Atomistry » Manganese » PDB 1lu1-1n0j » 1m0d
Atomistry »
  Manganese »
    PDB 1lu1-1n0j »
      1m0d »

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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Go back to Manganese Binding Sites List in 1m0d
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy