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Magnesium in PDB 1g8t: Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution

Enzymatic activity of Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution

All present enzymatic activity of Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution:
3.1.30.2;

Protein crystallography data

The structure of Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution, PDB code: 1g8t was solved by V.V.Lunin, M.Perbandt, C.H.Betzel, A.M.Mikhailov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 106.390, 73.670, 68.120, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 15.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution (pdb code 1g8t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution, PDB code: 1g8t:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1g8t

Go back to Magnesium Binding Sites List in 1g8t
Magnesium binding site 1 out of 2 in the Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg810

b:7.1
occ:1.00
O A:HOH1247 2.0 13.2 1.0
O A:HOH1250 2.1 13.1 1.0
OD1 A:ASN119 2.1 14.3 1.0
O A:HOH1249 2.1 11.2 1.0
O A:HOH1248 2.1 9.6 0.5
O A:HOH1246 2.1 8.4 0.7
O A:HOH1163 2.7 16.2 0.3
O A:HOH1164 3.0 24.4 0.5
CG A:ASN119 3.3 10.9 1.0
ND2 A:ASN119 3.9 14.9 1.0
OE2 A:GLU127 3.9 12.5 1.0
O3 A:SO4801 3.9 20.6 0.5
OE1 A:GLU127 4.0 12.8 1.0
N A:HIS89 4.0 8.1 1.0
O A:HOH1136 4.1 16.9 0.5
O A:ASN119 4.1 11.0 1.0
OE1 A:GLN114 4.2 8.1 1.0
O A:HOH856 4.2 17.0 1.0
CD1 A:TRP123 4.2 9.5 1.0
CD A:GLU127 4.4 11.3 1.0
ND1 A:HIS89 4.4 9.6 1.0
O2 A:SO4801 4.5 20.1 0.5
CA A:GLY88 4.5 8.8 1.0
CB A:ASN119 4.5 10.3 1.0
CB A:HIS89 4.6 8.1 1.0
O A:HIS89 4.6 8.0 1.0
O A:HOH1162 4.6 31.0 0.5
CA A:ASN119 4.7 9.8 1.0
C A:GLY88 4.7 7.5 1.0
C A:ASN119 4.7 10.1 1.0
NE1 A:TRP123 4.8 10.0 1.0
CA A:HIS89 4.8 7.8 1.0
S A:SO4801 4.8 18.5 0.5
CG A:HIS89 5.0 8.6 1.0

Magnesium binding site 2 out of 2 in 1g8t

Go back to Magnesium Binding Sites List in 1g8t
Magnesium binding site 2 out of 2 in the Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Sm Endonuclease From Seratia Marcenscens at 1.1 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg811

b:4.6
occ:1.00
OD1 B:ASN119 2.0 11.1 1.0
O B:HOH1217 2.0 9.8 1.0
O B:HOH1218 2.1 8.8 1.0
O B:HOH1220 2.1 9.8 1.0
O B:HOH1216 2.1 9.4 1.0
O B:HOH1219 2.1 13.7 1.0
CG B:ASN119 3.3 10.0 1.0
ND2 B:ASN119 3.9 11.5 1.0
OE2 B:GLU127 4.0 9.6 1.0
O3 B:SO4802 4.0 12.8 0.6
OE1 B:GLU127 4.0 10.1 1.0
N B:HIS89 4.0 7.4 1.0
O B:ASN119 4.1 10.8 1.0
O4 B:SO4802 4.1 14.7 0.6
OE1 B:GLN114 4.2 7.7 1.0
O B:HOH844 4.2 11.3 1.0
O B:HOH1182 4.3 15.1 0.3
CD1 B:TRP123 4.4 8.7 1.0
ND1 B:HIS89 4.4 8.3 1.0
CB B:ASN119 4.4 10.2 1.0
CD B:GLU127 4.4 8.8 1.0
O B:HIS89 4.5 7.7 1.0
CA B:GLY88 4.5 8.9 1.0
CB B:HIS89 4.6 7.6 1.0
CA B:ASN119 4.6 9.6 1.0
C B:ASN119 4.7 10.4 1.0
S B:SO4802 4.7 13.2 0.6
C B:GLY88 4.8 7.6 1.0
CA B:HIS89 4.8 7.4 1.0
NE1 B:TRP123 4.9 8.8 1.0
CG B:HIS89 5.0 7.6 1.0

Reference:

S.V.Shlyapnikov, V.V.Lunin, M.Perbandt, K.M.Polyakov, V.Y.Lunin, V.M.Levdikov, C.Betzel, A.M.Mikhailov. Atomic Structure of the Serratia Marcescens Endonuclease at 1.1 A Resolution and the Enzyme Reaction Mechanism. Acta Crystallogr.,Sect.D V. 56 567 2000.
ISSN: ISSN 0907-4449
PubMed: 10771425
DOI: 10.1107/S090744490000322X
Page generated: Mon Dec 14 05:57:31 2020

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