Magnesium in PDB 4kb1: Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Ct )

The structure of Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Ct ), PDB code: 4kb1 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)	28.62 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	60.556, 81.844, 73.744, 90.00, 105.71, 90.00
R / Rfree (%)	18.3 / 19.9

The binding sites of Magnesium atom in the Crystal Structure of Rnase T in Complex with A Bluge Dna (Two Nucleotide Insertion Ct ) (pdb code 4kb1). 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 Ct ), PDB code: 4kb1:
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 Ct )


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 Ct ) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:26.3 occ:1.00 OP1 C:DC18 2.1 17.0 1.0 OD2 A:ASP186 2.3 20.9 1.0 OE1 A:GLU25 2.4 29.5 1.0 O A:HOH502 2.5 36.3 1.0 OD1 A:ASP23 3.1 30.4 1.0 OD2 A:ASP23 3.2 27.3 1.0 CD A:GLU25 3.3 25.5 1.0 CG A:ASP186 3.4 25.2 1.0 O C:HOH209 3.4 27.1 1.0 MG C:MG101 3.5 19.4 1.0 CG A:ASP23 3.5 21.0 1.0 P C:DC18 3.5 16.2 1.0 OE2 A:GLU25 3.5 18.2 1.0 CB A:ASP186 3.8 22.1 1.0 O A:HOH424 3.9 20.6 1.0 CA A:HIS181 4.2 33.1 1.0 C A:HIS181 4.2 29.5 1.0 OP2 C:DC18 4.3 16.5 1.0 O5' C:DC18 4.3 17.6 1.0 O A:SER182 4.4 21.0 1.0 O A:HIS181 4.4 30.1 1.0 O A:HOH415 4.4 17.9 1.0 O3' C:DT17 4.5 13.6 1.0 OD1 A:ASP186 4.5 20.1 1.0 O A:VAL24 4.5 16.2 1.0 C A:SER182 4.5 27.4 1.0 C5' C:DC18 4.6 14.9 1.0 CA A:ALA183 4.6 23.5 1.0 N A:SER182 4.7 29.8 1.0 CG A:GLU25 4.7 21.5 1.0 N A:ALA183 4.7 23.3 1.0 O C:HOH202 4.8 18.3 1.0 N A:HIS181 4.9 34.2 1.0 CB A:ASP23 5.0 16.5 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 Ct )


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 Ct ) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg301 b:30.8 occ:1.00 OP1 D:DC18 2.1 17.6 1.0 OE1 B:GLU25 2.2 31.4 1.0 OD2 B:ASP186 2.2 35.6 1.0 CD B:GLU25 3.1 28.4 1.0 O D:HOH212 3.3 39.1 1.0 OE2 B:GLU25 3.3 23.4 1.0 CG B:ASP186 3.3 33.6 1.0 OD2 B:ASP23 3.4 24.7 1.0 P D:DC18 3.5 16.4 1.0 O B:ALA180 3.6 57.5 1.0 OD1 B:ASP23 3.7 18.6 1.0 MG D:MG101 3.8 17.4 1.0 CG B:ASP23 3.9 23.3 1.0 CB B:ASP186 4.0 19.3 1.0 OP2 D:DC18 4.2 19.0 1.0 O B:HOH424 4.2 19.3 1.0 O5' D:DC18 4.2 14.5 1.0 CA B:HIS181 4.2 44.0 1.0 O B:HIS181 4.2 50.4 1.0 OD1 B:ASP186 4.3 33.6 1.0 C B:HIS181 4.3 46.0 1.0 O B:VAL24 4.5 15.0 1.0 O3' D:DT17 4.5 14.0 1.0 CG B:GLU25 4.5 21.6 1.0 C5' D:DC18 4.5 11.9 1.0 C B:ALA180 4.5 47.3 1.0 O B:SER182 4.6 27.2 1.0 O B:HOH412 4.7 16.1 1.0 O D:HOH204 4.8 21.2 1.0 O B:HOH441 4.8 37.9 1.0 N B:HIS181 4.9 44.0 1.0 C B:SER182 4.9 32.8 1.0 N B:SER182 5.0 31.4 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 Ct )


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 Ct ) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg101 b:19.4 occ:1.00 OD2 A:ASP23 2.3 27.3 1.0 O A:HOH415 2.3 17.9 1.0 O A:HOH424 2.3 20.6 1.0 O3' C:DT17 2.4 13.6 1.0 O A:HOH402 2.4 15.6 1.0 OP1 C:DC18 2.5 17.0 1.0 P C:DC18 3.0 16.2 1.0 CG A:ASP23 3.5 21.0 1.0 MG A:MG301 3.5 26.3 1.0 C3' C:DT17 3.6 11.5 1.0 O A:HOH411 3.9 15.5 1.0 C4' C:DT17 3.9 10.6 1.0 O5' C:DC18 4.1 17.6 1.0 OD1 A:ASP23 4.1 30.4 1.0 OP2 C:DC18 4.2 16.5 1.0 C5' C:DC18 4.2 14.9 1.0 O A:HOH406 4.2 13.0 1.0 OD2 A:ASP125 4.2 16.1 1.0 C2' C:DT17 4.3 12.8 1.0 O A:VAL24 4.4 16.2 1.0 OD1 A:ASP125 4.5 17.2 1.0 CB A:ASP23 4.6 16.5 1.0 C5' C:DT17 4.6 14.5 1.0 O C:HOH202 4.6 18.3 1.0 O A:HIS120 4.7 15.5 1.0 OD2 A:ASP186 4.8 20.9 1.0 CG A:ASP125 4.8 18.9 1.0 O C:HOH209 4.9 27.1 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 Ct )


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 Ct ) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg101 b:17.4 occ:1.00 O B:HOH426 2.2 19.2 1.0 O B:HOH412 2.2 16.1 1.0 O B:HOH424 2.4 19.3 1.0 OD1 B:ASP23 2.4 18.6 1.0 O3' D:DT17 2.4 14.0 1.0 OP1 D:DC18 2.6 17.6 1.0 P D:DC18 3.1 16.4 1.0 CG B:ASP23 3.6 23.3 1.0 C3' D:DT17 3.6 12.2 1.0 MG B:MG301 3.8 30.8 1.0 O B:HOH415 3.8 17.5 1.0 C4' D:DT17 3.9 12.0 1.0 OD2 B:ASP125 4.0 17.9 1.0 C2' D:DT17 4.1 15.4 1.0 C5' D:DC18 4.1 11.9 1.0 O B:HOH405 4.2 13.8 1.0 O5' D:DC18 4.2 14.5 1.0 OD2 B:ASP23 4.2 24.7 1.0 OP2 D:DC18 4.3 19.0 1.0 O B:VAL24 4.3 15.0 1.0 OD1 B:ASP125 4.4 16.6 1.0 OD2 B:ASP186 4.4 35.6 1.0 O B:HIS120 4.6 13.5 1.0 CG B:ASP125 4.6 17.7 1.0 O D:HOH204 4.6 21.2 1.0 C5' D:DT17 4.7 18.7 1.0 CB B:ASP23 4.7 13.3 1.0 N B:VAL24 5.0 12.3 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