Manganese in PDB 1sx8: Ecorv Bound to Cognate Dna and MN2+

All present enzymatic activity of Ecorv Bound to Cognate Dna and MN2+:
3.1.21.4;

The structure of Ecorv Bound to Cognate Dna and MN2+, PDB code: 1sx8 was solved by N.C.Horton, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.15
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.800, 49.100, 63.700, 96.90, 108.90, 107.10
R / Rfree (%)	21.3 / 25.4

The binding sites of Manganese atom in the Ecorv Bound to Cognate Dna and MN2+ (pdb code 1sx8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Ecorv Bound to Cognate Dna and MN2+, PDB code: 1sx8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn246 b:55.3 occ:1.00 OP1 C:DA7 2.1 33.6 1.0 O A:HOH258 2.6 24.4 1.0 OD2 A:ASP74 2.6 23.1 1.0 OD1 A:ASP74 2.7 21.3 1.0 OD1 A:ASP90 2.9 27.4 1.0 CG A:ASP74 3.0 19.6 1.0 P C:DA7 3.3 31.3 1.0 CG A:ASP90 3.4 25.9 1.0 O C:HOH18 3.4 17.8 1.0 OD2 A:ASP90 3.5 29.2 1.0 C5' C:DA7 3.6 31.1 1.0 O3' C:DT6 3.7 28.2 1.0 O A:HOH315 3.7 44.3 1.0 O5' C:DA7 3.9 33.2 1.0 O C:HOH27 4.1 38.9 1.0 O A:ILE91 4.1 18.3 1.0 CB A:ASP74 4.5 18.0 1.0 N A:ASP74 4.5 19.0 1.0 N A:ILE91 4.5 19.8 1.0 CB A:ASP90 4.6 25.0 1.0 C4' C:DA7 4.7 30.1 1.0 OP2 C:DA7 4.7 29.1 1.0 CA A:ASP90 4.9 22.6 1.0 C3' C:DA7 4.9 31.2 1.0 CA A:ASP74 5.0 18.9 1.0

Manganese binding site 2 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn247 b:73.9 occ:1.00 O A:HOH257 2.4 39.1 1.0 OD2 A:ASP74 2.9 23.1 1.0 OE1 A:GLU45 3.0 38.2 1.0 CG A:ASP74 3.4 19.6 1.0 CB A:ASP74 3.6 18.0 1.0 CA A:ASP74 3.7 18.9 1.0 O A:HOH315 3.9 44.3 1.0 CD A:GLU45 4.1 36.2 1.0 OD1 A:ASP74 4.3 21.3 1.0 CD A:PRO66 4.6 34.1 1.0 OE2 A:GLU45 4.6 38.8 1.0 N A:ASP74 4.7 19.0 1.0 C A:ASP74 4.8 16.7 1.0 O A:ASP74 4.8 15.4 1.0 OD2 B:ASP36 4.8 50.0 1.0 CG B:ASP36 4.8 47.9 1.0 OE2 A:GLU65 5.0 30.8 1.0

Manganese binding site 3 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn248 b:72.0 occ:1.00 NE2 A:HIS71 2.6 36.9 1.0 CE1 A:HIS71 3.3 34.6 1.0 CD2 A:HIS71 3.7 34.9 1.0 N A:ASN120 4.4 25.5 1.0 ND1 A:HIS71 4.5 33.5 1.0 O A:THR118 4.7 26.9 1.0 CA A:ASN120 4.7 24.6 1.0 CG A:HIS71 4.7 33.9 1.0 O A:ILE121 4.8 15.7 1.0

Manganese binding site 4 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn246 b:57.2 occ:1.00 NE2 B:HIS71 2.2 25.1 1.0 OP1 C:DT11 2.3 43.1 1.0 CE1 B:HIS71 3.0 25.9 1.0 CD2 B:HIS71 3.3 24.7 1.0 P C:DT11 3.8 44.0 1.0 ND1 B:HIS71 4.2 26.4 1.0 CG B:HIS71 4.3 25.2 1.0 O3' C:DT10 4.5 41.4 1.0 O5' C:DT11 4.5 44.6 1.0 N B:ASN120 4.5 22.2 1.0 C5' C:DT11 4.6 49.6 1.0 O B:ILE121 4.7 16.6 1.0 CA B:ASN120 4.7 21.2 1.0 OP2 C:DT11 4.8 42.6 1.0 O B:THR118 4.8 26.8 1.0 N B:ILE121 4.8 19.0 1.0

Manganese binding site 5 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn247 b:46.7 occ:1.00 O B:HOH274 2.2 19.9 1.0 OP1 D:DA7 2.2 32.0 1.0 OD2 B:ASP90 2.5 22.9 1.0 O B:HOH257 2.5 19.8 1.0 OD2 B:ASP74 2.7 14.3 1.0 OD1 B:ASP90 2.9 22.1 1.0 CG B:ASP90 3.0 19.7 1.0 OD1 B:ASP74 3.2 7.3 1.0 CG B:ASP74 3.2 12.2 1.0 P D:DA7 3.5 31.6 1.0 O3' D:DT6 3.8 29.4 1.0 O B:ILE91 3.9 16.4 1.0 O B:HOH291 4.1 26.3 1.0 O D:HOH121 4.2 28.9 1.0 C5' D:DA7 4.2 30.3 1.0 O5' D:DA7 4.3 32.3 1.0 N B:ILE91 4.4 16.0 1.0 CB B:ASP90 4.4 20.7 1.0 O B:HOH258 4.5 26.4 1.0 CB B:ASP74 4.6 14.8 1.0 N B:ASP74 4.7 17.3 1.0 OP2 D:DA7 4.7 31.4 1.0 CA B:ASP90 4.8 17.8 1.0 C B:ILE91 4.9 13.0 1.0 O B:HOH289 5.0 32.9 1.0

Manganese binding site 6 out of 6 in the Ecorv Bound to Cognate Dna and MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Ecorv Bound to Cognate Dna and MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn248 b:43.0 occ:1.00 O B:HOH258 2.2 26.4 1.0 OE1 B:GLU45 2.4 30.1 1.0 OD1 B:ASP74 2.5 7.3 1.0 CD B:GLU45 3.3 28.9 1.0 CG B:ASP74 3.3 12.2 1.0 OE2 B:GLU45 3.4 28.9 1.0 CB B:ASP74 3.8 14.8 1.0 CA B:ASP74 3.9 17.3 1.0 OD2 A:ASP36 4.1 40.4 1.0 O B:HOH257 4.1 19.8 1.0 OD2 B:ASP74 4.1 14.3 1.0 CG A:ASP36 4.5 40.9 1.0 CG B:GLU45 4.7 26.6 1.0 OD1 A:ASP36 4.7 44.9 1.0 O B:ASP74 4.8 15.9 1.0 CD B:PRO66 4.8 24.7 1.0 C B:ASP74 4.9 16.2 1.0 OE1 B:GLU65 4.9 27.7 1.0 N B:ASP74 5.0 17.3 1.0

N.C.Horton, J.J.Perona. Dna Cleavage By Ecorv Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites Biochemistry V. 43 6841 2004.
ISSN: ISSN 0006-2960
PubMed: 15170321
DOI: 10.1021/BI0499056