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Magnesium in PDB 1fiu: Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna

Enzymatic activity of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna

All present enzymatic activity of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna:
3.1.21.4;

Protein crystallography data

The structure of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna, PDB code: 1fiu was solved by M.Deibert, S.Grazulis, G.Sasnauskas, V.Siksnys, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.26 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 90.400, 91.130, 149.520, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna (pdb code 1fiu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna, PDB code: 1fiu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1fiu

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Magnesium binding site 1 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg2222

b:23.5
occ:1.00
 OD1 B:ASP140 2.0 17.4 1.0
O B:HOH3345 2.1 27.5 1.0
O B:ACY3002 2.1 23.7 1.0
O I:HOH259 2.2 34.7 1.0
O B:HOH3403 2.3 26.1 1.0
OP2 I:DC5 2.3 20.6 1.0
OP3 I:DC5 3.1 22.9 1.0
CG B:ASP140 3.1 18.4 1.0
P I:DC5 3.2 18.5 1.0
C B:ACY3002 3.3 22.4 1.0
OD2 B:ASP140 3.5 19.3 1.0
MG B:MG3333 3.6 15.3 1.0
O B:HOH3384 3.9 24.7 1.0
O B:HOH3387 3.9 39.5 1.0
O B:HOH3402 3.9 28.2 1.0
OXT B:ACY3002 4.0 21.6 1.0
OP1 I:DC5 4.2 18.1 1.0
OE2 B:GLU201 4.3 29.4 1.0
OE1 B:GLU201 4.3 28.7 1.0
CH3 B:ACY3002 4.3 20.0 1.0
CB B:ASP140 4.4 18.7 1.0
N B:ASP140 4.4 16.1 1.0
O5' I:DC5 4.4 18.6 1.0
O3' E:DG4 4.4 20.7 1.0
CA B:ASP140 4.5 17.1 1.0
C5' I:DC5 4.6 19.1 1.0
O B:HOH3557 4.6 36.9 1.0
O B:HOH3390 4.7 20.5 1.0
CD B:GLU201 4.8 32.6 1.0
O B:THR138 4.8 28.5 1.0
OE2 B:GLU70 4.9 22.8 1.0
C B:PRO139 5.0 24.5 1.0

Magnesium binding site 2 out of 8 in 1fiu

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Magnesium binding site 2 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg4444

b:31.4
occ:1.00
 OXT A:ACY2001 2.1 25.4 1.0
OD1 A:ASP140 2.2 17.7 1.0
O F:HOH22 2.2 26.0 1.0
OP2 J:DC5 2.3 21.2 1.0
O A:HOH5562 2.3 40.0 1.0
O A:HOH5593 2.3 28.8 1.0
OP3 J:DC5 2.9 26.0 1.0
P J:DC5 3.1 20.3 1.0
CG A:ASP140 3.2 20.1 1.0
C A:ACY2001 3.3 26.0 1.0
OD2 A:ASP140 3.6 18.1 1.0
MG A:MG5555 3.7 15.9 1.0
O A:ACY2001 3.9 23.7 1.0
O A:HOH5559 4.0 30.5 1.0
O A:THR138 4.1 32.0 1.0
OP1 J:DC5 4.1 18.4 1.0
O A:HOH5602 4.1 24.9 1.0
O3' F:DG4 4.2 23.4 1.0
OE1 A:GLU201 4.3 30.8 1.0
O5' J:DC5 4.3 19.6 1.0
OE2 A:GLU201 4.4 36.1 1.0
CH3 A:ACY2001 4.4 21.7 1.0
N A:ASP140 4.4 19.4 1.0
CB A:ASP140 4.5 17.2 1.0
C5' J:DC5 4.5 22.9 1.0
CA A:ASP140 4.6 16.1 1.0
O A:HOH5601 4.7 39.4 1.0
O J:HOH450 4.7 36.2 1.0
CD A:GLU201 4.8 33.0 1.0
O A:HOH5564 4.8 18.2 1.0
C A:PRO139 4.9 22.1 1.0
O J:HOH221 5.0 18.2 1.0
OE2 A:GLU70 5.0 22.5 1.0

Magnesium binding site 3 out of 8 in 1fiu

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Magnesium binding site 3 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg6666

b:24.1
occ:1.00
 OD1 C:ASP140 2.1 15.0 1.0
OXT C:ACY4003 2.2 21.1 1.0
O K:HOH271 2.2 34.0 1.0
O C:HOH7779 2.2 26.9 1.0
OP2 K:DC5 2.3 16.5 1.0
O C:HOH7780 2.3 26.9 1.0
OP3 K:DC5 2.9 24.2 1.0
P K:DC5 3.1 16.8 1.0
CG C:ASP140 3.1 18.9 1.0
C C:ACY4003 3.3 22.3 1.0
OD2 C:ASP140 3.6 14.3 1.0
MG C:MG7777 3.7 13.9 1.0
O C:HOH7819 3.9 27.0 1.0
O C:ACY4003 3.9 17.8 1.0
O C:HOH7829 3.9 24.1 1.0
O C:THR138 4.1 33.2 1.0
OP1 K:DC5 4.2 16.4 1.0
OE1 C:GLU201 4.2 25.8 1.0
OE2 C:GLU201 4.3 33.8 1.0
O3' G:DG4 4.3 23.3 1.0
N C:ASP140 4.3 14.8 1.0
O5' K:DC5 4.4 14.4 1.0
CB C:ASP140 4.4 13.6 1.0
CH3 C:ACY4003 4.4 19.9 1.0
CA C:ASP140 4.6 14.9 1.0
C5' K:DC5 4.6 16.6 1.0
CD C:GLU201 4.7 31.7 1.0
O C:HOH7804 4.7 46.0 1.0
O C:HOH7781 4.8 17.6 1.0
C C:PRO139 4.8 24.4 1.0
O K:HOH238 4.9 31.3 1.0
OE2 C:GLU70 5.0 22.1 1.0
O K:HOH328 5.0 16.1 1.0

Magnesium binding site 4 out of 8 in 1fiu

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Magnesium binding site 4 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg8888

b:22.8
occ:1.00
 OD1 D:ASP140 2.1 14.8 1.0
O D:ACY5004 2.2 21.7 1.0
O D:HOH1118 2.2 20.9 1.0
O D:HOH1109 2.2 23.9 1.0
OP2 L:DC5 2.3 16.6 1.0
O D:HOH1026 2.4 24.3 1.0
OP3 L:DC5 3.1 21.7 1.0
P L:DC5 3.1 17.4 1.0
CG D:ASP140 3.2 19.8 1.0
C D:ACY5004 3.2 23.3 1.0
OD2 D:ASP140 3.5 14.9 1.0
MG D:MG9999 3.6 12.0 1.0
O D:HOH1119 3.8 22.6 1.0
OXT D:ACY5004 3.9 18.8 1.0
O D:HOH1020 3.9 23.9 1.0
O D:HOH1267 4.0 35.5 1.0
OP1 L:DC5 4.1 14.7 1.0
OE1 D:GLU201 4.2 23.6 1.0
CH3 D:ACY5004 4.3 19.6 1.0
OE2 D:GLU201 4.3 27.1 1.0
N D:ASP140 4.4 14.4 1.0
O5' L:DC5 4.4 15.3 1.0
CB D:ASP140 4.4 14.8 1.0
O D:THR138 4.5 24.7 1.0
CA D:ASP140 4.6 14.8 1.0
O3' H:DG4 4.6 25.9 1.0
C5' L:DC5 4.7 15.3 1.0
CD D:GLU201 4.7 25.9 1.0
O D:HOH1022 4.8 16.3 1.0
O L:HOH347 4.9 24.9 1.0
ND2 D:ASN197 5.0 10.8 1.0
O L:HOH55 5.0 16.1 1.0

Magnesium binding site 5 out of 8 in 1fiu

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Magnesium binding site 5 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5555

b:15.9
occ:1.00
 OP2 J:DC5 2.1 21.2 1.0
O J:HOH221 2.2 18.2 1.0
OD2 A:ASP140 2.2 18.1 1.0
O A:CYS186 2.2 17.5 1.0
O A:HOH5564 2.2 18.2 1.0
O A:ACY2001 2.3 23.7 1.0
C A:ACY2001 3.1 26.0 1.0
CG A:ASP140 3.1 20.1 1.0
OXT A:ACY2001 3.2 25.4 1.0
P J:DC5 3.3 20.3 1.0
C A:CYS186 3.4 15.6 1.0
OD1 A:ASP140 3.4 17.7 1.0
OP1 J:DC5 3.6 18.4 1.0
MG J:MG4444 3.7 31.4 1.0
N A:CYS186 3.7 15.1 1.0
O5' J:DC5 4.0 19.6 1.0
C5' J:DC5 4.1 22.9 1.0
CA A:CYS186 4.1 16.6 1.0
OE2 A:GLU70 4.2 22.5 1.0
OG A:SER185 4.2 29.0 1.0
CG A:LYS187 4.3 15.3 1.0
NZ A:LYS187 4.4 22.1 1.0
OP2 J:DC6 4.4 19.0 1.0
N A:LYS187 4.5 16.1 1.0
CB A:ASP140 4.5 17.2 1.0
O J:HOH43 4.5 15.9 1.0
CH3 A:ACY2001 4.6 21.7 1.0
CB A:CYS186 4.6 14.7 1.0
OP3 J:DC5 4.6 26.0 1.0
CA A:LYS187 4.7 17.2 1.0
C A:SER185 4.7 18.1 1.0
O3' J:DC5 4.9 15.7 1.0
P J:DC6 4.9 17.4 1.0

Magnesium binding site 6 out of 8 in 1fiu

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Magnesium binding site 6 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3333

b:15.3
occ:1.00
 OP2 I:DC5 2.2 20.6 1.0
O I:HOH57 2.2 18.3 1.0
OD2 B:ASP140 2.2 19.3 1.0
O B:CYS186 2.2 15.9 1.0
O B:HOH3390 2.3 20.5 1.0
OXT B:ACY3002 2.3 21.6 1.0
C B:ACY3002 3.0 22.4 1.0
CG B:ASP140 3.2 18.4 1.0
O B:ACY3002 3.2 23.7 1.0
P I:DC5 3.3 18.5 1.0
C B:CYS186 3.4 16.2 1.0
OD1 B:ASP140 3.4 17.4 1.0
MG I:MG2222 3.6 23.5 1.0
OP1 I:DC5 3.6 18.1 1.0
N B:CYS186 3.8 14.4 1.0
O5' I:DC5 4.0 18.6 1.0
C5' I:DC5 4.1 19.1 1.0
CA B:CYS186 4.1 15.7 1.0
OE2 B:GLU70 4.3 22.8 1.0
CG B:LYS187 4.3 16.1 1.0
NZ B:LYS187 4.3 19.0 1.0
OG B:SER185 4.3 33.4 1.0
OP2 I:DC6 4.4 17.2 1.0
O I:HOH56 4.4 17.5 1.0
N B:LYS187 4.5 15.2 1.0
CB B:ASP140 4.5 18.7 1.0
CH3 B:ACY3002 4.5 20.0 1.0
CB B:CYS186 4.6 15.4 1.0
OP3 I:DC5 4.6 22.9 1.0
C B:SER185 4.8 17.9 1.0
CA B:LYS187 4.8 17.1 1.0
O3' I:DC5 4.9 16.7 1.0
P I:DC6 4.9 17.4 1.0

Magnesium binding site 7 out of 8 in 1fiu

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Magnesium binding site 7 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg7777

b:13.9
occ:1.00
 OP2 K:DC5 2.1 16.5 1.0
O C:CYS186 2.2 13.5 1.0
OD2 C:ASP140 2.2 14.3 1.0
O C:HOH7781 2.2 17.6 1.0
O K:HOH328 2.2 16.1 1.0
O C:ACY4003 2.3 17.8 1.0
CG C:ASP140 3.1 18.9 1.0
C C:ACY4003 3.2 22.3 1.0
OXT C:ACY4003 3.3 21.1 1.0
P K:DC5 3.3 16.8 1.0
C C:CYS186 3.3 13.4 1.0
OD1 C:ASP140 3.4 15.0 1.0
MG K:MG6666 3.7 24.1 1.0
N C:CYS186 3.7 12.1 1.0
OP1 K:DC5 3.7 16.4 1.0
O5' K:DC5 3.9 14.4 1.0
CA C:CYS186 4.0 12.4 1.0
C5' K:DC5 4.1 16.6 1.0
OE2 C:GLU70 4.2 22.1 1.0
CG C:LYS187 4.3 12.8 1.0
NZ C:LYS187 4.3 19.1 1.0
OG C:SER185 4.4 30.0 1.0
OP2 K:DC6 4.4 15.6 1.0
N C:LYS187 4.4 12.8 1.0
O K:HOH67 4.4 13.9 1.0
CB C:ASP140 4.4 13.6 1.0
CB C:CYS186 4.5 13.9 1.0
OP3 K:DC5 4.6 24.2 1.0
CH3 C:ACY4003 4.6 19.9 1.0
C C:SER185 4.7 16.4 1.0
CA C:LYS187 4.7 13.1 1.0
O3' K:DC5 4.8 13.7 1.0
P K:DC6 4.9 14.1 1.0
OP1 K:DC6 5.0 15.0 1.0

Magnesium binding site 8 out of 8 in 1fiu

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Magnesium binding site 8 out of 8 in the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg9999

b:12.0
occ:1.00
 OP2 L:DC5 2.2 16.6 1.0
OD2 D:ASP140 2.2 14.9 1.0
O D:CYS186 2.2 12.2 1.0
O D:HOH1022 2.2 16.3 1.0
O L:HOH55 2.2 16.1 1.0
OXT D:ACY5004 2.3 18.8 1.0
C D:ACY5004 3.1 23.3 1.0
CG D:ASP140 3.2 19.8 1.0
O D:ACY5004 3.2 21.7 1.0
P L:DC5 3.4 17.4 1.0
C D:CYS186 3.4 12.7 1.0
OD1 D:ASP140 3.4 14.8 1.0
MG L:MG8888 3.6 22.8 1.0
N D:CYS186 3.7 10.9 1.0
OP1 L:DC5 3.7 14.7 1.0
O5' L:DC5 4.0 15.3 1.0
CA D:CYS186 4.1 11.5 1.0
C5' L:DC5 4.1 15.3 1.0
OE2 D:GLU70 4.2 19.8 1.0
CG D:LYS187 4.3 13.8 1.0
NZ D:LYS187 4.3 18.3 1.0
OP2 L:DC6 4.4 13.8 1.0
N D:LYS187 4.5 13.7 1.0
CB D:ASP140 4.5 14.8 1.0
O L:HOH52 4.5 14.2 1.0
CH3 D:ACY5004 4.6 19.6 1.0
CB D:CYS186 4.6 13.2 1.0
OP3 L:DC5 4.6 21.7 1.0
C D:SER185 4.7 13.1 1.0
CA D:LYS187 4.7 13.4 1.0
O3' L:DC5 4.9 12.9 1.0
P L:DC6 5.0 13.0 1.0
O D:HOH1119 5.0 22.6 1.0
CA D:SER185 5.0 12.6 1.0

Reference:

M.Deibert, S.Grazulis, G.Sasnauskas, V.Siksnys, R.Huber. Structure of the Tetrameric Restriction Endonuclease Ngomiv in Complex with Cleaved Dna. Nat.Struct.Biol. V. 7 792 2000.
ISSN: ISSN 1072-8368
PubMed: 10966652
DOI: 10.1038/79032
Page generated: Tue Aug 13 03:16:23 2024

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