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Manganese in PDB 1eo4: Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site

Enzymatic activity of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site

All present enzymatic activity of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site:
3.1.21.4;

Protein crystallography data

The structure of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site, PDB code: 1eo4 was solved by N.C.Horton, B.A.Connolly, J.J.Perona, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 4.90 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 47.700, 48.500, 63.700, 96.70, 109.60, 106.30
R / Rfree (%) 21.3 / 30.5

Manganese Binding Sites:

The binding sites of Manganese atom in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site (pdb code 1eo4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site, PDB code: 1eo4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1eo4

Go back to Manganese Binding Sites List in 1eo4
Manganese binding site 1 out of 5 in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:52.2
occ:1.00
 O A:HOH619 2.0 23.3 1.0
O A:HOH686 2.0 51.6 1.0
O A:HOH678 2.0 40.8 1.0
O B:HOH698 2.1 63.6 1.0
OE2 A:GLU45 2.3 37.2 1.0
OD1 A:ASP74 2.8 31.6 1.0
O B:HOH709 3.4 46.6 1.0
CG A:ASP74 3.4 27.7 1.0
CD A:GLU45 3.5 35.7 1.0
CB A:ASP74 3.8 28.7 1.0
CA A:ASP74 3.9 28.3 1.0
O B:HOH699 3.9 51.0 1.0
OE1 A:GLU45 4.0 40.5 1.0
OD2 A:ASP74 4.2 31.7 1.0
O A:HOH680 4.2 36.0 1.0
O A:ASP74 4.2 26.2 1.0
O A:HOH617 4.4 64.3 1.0
OE2 A:GLU65 4.5 41.1 1.0
C A:ASP74 4.6 28.4 1.0
O A:HOH618 4.6 57.4 1.0
CG A:GLU45 4.7 34.4 1.0
CD A:PRO66 4.9 36.6 1.0
OD1 B:ASP36 5.0 44.6 1.0

Manganese binding site 2 out of 5 in 1eo4

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Manganese binding site 2 out of 5 in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:61.0
occ:1.00
 O A:HOH710 2.0 43.7 1.0
O A:HOH687 2.0 63.9 1.0
O A:HOH719 2.1 61.0 1.0
O A:HOH624 2.1 47.8 1.0
NE2 A:HIS193 2.3 26.7 1.0
O A:LYS102 3.3 31.5 1.0
CE1 A:HIS193 3.3 26.4 1.0
CD2 A:HIS193 3.3 27.3 1.0
O A:HOH732 3.6 38.5 1.0
O A:HOH622 3.8 77.3 1.0
C A:LYS102 4.0 30.7 1.0
O A:HOH709 4.2 72.2 1.0
CB A:LYS102 4.2 30.8 1.0
ND1 A:HIS193 4.5 26.8 1.0
O A:HOH731 4.5 43.3 1.0
CG A:HIS193 4.5 24.4 1.0
O A:HOH663 4.6 56.6 1.0
CA A:LYS102 4.6 32.0 1.0
O A:HOH730 4.6 40.0 1.0
N A:ILE103 4.7 27.4 1.0
CA A:ILE103 4.9 25.1 1.0

Manganese binding site 3 out of 5 in 1eo4

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Manganese binding site 3 out of 5 in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn503

b:39.9
occ:1.00
 O A:HOH607 2.0 56.2 1.0
O A:HOH706 2.0 44.1 1.0
O A:HOH689 2.2 32.7 1.0
NE2 A:HIS71 2.2 44.0 1.0
CE1 A:HIS71 3.2 44.2 1.0
CD2 A:HIS71 3.2 42.6 1.0
ND1 A:HIS71 4.3 42.1 1.0
CG A:HIS71 4.4 41.8 1.0
N A:ASN120 4.4 27.7 1.0
O A:THR118 4.5 31.3 1.0
CA A:ASN120 4.8 27.9 1.0
O3' D:DT10 4.9 48.0 1.0

Manganese binding site 4 out of 5 in 1eo4

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Manganese binding site 4 out of 5 in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn504

b:55.4
occ:1.00
 O A:HOH662 2.0 75.2 1.0
O A:HOH618 2.0 57.4 1.0
O C:HOH23 2.1 34.2 1.0
OD2 A:ASP74 2.2 31.7 1.0
O A:ILE91 2.4 24.0 1.0
OE1 A:GLU45 2.8 40.5 1.0
CG A:ASP74 3.1 27.7 1.0
OD1 A:ASP74 3.3 31.6 1.0
C A:ILE91 3.5 23.2 1.0
O A:HOH619 3.8 23.3 1.0
O A:HOH646 3.8 52.4 1.0
CD A:GLU45 3.9 35.7 1.0
N A:ILE91 3.9 23.5 1.0
CB A:ILE91 4.0 26.6 1.0
CA A:ILE91 4.0 23.6 1.0
C5' C:DA7 4.4 32.9 1.0
O A:HOH659 4.4 31.6 1.0
OE2 A:GLU45 4.4 37.2 1.0
CB A:ASP74 4.5 28.7 1.0
OD1 A:ASP90 4.5 31.5 1.0
O C:HOH172 4.6 25.8 1.0
C4' C:DA7 4.6 31.9 1.0
OD2 A:ASP90 4.6 27.2 1.0
OP1 C:DT8 4.7 41.2 1.0
N A:LYS92 4.7 23.1 1.0
O3' C:DA7 4.7 35.2 1.0
OP2 C:DA7 4.7 40.7 1.0
C3' C:DA7 4.7 33.1 1.0
CG A:ASP90 4.7 27.2 1.0
CG2 A:ILE91 4.9 26.3 1.0
CG A:GLU45 5.0 34.4 1.0
C A:ASP90 5.0 23.3 1.0

Manganese binding site 5 out of 5 in 1eo4

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Manganese binding site 5 out of 5 in the Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Ecorv Bound to MN2+ and Cognate Dna Containing A 3'S Substition at the Cleavage Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn505

b:33.4
occ:1.00
 O C:HOH184 2.0 28.2 1.0
O C:HOH84 2.0 21.3 1.0
O B:HOH622 2.1 26.0 1.0
OP1 C:DT11 2.2 42.0 1.0
NE2 B:HIS71 2.3 32.4 1.0
CD2 B:HIS71 3.2 34.5 1.0
CE1 B:HIS71 3.4 35.7 1.0
P C:DT11 3.7 38.1 1.0
C5' C:DT11 4.1 45.3 1.0
O B:THR118 4.3 33.0 1.0
O5' C:DT11 4.3 41.6 1.0
O3' C:DT10 4.4 37.5 1.0
CG B:HIS71 4.4 33.4 1.0
N B:ASN120 4.4 24.6 1.0
ND1 B:HIS71 4.4 36.3 1.0
OP2 C:DT11 4.7 38.4 1.0
CA B:ASN120 4.8 25.1 1.0
O B:ILE121 4.8 25.1 1.0

Reference:

N.C.Horton, B.A.Connolly, J.J.Perona. Inhibition of Ecorv Endonuclease By Deoxyribo-3'-S-Phosphorothiolates: A High-Resolution X-Ray Crystallographic Study J.Am.Chem.Soc. V. 122 3314 2000.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA993719J
Page generated: Sat Oct 5 10:14:02 2024

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