Atomistry » Magnesium » PDB 4r0d-4rcr » 4r1f
Atomistry »
  Magnesium »
    PDB 4r0d-4rcr »
      4r1f »

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

Go back to Magnesium Binding Sites List in 4r1f
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

Go back to Magnesium Binding Sites List in 4r1f
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

Go back to Magnesium Binding Sites List in 4r1f
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

Go back to Magnesium Binding Sites List in 4r1f
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: Tue Aug 20 02:45:53 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy