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Manganese in PDB 3a4k: Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution

Enzymatic activity of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution

All present enzymatic activity of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution:
3.1.21.4;

Protein crystallography data

The structure of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution, PDB code: 3a4k was solved by N.Watanabe, C.Sato, Y.Takasaki, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.67 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 83.460, 132.211, 94.070, 90.00, 111.03, 90.00
R / Rfree (%) 17.8 / 22.6

Other elements in 3a4k:

The structure of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution (pdb code 3a4k). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution, PDB code: 3a4k:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3a4k

Go back to Manganese Binding Sites List in 3a4k
Manganese binding site 1 out of 4 in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:27.4
occ:1.00
 OP3 F:DA1 1.9 23.2 1.0
OD2 A:ASP93 2.0 22.6 1.0
O A:ALA109 2.0 22.3 1.0
O A:HOH570 2.1 23.8 1.0
OD2 A:ASP108 2.1 32.5 1.0
OP2 F:DA1 2.9 27.4 1.0
CG A:ASP93 3.0 24.7 1.0
CG A:ASP108 3.0 30.9 1.0
P F:DA1 3.0 26.5 1.0
C A:ALA109 3.1 21.7 1.0
N A:ALA109 3.4 22.6 1.0
OD1 A:ASP93 3.4 23.9 1.0
OD1 A:ASP108 3.6 30.9 1.0
CA A:ALA109 3.7 22.2 1.0
C A:ASP108 3.9 25.5 1.0
MG A:MG301 4.0 30.8 1.0
O5' F:DA1 4.0 25.4 1.0
O F:HOH71 4.1 17.0 1.0
OD1 A:ASP68 4.1 26.1 1.0
CB A:ASP108 4.1 27.7 1.0
OP1 F:DA1 4.1 23.9 1.0
CA A:ASP108 4.2 26.1 1.0
NZ A:LYS110 4.2 34.9 1.0
CB A:ALA109 4.2 21.0 1.0
C5' F:DA1 4.2 24.6 1.0
N A:LYS110 4.3 22.5 1.0
CB A:ASP93 4.3 24.8 1.0
CG A:LYS110 4.6 29.6 1.0
CA A:LYS110 4.6 22.8 1.0
O A:HOH320 4.7 25.3 1.0
O A:HOH386 4.7 19.2 1.0
O A:ASP108 4.8 23.9 1.0

Manganese binding site 2 out of 4 in 3a4k

Go back to Manganese Binding Sites List in 3a4k
Manganese binding site 2 out of 4 in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:33.0
occ:1.00
 OP1 H:DA1 2.0 27.3 1.0
OD2 C:ASP93 2.0 28.2 1.0
O C:ALA109 2.1 25.8 1.0
OD2 C:ASP108 2.2 31.3 1.0
O C:HOH573 2.3 32.4 1.0
OP3 H:DA1 2.7 33.2 1.0
P H:DA1 2.9 31.4 1.0
CG C:ASP93 3.0 27.6 1.0
CG C:ASP108 3.1 34.0 1.0
C C:ALA109 3.2 26.4 1.0
OD1 C:ASP93 3.2 27.0 1.0
N C:ALA109 3.4 28.1 1.0
OD1 C:ASP108 3.6 37.2 1.0
CA C:ALA109 3.8 26.9 1.0
MG C:MG301 3.9 34.8 1.0
O5' H:DA1 3.9 27.2 1.0
C C:ASP108 4.0 29.6 1.0
C5' H:DA1 4.0 26.7 1.0
NZ C:LYS110 4.1 33.9 1.0
OP2 H:DA1 4.1 32.1 1.0
OD1 C:ASP68 4.1 31.4 1.0
CG C:LYS110 4.2 34.6 1.0
O H:HOH171 4.2 25.4 1.0
CA C:ASP108 4.2 30.0 1.0
CB C:ASP108 4.2 30.9 1.0
CB C:ALA109 4.2 26.1 1.0
CB C:ASP93 4.3 28.5 1.0
N C:LYS110 4.4 25.6 1.0
O H:HOH84 4.4 27.8 1.0
O C:HOH421 4.4 31.6 1.0
CA C:LYS110 4.7 26.2 1.0
O C:ASP108 4.9 30.5 1.0
CE C:LYS110 4.9 36.1 1.0

Manganese binding site 3 out of 4 in 3a4k

Go back to Manganese Binding Sites List in 3a4k
Manganese binding site 3 out of 4 in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:32.0
occ:1.00
 OP3 J:DA1 2.0 25.9 1.0
OD2 B:ASP93 2.0 26.1 1.0
O B:ALA109 2.0 27.0 1.0
OD1 B:ASP108 2.2 29.1 1.0
O B:HOH494 2.2 23.1 1.0
OP2 J:DA1 2.6 32.1 1.0
P J:DA1 2.9 28.4 1.0
CG B:ASP93 3.0 26.2 1.0
CG B:ASP108 3.1 30.8 1.0
C B:ALA109 3.2 27.1 1.0
N B:ALA109 3.4 27.7 1.0
OD1 B:ASP93 3.4 25.5 1.0
OD2 B:ASP108 3.6 36.3 1.0
CA B:ALA109 3.8 27.3 1.0
C B:ASP108 3.9 28.8 1.0
O5' J:DA1 4.0 26.9 1.0
MG B:MG301 4.0 37.5 1.0
OP1 J:DA1 4.1 28.4 1.0
OD1 B:ASP68 4.1 28.3 1.0
O J:HOH85 4.1 25.3 1.0
C5' J:DA1 4.2 23.0 1.0
CB B:ASP108 4.2 30.9 1.0
CA B:ASP108 4.2 29.0 1.0
CE B:LYS110 4.3 41.8 1.0
CB B:ALA109 4.3 24.6 1.0
N B:LYS110 4.3 26.6 1.0
CB B:ASP93 4.3 27.5 1.0
O B:HOH333 4.4 32.2 1.0
O B:HOH342 4.5 26.0 1.0
NZ B:LYS110 4.6 44.9 1.0
CA B:LYS110 4.7 28.6 1.0
CG B:LYS110 4.7 36.3 1.0
O B:ASP108 4.8 29.2 1.0

Manganese binding site 4 out of 4 in 3a4k

Go back to Manganese Binding Sites List in 3a4k
Manganese binding site 4 out of 4 in the Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structural Analysis of Hindiii Restriction Endonuclease in Complex with Cognate Dna and Divalent Cations at 2.17 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:34.2
occ:1.00
 OP3 L:DA1 2.0 31.4 1.0
OD2 D:ASP93 2.1 29.1 1.0
O D:ALA109 2.1 25.8 1.0
O D:HOH571 2.2 25.4 1.0
OD2 D:ASP108 2.2 30.1 1.0
OP2 L:DA1 2.7 32.3 1.0
CG D:ASP93 3.0 26.5 1.0
P L:DA1 3.0 29.4 1.0
CG D:ASP108 3.1 31.7 1.0
C D:ALA109 3.2 26.3 1.0
OD1 D:ASP93 3.4 25.8 1.0
N D:ALA109 3.4 25.9 1.0
OD1 D:ASP108 3.7 35.6 1.0
CA D:ALA109 3.8 26.5 1.0
MG D:MG301 3.9 29.5 1.0
C D:ASP108 4.0 27.2 1.0
O D:HOH378 4.0 21.6 1.0
O5' L:DA1 4.1 30.2 1.0
OP1 L:DA1 4.1 29.5 1.0
OD1 D:ASP68 4.1 25.2 1.0
C5' L:DA1 4.2 25.8 1.0
NZ D:LYS110 4.2 35.8 1.0
CB D:ASP108 4.2 28.9 1.0
CA D:ASP108 4.2 27.7 1.0
CB D:ALA109 4.3 24.7 1.0
N D:LYS110 4.3 26.4 1.0
CB D:ASP93 4.3 26.5 1.0
O D:HOH572 4.4 26.2 1.0
O L:HOH168 4.4 22.0 1.0
CD D:LYS110 4.5 39.0 1.0
CA D:LYS110 4.7 27.4 1.0
O D:ASP108 4.9 26.9 1.0
CE D:LYS110 5.0 36.9 1.0

Reference:

N.Watanabe, Y.Takasaki, C.Sato, S.Ando, I.Tanaka. Structures of Restriction Endonuclease Hindiii in Complex with Its Cognate Dna and Divalent Cations Acta Crystallogr.,Sect.D V. 65 1326 2009.
ISSN: ISSN 0907-4449
PubMed: 19966419
DOI: 10.1107/S0907444909041134
Page generated: Sat Oct 5 15:38:58 2024

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