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Magnesium in PDB 1svm: Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp

Protein crystallography data

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm was solved by D.Gai, R.Zhao, C.V.Finkielstein, X.S.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 125.021, 89.377, 148.506, 90.00, 91.31, 90.00
R / Rfree (%) 21.8 / 24.1

Other elements in 1svm:

The structure of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp (pdb code 1svm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp, PDB code: 1svm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1svm

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Magnesium binding site 1 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg750

b:31.6
occ:1.00
 O1G A:ATP800 1.9 39.6 1.0
OG1 A:THR433 2.0 27.6 1.0
O A:HOH936 2.1 29.6 1.0
O A:HOH935 2.2 29.9 1.0
O A:HOH802 2.2 21.3 1.0
O2B A:ATP800 2.3 30.7 1.0
CB A:THR433 3.1 24.9 1.0
PG A:ATP800 3.3 48.3 1.0
PB A:ATP800 3.5 35.5 1.0
OE1 A:GLU473 3.6 38.5 1.0
O3B A:ATP800 3.7 36.1 1.0
OD2 F:ASP502 3.9 28.5 1.0
N A:THR433 3.9 23.6 1.0
O3A A:ATP800 4.0 33.7 1.0
PA A:ATP800 4.0 39.6 1.0
CA A:THR433 4.0 25.0 1.0
OD1 A:ASP474 4.1 47.1 1.0
O3G A:ATP800 4.1 41.8 1.0
CG2 A:THR433 4.1 24.9 1.0
O1A A:ATP800 4.2 41.6 1.0
O A:HOH818 4.3 28.9 1.0
OE2 A:GLU473 4.4 40.4 1.0
O A:HOH910 4.4 37.3 1.0
O2G A:ATP800 4.4 37.9 1.0
CD A:GLU473 4.4 36.9 1.0
NZ F:LYS418 4.5 23.6 1.0
NH1 F:ARG540 4.5 39.8 1.0
CG A:ASP474 4.6 45.9 1.0
O1B A:ATP800 4.8 40.4 1.0
CB A:LYS432 4.9 25.8 1.0
CE A:LYS432 4.9 22.6 1.0
O2A A:ATP800 4.9 36.6 1.0
NZ A:LYS432 5.0 26.3 1.0

Magnesium binding site 2 out of 6 in 1svm

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Magnesium binding site 2 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg750

b:28.6
occ:1.00
 O1G B:ATP800 1.8 35.6 1.0
OG1 B:THR433 2.0 24.3 1.0
O B:HOH938 2.1 20.2 1.0
O B:HOH937 2.2 16.5 1.0
O B:HOH939 2.2 24.0 1.0
O2B B:ATP800 2.3 24.8 1.0
CB B:THR433 3.1 21.8 1.0
PG B:ATP800 3.2 46.4 1.0
PB B:ATP800 3.4 30.4 1.0
O3B B:ATP800 3.6 32.4 1.0
OE1 B:GLU473 3.7 41.4 1.0
OD2 B:ASP474 3.7 63.6 1.0
O3A B:ATP800 3.9 29.7 1.0
N B:THR433 4.0 19.9 1.0
O3G B:ATP800 4.0 36.4 1.0
PA B:ATP800 4.0 33.6 1.0
CA B:THR433 4.1 21.8 1.0
CG2 B:THR433 4.1 20.9 1.0
O1A B:ATP800 4.1 32.3 1.0
NH2 A:ARG540 4.1 45.5 1.0
OD2 A:ASP502 4.1 57.1 1.0
OE2 B:GLU473 4.3 41.0 1.0
O2G B:ATP800 4.3 37.6 1.0
O B:HOH804 4.3 39.1 1.0
O B:HOH817 4.4 23.5 1.0
CD B:GLU473 4.4 38.4 1.0
NZ A:LYS418 4.5 25.5 1.0
CG B:ASP474 4.6 57.2 1.0
O1B B:ATP800 4.7 35.0 1.0
CE B:LYS432 4.8 22.6 1.0
CB B:LYS432 4.9 24.2 1.0
NZ B:LYS432 5.0 21.6 1.0

Magnesium binding site 3 out of 6 in 1svm

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Magnesium binding site 3 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg750

b:28.8
occ:1.00
 O1G C:ATP800 1.9 43.1 1.0
OG1 C:THR433 2.0 22.6 1.0
O C:HOH926 2.1 15.6 1.0
O2B C:ATP800 2.2 33.2 1.0
O C:HOH803 2.3 21.8 1.0
O C:HOH811 2.4 23.9 1.0
CB C:THR433 3.1 23.7 1.0
PG C:ATP800 3.2 51.3 1.0
PB C:ATP800 3.2 32.6 1.0
O3B C:ATP800 3.6 36.2 1.0
OD2 C:ASP474 3.7 41.9 1.0
O2A C:ATP800 3.8 24.5 1.0
N C:THR433 3.9 25.3 1.0
O3G C:ATP800 3.9 41.2 1.0
NH2 B:ARG540 4.0 24.4 1.0
O3A C:ATP800 4.0 29.6 1.0
CA C:THR433 4.0 24.1 1.0
OD2 B:ASP502 4.1 28.6 1.0
CG2 C:THR433 4.2 24.1 1.0
OE2 C:GLU473 4.2 42.8 1.0
O C:HOH862 4.3 39.5 1.0
O2G C:ATP800 4.3 39.3 1.0
NZ B:LYS418 4.4 23.4 1.0
PA C:ATP800 4.4 27.1 1.0
OE1 C:GLU473 4.4 42.0 1.0
CD C:GLU473 4.4 39.8 1.0
O C:HOH824 4.5 26.4 1.0
CG C:ASP474 4.6 41.0 1.0
O1B C:ATP800 4.6 35.0 1.0
CE C:LYS432 4.8 22.7 1.0
O1A C:ATP800 4.8 26.0 1.0
NZ C:LYS432 4.8 24.7 1.0
CB C:LYS432 4.8 25.1 1.0
C C:LYS432 5.0 25.1 1.0

Magnesium binding site 4 out of 6 in 1svm

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Magnesium binding site 4 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg750

b:32.2
occ:1.00
 O1G D:ATP800 1.9 37.4 1.0
OG1 D:THR433 2.1 25.0 1.0
O D:HOH801 2.2 23.5 1.0
O D:HOH922 2.2 24.7 1.0
O D:HOH921 2.2 18.7 1.0
O2B D:ATP800 2.3 30.2 1.0
CB D:THR433 3.1 24.5 1.0
PG D:ATP800 3.2 47.9 1.0
PB D:ATP800 3.3 32.2 1.0
O3B D:ATP800 3.6 33.1 1.0
O2A D:ATP800 3.8 26.9 1.0
OE1 D:GLU473 3.8 38.0 1.0
O3G D:ATP800 3.9 37.3 1.0
OD1 D:ASP474 3.9 53.0 1.0
OD2 C:ASP502 3.9 28.4 1.0
N D:THR433 4.0 26.3 1.0
O3A D:ATP800 4.0 27.6 1.0
CA D:THR433 4.1 24.8 1.0
CG2 D:THR433 4.2 23.9 1.0
OE2 D:GLU473 4.2 36.8 1.0
O2G D:ATP800 4.4 36.7 1.0
NH1 C:ARG540 4.4 42.0 1.0
PA D:ATP800 4.4 27.4 1.0
CG D:ASP474 4.4 48.7 1.0
NZ C:LYS418 4.4 26.3 1.0
CD D:GLU473 4.5 34.5 1.0
O D:HOH808 4.5 28.9 1.0
O1B D:ATP800 4.7 34.6 1.0
OD2 D:ASP474 4.7 53.6 1.0
O1A D:ATP800 4.8 24.2 1.0
CE D:LYS432 4.8 29.1 1.0
CB D:LYS432 4.9 29.2 1.0
NZ D:LYS432 4.9 25.1 1.0

Magnesium binding site 5 out of 6 in 1svm

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Magnesium binding site 5 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg750

b:72.7
occ:1.00
 O1G E:ATP800 2.0 52.9 1.0
OG1 E:THR433 2.0 24.2 1.0
O E:HOH958 2.1 62.3 1.0
O E:HOH957 2.3 24.9 1.0
O D:HOH823 2.3 58.6 1.0
O2B E:ATP800 2.6 24.3 1.0
CB E:THR433 3.2 21.5 1.0
PG E:ATP800 3.3 57.4 1.0
OD2 E:ASP474 3.6 47.9 1.0
PB E:ATP800 3.6 24.4 1.0
OE1 E:GLU473 3.6 40.1 1.0
O3B E:ATP800 3.9 21.6 1.0
O3G E:ATP800 3.9 49.8 1.0
OE2 E:GLU473 3.9 40.4 1.0
O2A E:ATP800 4.1 25.9 1.0
N E:THR433 4.1 20.8 1.0
CA E:THR433 4.2 21.8 1.0
CG2 E:THR433 4.2 22.6 1.0
CD E:GLU473 4.2 36.9 1.0
O E:HOH950 4.3 39.2 1.0
OD1 D:ASP502 4.3 55.7 1.0
CG E:ASP474 4.3 42.1 1.0
O3A E:ATP800 4.4 26.5 1.0
NH1 D:ARG540 4.5 36.9 1.0
O2G E:ATP800 4.5 50.1 1.0
NZ D:LYS418 4.7 20.6 1.0
PA E:ATP800 4.7 25.1 1.0
CB E:ASP474 4.9 36.5 1.0
OG1 E:THR527 4.9 25.6 1.0
CE E:LYS432 5.0 23.2 1.0

Magnesium binding site 6 out of 6 in 1svm

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Magnesium binding site 6 out of 6 in the Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Co-Crystal Structure of SV40 Large T Antigen Helicase Domain and Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg750

b:50.2
occ:1.00
 O1G F:ATP800 1.9 55.9 1.0
OG1 F:THR433 2.0 25.2 1.0
O F:HOH922 2.2 27.2 1.0
O2B F:ATP800 2.2 21.9 1.0
O F:HOH805 2.3 21.1 1.0
O F:HOH808 2.4 25.3 1.0
CB F:THR433 3.1 23.6 1.0
PG F:ATP800 3.2 60.1 1.0
PB F:ATP800 3.2 23.4 1.0
O3B F:ATP800 3.6 23.1 1.0
O3G F:ATP800 3.8 53.6 1.0
OE2 F:GLU473 3.8 42.3 1.0
OD1 F:ASP474 3.9 41.9 1.0
O2A F:ATP800 3.9 23.3 1.0
N F:THR433 3.9 23.3 1.0
OD2 E:ASP502 4.0 30.2 1.0
CA F:THR433 4.0 22.4 1.0
O3A F:ATP800 4.0 24.0 1.0
CG2 F:THR433 4.1 24.3 1.0
CD F:GLU473 4.2 37.7 1.0
O F:HOH818 4.2 32.3 1.0
NH1 E:ARG540 4.3 44.7 1.0
OE1 F:GLU473 4.3 39.2 1.0
O2G F:ATP800 4.4 53.4 1.0
NZ E:LYS418 4.5 25.6 1.0
PA F:ATP800 4.5 26.1 1.0
O F:HOH812 4.5 24.3 1.0
CG F:ASP474 4.6 40.2 1.0
O1B F:ATP800 4.6 22.4 1.0
O1A F:ATP800 4.9 22.4 1.0
CB F:LYS432 4.9 24.3 1.0
CE F:LYS432 4.9 25.4 1.0

Reference:

D.Gai, R.Zhao, D.Li, C.V.Finkielstein, X.S.Chen. Mechanisms of Conformational Change For A Replicative Hexameric Helicase of SV40 Large Tumor Antigen. Cell(Cambridge,Mass.) V. 119 47 2004.
ISSN: ISSN 0092-8674
PubMed: 15454080
DOI: 10.1016/J.CELL.2004.09.017
Page generated: Tue Aug 13 14:19:44 2024

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