Cadmium in PDB 2oa9: Restriction Endonuclease Mvai in the Absence of Dna

The structure of Restriction Endonuclease Mvai in the Absence of Dna, PDB code: 2oa9 was solved by M.Kaus-Drobek, H.Czapinska, M.Sokolowska, G.Tamulaitis, R.H.Szczepanowski, K.Urbanke, V.Siksnys, M.Bochtler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.499, 63.281, 71.892, 90.00, 100.77, 90.00
R / Rfree (%)	18.4 / 21.2

The structure of Restriction Endonuclease Mvai in the Absence of Dna also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Cadmium atom in the Restriction Endonuclease Mvai in the Absence of Dna (pdb code 2oa9). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 15 binding sites of Cadmium where determined in the Restriction Endonuclease Mvai in the Absence of Dna, PDB code: 2oa9:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd900 b:17.5 occ:1.00 OD2 B:ASP203 2.2 11.8 1.0 OE2 A:GLU234 2.3 17.6 1.0 ND1 A:HIS59 2.3 14.6 1.0 OE1 B:GLU238 2.4 15.6 1.0 OE2 B:GLU238 2.4 15.5 1.0 OE1 A:GLU234 2.4 18.0 1.0 CD A:GLU234 2.7 18.2 1.0 CD B:GLU238 2.8 14.9 1.0 CE1 A:HIS59 3.2 18.8 1.0 CG B:ASP203 3.3 11.6 1.0 CG A:HIS59 3.3 13.5 1.0 OD1 B:ASP203 3.6 12.2 1.0 CB A:HIS59 3.7 16.3 1.0 OH B:TYR239 3.8 10.9 1.0 CD1 A:LEU237 4.2 14.3 1.0 CG A:GLU234 4.2 16.8 1.0 CG B:GLU238 4.3 16.3 1.0 NE2 A:HIS59 4.3 17.8 1.0 CD2 A:HIS59 4.4 15.9 1.0 CA A:HIS59 4.5 15.4 1.0 O A:HOH944 4.5 22.5 1.0 CE2 B:TYR239 4.6 11.4 1.0 CZ B:TYR239 4.6 11.5 1.0 CB B:ASP203 4.6 11.3 1.0 O B:HOH939 4.6 26.7 1.0 NZ B:LYS235 4.7 27.0 1.0 CB A:GLU234 4.9 16.1 1.0 O B:HOH954 5.0 24.0 1.0

Cadmium binding site 2 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd903 b:23.7 occ:1.00 O A:HOH935 2.2 25.1 1.0 NE2 A:HIS100 2.3 18.8 1.0 OD2 A:ASP207 2.3 18.3 1.0 OD1 A:ASP207 2.3 19.8 1.0 O A:HOH966 2.3 31.2 1.0 O A:HOH919 2.4 25.1 1.0 CG A:ASP207 2.7 18.7 1.0 CE1 A:HIS100 3.2 14.6 1.0 CD2 A:HIS100 3.2 16.4 1.0 NH1 A:ARG230 4.1 20.3 1.0 CB A:ASP207 4.1 14.3 1.0 O A:HOH987 4.3 39.5 1.0 O A:HOH978 4.3 35.7 1.0 ND1 A:HIS100 4.3 19.3 1.0 NE A:ARG209 4.3 38.0 1.0 CG A:HIS100 4.4 14.0 1.0 OG1 A:THR102 4.4 18.7 1.0 O A:HOH954 4.6 29.7 1.0 CB A:ARG209 4.9 15.9 1.0 NH2 A:ARG209 5.0 41.6 1.0

Cadmium binding site 3 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd904 b:24.4 occ:1.00 O A:HOH988 2.2 27.8 1.0 OE2 B:GLU169 2.2 28.4 1.0 OD1 A:ASP121 2.3 15.7 1.0 OE1 B:GLU169 2.4 25.9 1.0 OD2 A:ASP121 2.6 17.8 1.0 CD B:GLU169 2.7 25.8 1.0 CG A:ASP121 2.8 14.5 1.0 O A:HOH938 3.9 21.9 1.0 O A:HOH1060 4.0 48.9 1.0 CG B:GLU169 4.2 23.0 1.0 CB A:ASP121 4.3 13.4 1.0 O A:ILE122 4.4 15.6 1.0 CE B:LYS180 4.7 31.5 1.0 NZ B:LYS180 4.7 35.5 1.0 O A:HOH961 4.8 29.7 1.0 O A:HOH995 4.9 31.3 1.0

Cadmium binding site 4 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd906 b:31.1 occ:0.80 OE2 A:GLU169 2.2 33.5 1.0 OD2 B:ASP121 2.3 24.5 1.0 O B:HOH951 2.3 26.9 1.0 O A:HOH1064 2.4 35.5 1.0 O A:HOH1059 2.4 45.4 1.0 O B:HOH1007 2.6 48.2 1.0 OD1 B:ASP121 2.6 30.2 1.0 OE1 A:GLU169 2.8 35.3 1.0 CG B:ASP121 2.8 22.1 1.0 CD A:GLU169 2.8 31.3 1.0 O B:HOH958 4.1 26.4 1.0 O B:HOH1002 4.1 34.5 1.0 O B:ILE122 4.3 14.5 1.0 CB B:ASP121 4.3 16.0 1.0 CG A:GLU169 4.3 26.0 1.0 O B:HOH967 4.5 30.2 1.0 O B:HOH920 4.5 35.7 1.0

Cadmium binding site 5 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd907 b:33.5 occ:0.80 NE2 A:HIS52 2.2 27.1 1.0 OE1 A:GLU43 2.3 25.3 1.0 O A:HOH998 2.3 40.2 1.0 OE2 A:GLU40 2.4 29.0 1.0 OE1 A:GLU40 2.5 29.9 1.0 OE2 A:GLU43 2.6 24.9 1.0 CD A:GLU40 2.8 27.9 1.0 CD A:GLU43 2.8 26.6 1.0 CE1 A:HIS52 3.2 28.2 1.0 CD2 A:HIS52 3.2 25.5 1.0 OD1 A:ASP50 3.3 23.2 1.0 CG A:ASP50 3.8 25.3 1.0 CD A:CD909 4.0 32.0 0.7 CB A:ASP50 4.3 24.8 1.0 CG A:GLU40 4.3 25.5 1.0 ND1 A:HIS52 4.3 25.9 1.0 CG A:GLU43 4.3 26.7 1.0 CG A:HIS52 4.3 27.2 1.0 OD2 A:ASP50 4.4 23.9 1.0 CA A:ASP50 4.7 24.9 1.0 CB A:GLU43 5.0 25.9 1.0

Cadmium binding site 6 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd909 b:32.0 occ:0.70 O A:HOH998 2.3 40.2 1.0 OD2 A:ASP50 2.3 23.9 1.0 OD1 A:ASP50 2.3 23.2 1.0 CG A:ASP50 2.7 25.3 1.0 O A:HOH1022 3.9 41.1 1.0 CD A:CD907 4.0 33.5 0.8 CB A:ASP50 4.2 24.8 1.0 OE1 A:GLU43 4.3 25.3 1.0 CE1 A:HIS52 4.5 28.2 1.0 NE2 A:HIS52 4.7 27.1 1.0 CA A:ASP50 5.0 24.9 1.0

Cadmium binding site 7 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd911 b:25.4 occ:0.50 OD1 A:ASP17 2.2 25.2 1.0 O A:VAL246 2.3 29.6 1.0 CL A:CL800 2.3 30.3 1.0 OXT A:VAL246 2.6 25.6 1.0 C A:VAL246 2.9 25.8 1.0 CG A:ASP17 3.2 24.5 1.0 OD2 A:ASP17 3.6 25.9 1.0 NE2 A:GLN13 3.9 22.8 1.0 O A:HOH948 4.1 39.1 1.0 CB A:ASP17 4.4 23.1 1.0 CA A:VAL246 4.5 23.8 1.0 CG1 A:VAL16 4.5 22.8 1.0 CA A:ASP17 4.7 23.1 1.0 CG2 A:VAL246 4.8 28.5 1.0 N A:ASP17 5.0 22.0 1.0

Cadmium binding site 8 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd912 b:45.5 occ:0.80 NE2 A:HIS225 2.2 34.3 1.0 NE2 A:HIS223 2.3 23.5 1.0 CE1 A:HIS225 2.7 34.3 1.0 CE1 A:HIS223 3.3 23.7 1.0 CD2 A:HIS223 3.3 22.8 1.0 CD2 A:HIS225 3.5 32.0 1.0 ND1 A:HIS225 3.9 35.8 1.0 CG A:HIS225 4.4 29.6 1.0 ND1 A:HIS223 4.4 22.3 1.0 CG A:HIS223 4.4 18.3 1.0 OH A:TYR213 4.5 25.9 1.0 O A:HOH990 4.8 32.1 1.0

Cadmium binding site 9 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd913 b:28.9 occ:0.50 ND1 A:HIS21 2.3 22.7 1.0 CL A:CL801 2.4 45.1 1.0 O A:HOH1055 2.4 38.6 1.0 CE1 A:HIS21 3.0 23.9 1.0 CG A:HIS21 3.5 23.7 1.0 CB A:HIS21 4.0 23.3 1.0 CD2 A:LEU38 4.1 24.8 1.0 NE2 A:HIS21 4.2 23.4 1.0 CA A:HIS21 4.3 23.4 1.0 CD2 A:HIS21 4.4 22.1 1.0 O A:GLY18 4.5 23.8 1.0 O A:TRP20 4.6 23.1 1.0

Cadmium binding site 10 out of 15 in the Restriction Endonuclease Mvai in the Absence of Dna


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd915 b:37.8 occ:0.25 OD1 A:ASP47 2.4 31.3 0.5 OD2 A:ASP47 2.5 32.4 0.5 CG A:ASP47 2.8 32.2 0.5 O A:ASP44 3.8 31.7 1.0 CB A:ASP47 4.3 32.1 1.0 C A:ASP44 4.9 30.9 1.0

M.Kaus-Drobek, H.Czapinska, M.Sokolowska, G.Tamulaitis, R.H.Szczepanowski, C.Urbanke, V.Siksnys, M.Bochtler. Restriction Endonuclease Mvai Is A Monomer That Recognizes Its Target Sequence Asymmetrically. Nucleic Acids Res. V. 35 2035 2007.
ISSN: ISSN 0305-1048
PubMed: 17344322
DOI: 10.1093/NAR/GKM064