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

Protein crystallography data

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

Other elements in 2oa9:

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

Chlorine (Cl) 2 atoms

Cadmium 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; 11; 12; 13; 14; 15;

Cadmium binding site 1 out of 15 in 2oa9

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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 2oa9

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


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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 2oa9

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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 2oa9

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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 2oa9

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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 2oa9

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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 2oa9

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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 2oa9

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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 2oa9

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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 2oa9

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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

Cadmium binding site 11 out of 15 in 2oa9

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Cadmium binding site 11 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 11 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd901

b:18.1
occ:1.00
OD2 A:ASP203 2.3 10.8 1.0
OE2 B:GLU234 2.3 16.6 1.0
ND1 B:HIS59 2.3 20.2 1.0
OE1 A:GLU238 2.4 13.4 1.0
OE2 A:GLU238 2.5 16.6 1.0
OE1 B:GLU234 2.5 16.7 1.0
CD B:GLU234 2.7 17.2 1.0
CD A:GLU238 2.8 14.3 1.0
CE1 B:HIS59 3.2 23.6 1.0
CG B:HIS59 3.3 15.3 1.0
CG A:ASP203 3.3 13.7 1.0
CB B:HIS59 3.6 15.8 1.0
OD1 A:ASP203 3.6 15.2 1.0
OH A:TYR239 3.9 11.1 1.0
CD1 B:LEU237 4.2 15.6 1.0
CG B:GLU234 4.2 16.5 1.0
CG A:GLU238 4.3 15.6 1.0
NE2 B:HIS59 4.4 19.3 1.0
O A:HOH924 4.4 21.9 1.0
CD2 B:HIS59 4.4 17.5 1.0
CA B:HIS59 4.5 14.6 1.0
NZ A:LYS235 4.5 25.9 1.0
CE2 A:TYR239 4.6 11.7 1.0
CZ A:TYR239 4.6 10.0 1.0
O A:HOH931 4.6 25.1 1.0
CB A:ASP203 4.6 12.4 1.0
O A:HOH933 4.9 25.4 1.0
CG1 B:VAL165 5.0 14.6 1.0

Cadmium binding site 12 out of 15 in 2oa9

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Cadmium binding site 12 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 12 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd902

b:21.7
occ:1.00
OD2 B:ASP207 2.2 18.4 1.0
O B:HOH1030 2.3 27.1 1.0
O B:HOH938 2.3 21.3 1.0
NE2 B:HIS100 2.3 13.0 1.0
O B:HOH935 2.4 25.8 1.0
OD1 B:ASP207 2.9 24.1 1.0
CG B:ASP207 2.9 18.9 1.0
CD2 B:HIS100 3.3 14.1 1.0
CE1 B:HIS100 3.3 13.4 1.0
O B:HOH949 3.5 28.3 1.0
OG1 B:THR102 4.1 15.5 1.0
NE B:ARG209 4.3 18.9 1.0
CB B:ASP207 4.3 12.8 1.0
ND1 B:HIS100 4.4 14.3 1.0
CG B:HIS100 4.4 12.9 1.0
NH2 B:ARG209 4.5 19.6 1.0
CZ B:ARG209 4.8 19.1 1.0
CH3 B:ACT600 4.9 28.5 1.0
CG B:ARG209 4.9 18.4 1.0

Cadmium binding site 13 out of 15 in 2oa9

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Cadmium binding site 13 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 13 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd908

b:29.5
occ:0.50
OE2 B:GLU40 2.2 33.5 1.0
ND1 B:HIS52 2.3 22.7 1.0
OE2 B:GLU43 2.5 25.9 1.0
OE1 B:GLU43 2.5 30.7 1.0
OE1 B:GLU40 2.7 31.6 1.0
CD B:GLU40 2.8 29.9 1.0
CD B:GLU43 2.8 26.5 1.0
CE1 B:HIS52 3.1 23.7 1.0
CG B:HIS52 3.4 27.3 1.0
CB B:HIS52 3.9 28.4 1.0
CG B:GLU40 4.2 28.0 1.0
NE2 B:HIS52 4.3 22.3 1.0
CG B:GLU43 4.3 25.2 1.0
CD2 B:HIS52 4.5 26.6 1.0
N B:HIS52 4.5 28.4 1.0
CA B:ASP50 4.8 30.0 1.0
CA B:HIS52 4.8 28.6 1.0
N B:ASP50 4.9 31.3 1.0

Cadmium binding site 14 out of 15 in 2oa9

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Cadmium binding site 14 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 14 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd910

b:20.3
occ:0.50
OXT B:ACT600 2.2 29.1 1.0
O B:HOH985 2.4 26.6 1.0
O B:ACT600 2.5 29.0 1.0
O B:ACT601 2.5 35.9 1.0
C B:ACT600 2.8 29.7 1.0
C B:ACT601 3.4 32.8 1.0
CH3 B:ACT601 4.0 36.3 1.0
OXT B:ACT601 4.1 35.2 1.0
CH3 B:ACT600 4.2 28.5 1.0
NE2 B:GLN101 4.5 16.4 1.0
O B:HOH955 4.6 23.1 1.0
OG B:SER113 4.6 19.9 1.0

Cadmium binding site 15 out of 15 in 2oa9

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Cadmium binding site 15 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 15 of Restriction Endonuclease Mvai in the Absence of Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd914

b:31.4
occ:0.50
OD1 B:ASP17 2.2 25.8 1.0
OXT B:VAL246 2.3 27.6 1.0
O B:VAL246 2.7 23.4 1.0
C B:VAL246 2.9 24.6 1.0
CG B:ASP17 3.2 22.2 1.0
OD2 B:ASP17 3.4 29.1 1.0
NE2 B:GLN13 3.7 31.8 1.0
CA B:VAL246 4.4 23.6 1.0
CB B:ASP17 4.5 17.9 1.0
CG1 B:VAL246 4.6 23.9 0.0
CB B:VAL246 4.8 23.8 1.0
CD B:GLN13 5.0 26.1 1.0

Reference:

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
Page generated: Wed Oct 28 09:59:56 2020
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