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Magnesium in PDB 1mx0: Structure of Topoisomerase Subunit

Enzymatic activity of Structure of Topoisomerase Subunit

All present enzymatic activity of Structure of Topoisomerase Subunit:
5.99.1.3;

Protein crystallography data

The structure of Structure of Topoisomerase Subunit, PDB code: 1mx0 was solved by K.D.Corbett, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 146.655, 219.192, 106.921, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 26.3

Other elements in 1mx0:

The structure of Structure of Topoisomerase Subunit also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Topoisomerase Subunit (pdb code 1mx0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Topoisomerase Subunit, PDB code: 1mx0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1mx0

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Magnesium binding site 1 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:43.4
occ:1.00
 O1B A:ANP900 2.0 45.1 1.0
O2G A:ANP900 2.0 45.3 1.0
O A:HOH915 2.1 46.5 1.0
O1A A:ANP900 2.1 44.1 1.0
OD1 A:ASN42 2.2 8.6 1.0
O A:HOH913 2.2 42.3 1.0
PB A:ANP900 3.0 40.8 1.0
CG A:ASN42 3.0 5.7 1.0
PA A:ANP900 3.2 44.7 1.0
PG A:ANP900 3.3 44.2 1.0
ND2 A:ASN42 3.3 3.6 1.0
O3A A:ANP900 3.3 46.9 1.0
N3B A:ANP900 3.5 46.0 1.0
O5' A:ANP900 3.9 45.1 1.0
OE2 A:GLU38 3.9 15.7 1.0
O A:HOH930 4.1 54.8 1.0
NZ A:LYS98 4.2 2.5 1.0
O1G A:ANP900 4.2 46.6 1.0
O3G A:ANP900 4.2 45.2 1.0
O2B A:ANP900 4.3 47.4 1.0
CA A:GLY111 4.4 6.4 1.0
O2A A:ANP900 4.4 47.5 1.0
O A:GLU38 4.4 6.5 1.0
CB A:ASN42 4.4 5.3 1.0
CA A:GLY106 4.5 7.0 1.0
N A:GLY111 4.7 7.4 1.0
N A:VAL112 4.8 6.9 1.0
CA A:ASN42 4.8 5.9 1.0
N A:ASN42 4.9 6.6 1.0

Magnesium binding site 2 out of 6 in 1mx0

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Magnesium binding site 2 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:42.1
occ:1.00
 O2G B:ANP910 2.0 41.0 1.0
O1A B:ANP910 2.0 43.0 1.0
O1B B:ANP910 2.1 40.6 1.0
O B:HOH985 2.2 50.4 1.0
OD1 B:ASN42 2.4 8.7 1.0
O B:HOH949 2.4 39.6 1.0
PB B:ANP910 3.0 38.8 1.0
PA B:ANP910 3.1 42.1 1.0
PG B:ANP910 3.2 42.1 1.0
CG B:ASN42 3.3 8.2 1.0
O3A B:ANP910 3.3 43.7 1.0
ND2 B:ASN42 3.5 5.0 1.0
N3B B:ANP910 3.5 42.7 1.0
O5' B:ANP910 3.8 41.0 1.0
O B:HOH998 4.1 53.2 1.0
O1G B:ANP910 4.1 43.6 1.0
OE1 B:GLU38 4.1 15.4 1.0
O3G B:ANP910 4.2 43.3 1.0
NZ B:LYS98 4.3 2.0 1.0
O2A B:ANP910 4.3 41.5 1.0
O2B B:ANP910 4.4 41.9 1.0
O B:GLU38 4.4 9.1 1.0
CA B:GLY106 4.5 6.0 1.0
CB B:ASN42 4.7 8.6 1.0
CA B:GLY111 4.7 6.4 1.0
N B:GLY111 4.8 7.3 1.0
NZ B:LYS427 4.8 23.2 1.0
N B:VAL112 4.9 5.9 1.0

Magnesium binding site 3 out of 6 in 1mx0

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Magnesium binding site 3 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:49.5
occ:1.00
 O2G C:ANP920 2.0 44.2 1.0
O1A C:ANP920 2.0 46.1 1.0
O C:HOH1048 2.0 62.3 1.0
O C:HOH948 2.0 50.3 1.0
O1B C:ANP920 2.2 46.2 1.0
OD1 C:ASN42 2.2 9.0 1.0
PB C:ANP920 3.0 43.3 1.0
PA C:ANP920 3.1 46.1 1.0
CG C:ASN42 3.1 8.2 1.0
PG C:ANP920 3.2 45.8 1.0
O3A C:ANP920 3.2 45.0 1.0
ND2 C:ASN42 3.3 2.0 1.0
N3B C:ANP920 3.5 48.0 1.0
O5' C:ANP920 3.8 48.6 1.0
O1G C:ANP920 4.1 44.9 1.0
OE2 C:GLU38 4.1 18.4 1.0
O C:HOH955 4.2 51.0 1.0
NZ C:LYS98 4.2 13.8 1.0
O3G C:ANP920 4.2 46.1 1.0
O2A C:ANP920 4.2 42.2 1.0
O2B C:ANP920 4.4 48.7 1.0
O C:GLU38 4.5 9.4 1.0
CA C:GLY106 4.5 8.4 1.0
CB C:ASN42 4.5 9.0 1.0
CA C:GLY111 4.5 10.2 1.0
N C:VAL112 4.6 8.9 1.0
N C:GLY111 4.7 11.5 1.0
CA C:ASN42 4.9 10.4 1.0
N C:ASN42 4.9 11.2 1.0

Magnesium binding site 4 out of 6 in 1mx0

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Magnesium binding site 4 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:45.1
occ:1.00
 O1B D:ANP930 1.9 42.8 1.0
O D:HOH932 2.0 51.2 1.0
O2G D:ANP930 2.1 43.5 1.0
O1A D:ANP930 2.1 43.1 1.0
OD1 D:ASN42 2.1 3.6 1.0
O D:HOH1045 2.4 47.2 1.0
PB D:ANP930 3.0 41.7 1.0
CG D:ASN42 3.0 3.4 1.0
PA D:ANP930 3.1 43.5 1.0
PG D:ANP930 3.3 43.4 1.0
O3A D:ANP930 3.3 44.7 1.0
ND2 D:ASN42 3.3 2.0 1.0
N3B D:ANP930 3.5 43.5 1.0
O5' D:ANP930 3.8 43.9 1.0
NZ D:LYS98 3.9 8.7 1.0
O1G D:ANP930 4.2 42.5 1.0
O2B D:ANP930 4.3 44.0 1.0
O3G D:ANP930 4.3 43.0 1.0
OE2 D:GLU38 4.3 12.9 1.0
O2A D:ANP930 4.4 43.8 1.0
CA D:GLY106 4.4 6.0 1.0
CB D:ASN42 4.4 5.2 1.0
O D:GLU38 4.5 7.0 1.0
CA D:GLY111 4.6 6.8 1.0
CA D:ASN42 4.8 6.5 1.0
N D:VAL112 4.8 7.2 1.0
N D:ASN42 4.9 6.8 1.0
N D:GLY111 4.9 7.3 1.0
NZ D:LYS427 5.0 29.2 1.0

Magnesium binding site 5 out of 6 in 1mx0

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Magnesium binding site 5 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg501

b:51.7
occ:1.00
 O2G E:ANP940 2.0 45.5 1.0
O1A E:ANP940 2.1 48.3 1.0
O1B E:ANP940 2.1 46.0 1.0
OD1 E:ASN42 2.2 6.7 1.0
O E:HOH976 2.3 44.9 1.0
PB E:ANP940 3.1 44.0 1.0
PA E:ANP940 3.1 47.2 1.0
CG E:ASN42 3.1 7.6 1.0
O3A E:ANP940 3.3 47.3 1.0
PG E:ANP940 3.3 45.8 1.0
ND2 E:ASN42 3.5 5.6 1.0
N3B E:ANP940 3.6 46.4 1.0
O5' E:ANP940 3.8 47.5 1.0
OE2 E:GLU38 4.0 18.7 1.0
NZ E:LYS98 4.0 10.2 1.0
O1G E:ANP940 4.2 45.7 1.0
O3G E:ANP940 4.3 45.0 1.0
O2A E:ANP940 4.3 47.0 1.0
O2B E:ANP940 4.4 47.2 1.0
CA E:GLY106 4.4 10.9 1.0
O E:GLU38 4.5 6.9 1.0
CB E:ASN42 4.5 5.1 1.0
NZ E:LYS427 4.6 22.3 1.0
CA E:GLY111 4.6 11.1 1.0
N E:VAL112 4.7 9.2 1.0
N E:GLY111 4.8 12.8 1.0
CA E:ASN42 4.8 5.7 1.0
N E:ASN42 4.8 5.0 1.0

Magnesium binding site 6 out of 6 in 1mx0

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Magnesium binding site 6 out of 6 in the Structure of Topoisomerase Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Topoisomerase Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:80.5
occ:1.00
 O1A F:ANP950 1.6 67.4 1.0
O1B F:ANP950 1.7 59.8 1.0
O2G F:ANP950 2.2 68.2 1.0
PB F:ANP950 2.6 64.1 1.0
PA F:ANP950 2.7 68.1 1.0
O F:HOH982 2.7 73.4 1.0
OD1 F:ASN42 2.8 46.1 1.0
O3A F:ANP950 2.8 68.7 1.0
ND2 F:ASN42 3.1 48.0 1.0
PG F:ANP950 3.1 68.7 1.0
N3B F:ANP950 3.2 68.1 1.0
CG F:ASN42 3.2 45.2 1.0
O5' F:ANP950 3.5 71.0 1.0
O2A F:ANP950 3.8 66.6 1.0
O1G F:ANP950 3.9 69.8 1.0
O2B F:ANP950 4.0 62.2 1.0
NZ F:LYS98 4.2 36.2 1.0
O3G F:ANP950 4.3 71.4 1.0
CA F:GLY111 4.4 35.7 1.0
N F:GLY111 4.4 36.6 1.0
CB F:ASN42 4.6 44.6 1.0
CA F:GLY106 4.7 35.1 1.0
C5' F:ANP950 4.7 73.6 1.0
CE F:LYS98 4.8 35.1 1.0
OE2 F:GLU38 4.9 47.1 1.0
C3' F:ANP950 4.9 77.8 1.0
N F:VAL112 4.9 34.6 1.0
CA F:ASN42 5.0 44.3 1.0

Reference:

K.D.Corbett, J.M.Berger. Structure of the Topoisomerase VI-B Subunit: Implications For Type II Topoisomerase Mechanism and Evolution Embo J. V. 22 151 2003.
ISSN: ISSN 0261-4189
PubMed: 12505993
DOI: 10.1093/EMBOJ/CDG008
Page generated: Tue Aug 13 09:16:09 2024

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