Atomistry » Magnesium » PDB 1f7d-1fnt » 1fiu
Atomistry »
  Magnesium »
    PDB 1f7d-1fnt »
      1fiu »

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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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

Go back to Magnesium Binding Sites List in 1fiu
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: Sat Aug 9 20:58:56 2025

Last articles

Mg in 4OKM
Mg in 4OLS
Mg in 4OL0
Mg in 4OKK
Mg in 4OKJ
Mg in 4OKQ
Mg in 4OK9
Mg in 4OKE
Mg in 4OJI
Mg in 4OJU
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy