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Manganese in PDB 1m0d: Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions

Enzymatic activity of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions

All present enzymatic activity of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions:
3.1.21.2;

Protein crystallography data

The structure of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions, PDB code: 1m0d was solved by J.M.Hadden, A.C.Declais, S.E.Phillips, D.M.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.80 / 1.90
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.810, 133.960, 61.460, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 23.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions (pdb code 1m0d). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions, PDB code: 1m0d:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 1m0d

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Manganese binding site 1 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:26.9
occ:1.00
 OE2 A:GLU65 2.1 26.4 1.0
OD2 A:ASP55 2.1 27.8 1.0
O A:HOH1002 2.2 30.0 1.0
O A:THR66 2.2 28.2 1.0
O B:HOH1003 2.3 26.8 1.0
O A:HOH1003 2.4 27.9 1.0
CG A:ASP55 3.0 37.1 1.0
CD A:GLU65 3.1 24.4 1.0
OD1 A:ASP55 3.3 33.4 1.0
O A:HOH1108 3.4 57.1 1.0
C A:THR66 3.4 24.4 1.0
MN A:MN2 3.6 35.0 0.8
OG1 A:THR66 3.7 24.6 1.0
N A:THR66 3.7 21.4 1.0
OE1 A:GLU65 3.8 26.6 1.0
O A:HOH1004 3.8 33.5 1.0
CG A:GLU65 4.0 21.8 1.0
CA A:THR66 4.1 23.4 1.0
NZ A:LYS67 4.2 29.9 1.0
OE2 B:GLU20 4.2 43.8 1.0
O1 A:SO41001 4.2 37.7 1.0
O2 A:SO41001 4.3 39.2 1.0
CE A:LYS67 4.4 24.2 1.0
N A:LYS67 4.4 24.1 1.0
CB A:ASP55 4.4 25.8 1.0
CB A:THR66 4.4 22.5 1.0
C A:GLU65 4.5 24.7 1.0
CA A:LYS67 4.6 26.5 1.0
O B:HOH1005 4.7 44.0 1.0
O A:HOH1005 4.7 41.2 1.0
S A:SO41001 4.8 56.5 1.0
CA A:GLU65 4.8 21.6 1.0
CB A:GLU65 5.0 20.7 1.0

Manganese binding site 2 out of 8 in 1m0d

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Manganese binding site 2 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:35.0
occ:0.75
 O A:HOH1002 1.8 30.0 1.0
O B:HOH1004 2.2 42.2 1.0
O B:HOH1005 2.2 44.0 1.0
OD1 A:ASP55 2.2 33.4 1.0
O A:HOH1004 2.2 33.5 1.0
O A:HOH1005 2.5 41.2 1.0
CG A:ASP55 3.2 37.1 1.0
OE2 B:GLU37 3.5 53.5 1.0
MN A:MN1 3.6 26.9 1.0
OD2 A:ASP55 3.6 27.8 1.0
O A:HOH1108 3.7 57.1 1.0
O A:THR53 3.9 28.7 1.0
OE2 A:GLU65 4.1 26.4 1.0
OE2 B:GLU20 4.2 43.8 1.0
CB A:ASP55 4.4 25.8 1.0
OE1 A:GLU65 4.4 26.6 1.0
CA A:ASP55 4.5 24.2 1.0
O B:HOH1003 4.5 26.8 1.0
N A:ASP55 4.5 26.0 1.0
CD B:GLU37 4.6 43.6 1.0
CD A:GLU65 4.7 24.4 1.0
O A:HOH1003 4.8 27.9 1.0
CG B:GLU37 4.8 42.0 1.0
O A:HOH1095 5.0 42.7 1.0

Manganese binding site 3 out of 8 in 1m0d

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Manganese binding site 3 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:27.5
occ:1.00
 O B:HOH1006 2.1 30.5 1.0
OE2 B:GLU65 2.1 26.5 1.0
O A:HOH1006 2.2 31.9 1.0
OD2 B:ASP55 2.2 28.1 1.0
O B:THR66 2.3 23.2 1.0
O B:HOH1007 2.3 27.0 1.0
CG B:ASP55 3.1 34.1 1.0
CD B:GLU65 3.1 36.4 1.0
OD1 B:ASP55 3.3 37.1 1.0
C B:THR66 3.4 31.9 1.0
MN B:MN4 3.5 43.3 0.8
O B:HOH1144 3.7 57.1 1.0
OG1 B:THR66 3.7 25.9 1.0
N B:THR66 3.7 24.3 1.0
OE1 B:GLU65 3.8 27.9 1.0
O B:HOH1008 4.0 29.9 1.0
CG B:GLU65 4.0 25.8 1.0
OE1 A:GLU20 4.0 42.0 1.0
NZ B:LYS67 4.1 26.5 1.0
CA B:THR66 4.1 25.9 1.0
O1 B:SO41002 4.3 35.4 1.0
CE B:LYS67 4.3 28.4 1.0
O2 B:SO41002 4.4 39.1 1.0
CB B:THR66 4.5 23.4 1.0
N B:LYS67 4.5 23.8 1.0
CB B:ASP55 4.5 27.6 1.0
C B:GLU65 4.5 22.9 1.0
O A:HOH1008 4.6 39.7 1.0
CA B:LYS67 4.7 24.3 1.0
S B:SO41002 4.8 46.3 1.0
CA B:GLU65 4.9 22.2 1.0
CD A:GLU20 5.0 44.6 1.0

Manganese binding site 4 out of 8 in 1m0d

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Manganese binding site 4 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn4

b:43.3
occ:0.75
 O B:HOH1006 1.9 30.5 1.0
OD1 B:ASP55 2.2 37.1 1.0
O A:HOH1008 2.3 39.7 1.0
O B:HOH1008 2.5 29.9 1.0
O A:HOH1007 2.5 47.0 1.0
CG B:ASP55 3.2 34.1 1.0
OE2 A:GLU37 3.3 54.5 1.0
MN B:MN3 3.5 27.5 1.0
OD2 B:ASP55 3.6 28.1 1.0
O B:HOH1144 3.8 57.1 1.0
OE1 A:GLU20 3.9 42.0 1.0
O B:THR53 4.1 28.4 1.0
OE2 B:GLU65 4.2 26.5 1.0
O A:HOH1006 4.2 31.9 1.0
CD A:GLU37 4.3 53.8 1.0
CB B:ASP55 4.3 27.6 1.0
CA B:ASP55 4.5 24.9 1.0
N B:ASP55 4.6 25.1 1.0
OE1 B:GLU65 4.6 27.9 1.0
CG A:GLU37 4.6 42.9 1.0
O B:HOH1007 4.7 27.0 1.0
CD B:GLU65 4.8 36.4 1.0
CD A:GLU20 4.9 44.6 1.0

Manganese binding site 5 out of 8 in 1m0d

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Manganese binding site 5 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn5

b:51.1
occ:1.00
 O C:HOH1005 1.6 31.9 1.0
OD2 C:ASP55 1.7 51.8 1.0
OE2 C:GLU65 2.2 42.2 1.0
O C:THR66 2.4 48.2 1.0
O C:HOH1006 2.4 53.0 1.0
CG C:ASP55 2.4 58.9 1.0
OD1 C:ASP55 2.6 74.3 1.0
O C:HOH1004 2.7 52.5 1.0
CD C:GLU65 3.0 47.9 1.0
MN C:MN6 3.3 63.1 0.8
OG1 C:THR66 3.4 58.4 1.0
C C:THR66 3.5 52.0 1.0
N C:THR66 3.5 43.3 1.0
OE1 C:GLU65 3.7 51.3 1.0
O C:HOH1007 3.8 55.1 1.0
CB C:ASP55 3.9 61.3 1.0
CG C:GLU65 4.0 36.9 1.0
CA C:THR66 4.0 55.4 1.0
O1 C:SO41003 4.1 89.5 1.0
C C:GLU65 4.3 47.0 1.0
CB C:THR66 4.3 61.9 1.0
O2 C:SO41003 4.5 93.0 1.0
CD C:LYS67 4.5 41.4 1.0
CA C:GLU65 4.6 41.5 1.0
O3 C:SO41003 4.6 0.5 1.0
N C:LYS67 4.6 43.7 1.0
O C:HOH1008 4.6 45.9 1.0
S C:SO41003 4.6 97.7 1.0
NZ C:LYS67 4.7 54.2 1.0
OE2 D:GLU20 4.8 83.4 1.0
CB C:GLU65 4.8 36.7 1.0
N C:ASP55 4.9 67.2 1.0
CA C:ASP55 4.9 64.8 1.0
CA C:LYS67 4.9 44.4 1.0

Manganese binding site 6 out of 8 in 1m0d

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Manganese binding site 6 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn6

b:63.1
occ:0.75
 OD1 C:ASP55 2.0 74.3 1.0
O C:HOH1004 2.3 52.5 1.0
O C:HOH1007 2.3 55.1 1.0
O C:HOH1008 2.4 45.9 1.0
CG C:ASP55 2.9 58.9 1.0
MN C:MN5 3.3 51.1 1.0
OD2 C:ASP55 3.4 51.8 1.0
O C:THR53 3.8 56.1 1.0
OE2 C:GLU65 4.0 42.2 1.0
O C:HOH1005 4.0 31.9 1.0
CB C:ASP55 4.0 61.3 1.0
CA C:ASP55 4.0 64.8 1.0
N C:ASP55 4.0 67.2 1.0
OE1 C:GLU65 4.3 51.3 1.0
OE2 D:GLU20 4.3 83.4 1.0
O C:HOH1006 4.3 53.0 1.0
CD C:GLU65 4.5 47.9 1.0
C C:PRO54 4.7 63.8 1.0
OE1 D:GLU37 4.9 0.8 1.0
CD D:GLU37 4.9 86.7 1.0

Manganese binding site 7 out of 8 in 1m0d

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Manganese binding site 7 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn7

b:26.4
occ:1.00
 OE2 D:GLU65 2.1 24.8 1.0
OD2 D:ASP55 2.1 26.7 1.0
O C:HOH1009 2.2 25.5 1.0
O D:HOH1005 2.2 28.0 1.0
O D:HOH1006 2.3 23.5 1.0
O D:THR66 2.3 22.9 1.0
CG D:ASP55 3.0 30.8 1.0
CD D:GLU65 3.1 32.2 1.0
OD1 D:ASP55 3.2 31.2 1.0
C D:THR66 3.4 28.6 1.0
MN D:MN8 3.5 43.7 0.8
N D:THR66 3.7 21.1 1.0
OG1 D:THR66 3.7 24.8 1.0
O D:HOH1159 3.8 55.4 1.0
OE1 D:GLU65 3.8 27.7 1.0
O D:HOH1007 3.9 30.6 1.0
CG D:GLU65 4.0 23.9 1.0
CA D:THR66 4.0 21.8 1.0
OE1 C:GLU20 4.2 31.1 1.0
O1 D:SO41004 4.2 26.3 1.0
NZ D:LYS67 4.2 28.6 1.0
O2 D:SO41004 4.3 31.3 1.0
CE D:LYS67 4.3 29.5 1.0
CB D:THR66 4.4 23.1 1.0
CB D:ASP55 4.4 26.0 1.0
N D:LYS67 4.5 20.9 1.0
C D:GLU65 4.5 27.5 1.0
CA D:LYS67 4.7 17.2 1.0
O C:HOH1011 4.7 47.1 1.0
S D:SO41004 4.7 33.8 1.0
CA D:GLU65 4.8 21.3 1.0
CB D:GLU65 5.0 20.4 1.0

Manganese binding site 8 out of 8 in 1m0d

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Manganese binding site 8 out of 8 in the Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Bacteriophage T7 Endonuclease I with A Wild-Type Active Site and Bound Manganese Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn8

b:43.7
occ:0.75
 O D:HOH1005 2.0 28.0 1.0
OD1 D:ASP55 2.1 31.2 1.0
O C:HOH1011 2.3 47.1 1.0
O D:HOH1007 2.5 30.6 1.0
O C:HOH1010 2.6 45.7 1.0
CG D:ASP55 3.1 30.8 1.0
MN D:MN7 3.5 26.4 1.0
OD2 D:ASP55 3.6 26.7 1.0
OE1 C:GLU20 4.1 31.1 1.0
OE2 D:GLU65 4.2 24.8 1.0
O D:THR53 4.2 26.4 1.0
O D:HOH1159 4.3 55.4 1.0
OE1 C:GLU37 4.3 75.7 1.0
CB D:ASP55 4.3 26.0 1.0
O C:HOH1009 4.3 25.5 1.0
CA D:ASP55 4.4 24.4 1.0
CD C:GLU37 4.4 66.8 1.0
N D:ASP55 4.5 24.4 1.0
OE1 D:GLU65 4.6 27.7 1.0
O D:HOH1006 4.7 23.5 1.0
CD C:GLU20 4.7 34.4 1.0
CG C:GLU37 4.7 57.6 1.0
CD D:GLU65 4.8 32.2 1.0
OE2 C:GLU20 4.8 38.4 1.0
OE2 C:GLU37 4.9 64.7 1.0

Reference:

J.M.Hadden, A.C.Declais, S.E.Phillips, D.M.Lilley. Metal Ions Bound at the Active Site of the Junction-Resolving Enzyme T7 Endonuclease I. Embo J. V. 21 3505 2002.
ISSN: ISSN 0261-4189
PubMed: 12093751
DOI: 10.1093/EMBOJ/CDF337
Page generated: Sat Oct 5 11:37:55 2024

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