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Magnesium in PDB 4r1f: Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4

Enzymatic activity of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4

All present enzymatic activity of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4:
5.99.1.3;

Protein crystallography data

The structure of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4, PDB code: 4r1f was solved by F.V.Stanger, T.Schirmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.51
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.015, 90.492, 148.293, 90.00, 89.97, 90.00
R / Rfree (%) 20.8 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4 (pdb code 4r1f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4, PDB code: 4r1f:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4r1f

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Magnesium binding site 1 out of 4 in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:43.7
occ:1.00
 OD1 A:ASN91 2.1 44.5 1.0
O1A A:ADP502 2.1 47.5 1.0
O A:HOH601 2.1 41.7 1.0
O A:HOH633 2.1 49.5 1.0
O3B A:ADP502 2.1 49.8 1.0
O A:HOH635 2.2 60.1 1.0
CG A:ASN91 3.0 40.4 1.0
PA A:ADP502 3.2 48.1 1.0
ND2 A:ASN91 3.3 43.7 1.0
PB A:ADP502 3.3 43.5 1.0
O3A A:ADP502 3.5 43.3 1.0
O1B A:ADP502 3.9 44.3 1.0
OE1 A:GLU87 3.9 56.2 1.0
O A:GLU87 4.1 41.1 1.0
CA A:GLY161 4.3 58.2 1.0
O2A A:ADP502 4.3 53.4 1.0
CB A:ASN91 4.4 41.9 1.0
OD2 A:ASP94 4.4 56.5 1.0
O5' A:ADP502 4.4 51.2 1.0
O2B A:ADP502 4.5 43.3 1.0
CA A:GLY166 4.6 38.8 1.0
C5' A:ADP502 4.7 53.8 1.0
CA A:ASN91 4.7 40.7 1.0
N A:GLY161 4.9 57.5 1.0
N A:ASN91 4.9 43.3 1.0
N A:GLY166 4.9 39.9 1.0
N A:ALA167 4.9 43.5 1.0
O1 A:GOL503 5.0 59.0 1.0

Magnesium binding site 2 out of 4 in 4r1f

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Magnesium binding site 2 out of 4 in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:40.3
occ:1.00
 O B:HOH645 2.1 39.5 1.0
OD1 B:ASN91 2.1 35.8 1.0
O B:HOH646 2.1 35.4 1.0
O1A B:ADP503 2.1 42.4 1.0
O B:HOH644 2.1 48.1 1.0
O1B B:ADP503 2.2 37.3 1.0
CG B:ASN91 3.0 37.4 1.0
PA B:ADP503 3.2 41.7 1.0
PB B:ADP503 3.2 39.5 1.0
ND2 B:ASN91 3.3 36.1 1.0
O3A B:ADP503 3.6 38.4 1.0
O B:HOH606 3.7 39.0 1.0
O2B B:ADP503 3.7 33.8 1.0
OE1 B:GLU87 4.0 71.0 1.0
CA B:GLY161 4.2 55.7 1.0
O B:GLU87 4.2 38.6 1.0
O2A B:ADP503 4.4 46.2 1.0
CB B:ASN91 4.4 38.2 1.0
O5' B:ADP503 4.4 50.0 1.0
OD2 B:ASP94 4.4 48.1 1.0
O3B B:ADP503 4.5 39.1 1.0
C5' B:ADP503 4.6 46.1 1.0
CA B:GLY166 4.7 45.7 1.0
O1 B:SO4502 4.7 82.5 1.0
CA B:ASN91 4.7 35.4 1.0
N B:GLY161 4.8 50.9 1.0
N B:ASN91 4.9 34.9 1.0
N B:GLY166 5.0 44.4 1.0
N B:ALA167 5.0 44.4 1.0

Magnesium binding site 3 out of 4 in 4r1f

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Magnesium binding site 3 out of 4 in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:45.2
occ:1.00
 O C:HOH607 2.1 49.0 1.0
OD1 C:ASN91 2.1 46.3 1.0
O C:HOH638 2.1 46.8 1.0
O1B C:ADP502 2.2 48.1 1.0
O1A C:ADP502 2.2 53.9 1.0
O C:HOH602 2.2 53.4 1.0
CG C:ASN91 3.0 41.6 1.0
PB C:ADP502 3.3 51.0 1.0
ND2 C:ASN91 3.4 40.2 1.0
PA C:ADP502 3.5 47.3 1.0
O2B C:ADP502 3.7 45.2 1.0
O3A C:ADP502 3.8 42.6 1.0
OE1 C:GLU87 3.9 64.1 1.0
O C:HOH610 3.9 44.4 1.0
O C:HOH639 4.0 62.1 1.0
CA C:GLY161 4.1 67.0 1.0
O C:GLU87 4.2 46.5 1.0
OD2 C:ASP94 4.3 51.4 1.0
CB C:ASN91 4.4 42.7 1.0
C5' C:ADP502 4.4 55.4 1.0
O2A C:ADP502 4.5 52.6 1.0
O5' C:ADP502 4.6 50.6 1.0
O3B C:ADP502 4.6 50.9 1.0
CA C:ASN91 4.7 42.1 1.0
N C:GLY161 4.7 69.4 1.0
CA C:GLY166 4.7 41.6 1.0
O1 C:SO4503 4.7 82.4 1.0
O4 C:SO4503 4.8 83.2 1.0
N C:ASN91 4.8 42.4 1.0
N C:GLY166 5.0 40.2 1.0

Magnesium binding site 4 out of 4 in 4r1f

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Magnesium binding site 4 out of 4 in the Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Re-Refined Human Dna Topoisomerase Iia (Atpase and Transducer Domains) in Complex with Adp and SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:50.3
occ:1.00
 O D:HOH609 2.1 51.4 1.0
O D:HOH610 2.1 52.4 1.0
O3B D:ADP503 2.1 54.0 1.0
O1A D:ADP503 2.2 49.0 1.0
O D:HOH611 2.2 57.1 1.0
OD1 D:ASN91 2.2 62.0 1.0
CG D:ASN91 3.1 53.3 1.0
PB D:ADP503 3.3 58.8 1.0
ND2 D:ASN91 3.5 53.4 1.0
PA D:ADP503 3.5 52.6 1.0
O1B D:ADP503 3.6 59.5 1.0
O3A D:ADP503 3.8 46.5 1.0
CA D:GLY161 3.8 71.8 1.0
OE1 D:GLU87 4.0 80.5 1.0
OD2 D:ASP94 4.0 70.8 1.0
O D:GLU87 4.3 55.6 1.0
N D:GLY161 4.4 71.6 1.0
CB D:ASN91 4.4 57.7 1.0
O5' D:ADP503 4.5 59.4 1.0
C5' D:ADP503 4.5 66.3 1.0
O2B D:ADP503 4.6 56.3 1.0
CA D:ASN91 4.7 55.5 1.0
O2A D:ADP503 4.7 48.7 1.0
O2 D:SO4502 4.8 0.3 1.0
N D:ASN91 4.8 55.8 1.0
CA D:GLY166 4.9 56.0 1.0

Reference:

F.V.Stanger, C.Dehio, T.Schirmer. Structure of the N-Terminal Gyrase B Fragment in Complex with Adppi Reveals Rigid-Body Motion Induced By Atp Hydrolysis Plos One V. 9 07289 2014.
ISSN: ESSN 1932-6203
PubMed: 25202966
DOI: 10.1371/JOURNAL.PONE.0107289
Page generated: Mon Dec 14 19:29:29 2020

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