 3.1 34.7 1.0 CG B:ASP186 3.2 29.7 1.0 OE2 B:GLU25 3.3 27.8 1.0 OD2 B:ASP23 3.4 29.8 1.0 CA B:HIS181 3.4 46.1 1.0 P D:DC18 3.5 21.1 1.0 OD1 B:ASP23 3.5 23.9 1.0 MG D:MG101 3.6 26.1 1.0 CG B:ASP23 3.8 29.0 1.0 CB B:ASP186 3.9 20.5 1.0 C B:HIS181 3.9 44.4 1.0 O B:HOH433 4.0 22.6 1.0 N B:HIS181 4.0 44.4 1.0 OD1 B:ASP186 4.1 34.2 1.0 O B:HIS181 4.2 45.6 1.0 O5' D:DC18 4.3 19.4 1.0 OP2 D:DC18 4.3 22.5 1.0 CB B:HIS181 4.4 45.3 1.0 O3' D:DC17 4.4 15.7 1.0 O B:VAL24 4.4 13.1 1.0 ND1 B:HIS181 4.4 57.5 1.0 N B:SER182 4.5 39.5 1.0 CG B:GLU25 4.5 23.8 1.0 C5' D:DC18 4.5 18.4 1.0 O B:HOH417 4.6 17.0 1.0 O B:HOH507 4.6 29.7 1.0 O B:SER182 4.7 30.2 1.0 O D:HOH205 4.8 24.4 1.0 C B:SER182 4.8 29.7 1.0 CG B:HIS181 4.9 53.8 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc )


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 Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:29.9 occ:1.00 O3' C:DC17 2.3 15.0 1.0 O A:HOH402 2.4 19.1 1.0 OD2 A:ASP23 2.4 30.3 1.0 OP1 C:DC18 2.4 20.2 1.0 O A:HOH529 2.4 23.7 1.0 O A:HOH401 2.7 17.8 1.0 P C:DC18 2.9 19.6 1.0 MG A:MG301 3.2 27.4 1.0 CG A:ASP23 3.5 24.5 1.0 C3' C:DC17 3.6 15.6 1.0 C5' C:DC18 3.9 14.3 1.0 O5' C:DC18 3.9 18.2 1.0 OD1 A:ASP23 4.0 26.2 1.0 C4' C:DC17 4.0 16.2 1.0 O A:HOH410 4.0 15.5 1.0 OP2 C:DC18 4.1 19.4 1.0 C2' C:DC17 4.1 20.0 1.0 O A:VAL24 4.2 24.6 1.0 OD2 A:ASP125 4.2 21.6 1.0 O A:HOH408 4.4 13.1 1.0 O C:HOH202 4.6 16.3 1.0 OD2 A:ASP186 4.6 34.5 1.0 OD1 A:ASP125 4.6 22.2 1.0 CB A:ASP23 4.7 15.7 1.0 C5' C:DC17 4.8 15.2 1.0 O A:HOH548 4.8 31.5 1.0 OE1 A:GLU25 4.9 36.4 1.0 CG A:ASP125 4.9 18.8 1.0 N A:VAL24 5.0 14.5 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc )


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Cc ) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:26.1 occ:1.00 O B:HOH417 2.1 17.0 1.0 O3' D:DC17 2.4 15.7 1.0 OD1 B:ASP23 2.4 23.9 1.0 O B:HOH433 2.4 22.6 1.0 O B:HOH505 2.5 25.2 1.0 OP1 D:DC18 2.7 19.8 1.0 P D:DC18 3.2 21.1 1.0 C3' D:DC17 3.6 15.7 1.0 CG B:ASP23 3.6 29.0 1.0 MG B:MG301 3.6 31.2 1.0 O B:HOH436 3.8 23.1 1.0 C4' D:DC17 3.9 21.0 1.0 C2' D:DC17 4.0 16.6 1.0 OD2 B:ASP125 4.1 18.7 1.0 C5' D:DC18 4.1 18.4 1.0 O5' D:DC18 4.2 19.4 1.0 O B:HOH420 4.2 16.1 1.0 OD2 B:ASP23 4.2 29.8 1.0 O D:HOH205 4.3 24.4 1.0 OP2 D:DC18 4.3 22.5 1.0 O B:VAL24 4.3 13.1 1.0 OD2 B:ASP186 4.3 32.8 1.0 OD1 B:ASP125 4.5 25.1 1.0 CB B:ASP23 4.7 13.1 1.0 C5' D:DC17 4.8 18.4 1.0 CG B:ASP125 4.8 22.9 1.0 O B:HIS120 4.8 14.1 1.0 OE1 B:GLU25 5.0 36.4 1.0

Y.Y.Hsiao, W.H.Fang, C.C.Lee, Y.P.Chen, H.S.Yuan. Structural Insights Into Dna Repair By Rnase T--An Exonuclease Processing 3' End of Structured Dna in Repair Pathways. Plos Biol. V. 12 01803 2014.
ISSN: ISSN 1544-9173
PubMed: 24594808
DOI: 10.1371/JOURNAL.PBIO.1001803