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Magnesium in PDB 8s09: H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna

Enzymatic activity of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna

All present enzymatic activity of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna:
3.6.4.12;

Other elements in 8s09:

The structure of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna also contains other interesting chemical elements:

Zinc (Zn) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna (pdb code 8s09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna, PDB code: 8s09:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8s09

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Magnesium binding site 1 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg1002

b:27.8
occ:1.00
 OG 2:SER530 2.1 26.5 1.0
O1G 2:ATP1001 2.3 32.4 1.0
O1B 2:ATP1001 2.3 32.4 1.0
CB 2:SER530 3.4 26.5 1.0
PB 2:ATP1001 3.5 32.4 1.0
PG 2:ATP1001 3.5 32.4 1.0
OD2 2:ASP587 3.6 28.4 1.0
O3B 2:ATP1001 3.7 32.4 1.0
O2A 2:ATP1001 3.8 32.4 1.0
OD1 2:ASP587 3.9 28.4 1.0
CG 2:ASP587 4.2 28.4 1.0
O3A 2:ATP1001 4.3 32.4 1.0
N 2:SER530 4.4 26.5 1.0
CA 2:SER530 4.5 26.5 1.0
O2G 2:ATP1001 4.5 32.4 1.0
O3G 2:ATP1001 4.6 32.4 1.0
PA 2:ATP1001 4.7 32.4 1.0
O2B 2:ATP1001 4.8 32.4 1.0

Magnesium binding site 2 out of 8 in 8s09

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Magnesium binding site 2 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg902

b:23.6
occ:1.00
 OG 3:SER352 2.1 31.1 1.0
O1B 3:ADP901 2.3 41.1 1.0
O3B 3:ADP901 2.8 41.1 1.0
PB 3:ADP901 3.0 41.1 1.0
OE1 5:GLU463 3.1 39.3 1.0
CB 3:SER352 3.4 31.1 1.0
O2A 3:ADP901 3.7 41.1 1.0
OD2 3:ASP409 4.1 30.8 1.0
O2B 3:ADP901 4.1 41.1 1.0
N 3:SER352 4.1 31.1 1.0
OD1 3:ASP409 4.1 30.8 1.0
O3A 3:ADP901 4.2 41.1 1.0
CD 5:GLU463 4.3 39.3 1.0
CA 3:SER352 4.3 31.1 1.0
PA 3:ADP901 4.4 41.1 1.0
NH2 5:ARG513 4.5 39.0 1.0
CG 3:ASP409 4.6 30.8 1.0
OE2 5:GLU463 4.8 39.3 1.0
O1A 3:ADP901 4.8 41.1 1.0
CE 3:LYS351 4.8 32.3 1.0

Magnesium binding site 3 out of 8 in 8s09

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Magnesium binding site 3 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Mg901

b:36.5
occ:1.00
 OG 6:SER403 2.1 37.0 1.0
O1B 4:ADP902 2.3 42.2 1.0
O3B 4:ADP902 2.3 42.2 1.0
PB 4:ADP902 2.8 42.2 1.0
CB 6:SER403 3.4 37.0 1.0
OD2 6:ASP460 3.7 35.8 1.0
O2A 4:ADP902 3.7 42.2 1.0
O2B 4:ADP902 3.9 42.2 1.0
O3A 4:ADP902 4.0 42.2 1.0
OD1 6:ASP460 4.2 35.8 1.0
OE2 6:GLU461 4.3 38.4 1.0
N 6:SER403 4.3 37.0 1.0
PA 4:ADP902 4.3 42.2 1.0
CA 6:SER403 4.4 37.0 1.0
CG 6:ASP460 4.4 35.8 1.0
NH2 4:ARG643 4.5 32.7 1.0
O1A 4:ADP902 4.8 42.2 1.0
CE 6:LYS402 4.8 38.3 1.0

Magnesium binding site 4 out of 8 in 8s09

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Magnesium binding site 4 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Mg802

b:46.2
occ:1.00
 O3B 7:ADP801 2.0 51.6 1.0
OG 7:SER388 2.1 39.4 1.0
O1B 7:ADP801 2.1 51.6 1.0
PB 7:ADP801 2.4 51.6 1.0
OE2 7:GLU446 3.1 38.8 1.0
O2A 7:ADP801 3.4 51.6 1.0
CB 7:SER388 3.5 39.4 1.0
O3A 7:ADP801 3.6 51.6 1.0
O2B 7:ADP801 3.6 51.6 1.0
OD2 7:ASP445 3.7 35.2 1.0
PA 7:ADP801 3.9 51.6 1.0
NE2 3:HIS423 4.0 40.3 1.0
OD1 7:ASP445 4.0 35.2 1.0
N 7:SER388 4.3 39.4 1.0
CG 7:ASP445 4.3 35.2 1.0
O1A 7:ADP801 4.3 51.6 1.0
CD 7:GLU446 4.4 38.8 1.0
CA 7:SER388 4.4 39.4 1.0
CE1 3:HIS423 4.7 40.3 1.0

Magnesium binding site 5 out of 8 in 8s09

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Magnesium binding site 5 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1002

b:27.8
occ:1.00
 OG A:SER530 2.1 26.5 1.0
O1G A:ATP1001 2.3 32.4 1.0
O1B A:ATP1001 2.3 32.4 1.0
CB A:SER530 3.4 26.5 1.0
PB A:ATP1001 3.5 32.4 1.0
PG A:ATP1001 3.5 32.4 1.0
OD2 A:ASP587 3.6 28.4 1.0
O3B A:ATP1001 3.7 32.4 1.0
O2A A:ATP1001 3.8 32.4 1.0
OD1 A:ASP587 3.9 28.4 1.0
CG A:ASP587 4.2 28.4 1.0
O3A A:ATP1001 4.3 32.4 1.0
N A:SER530 4.4 26.5 1.0
CA A:SER530 4.5 26.5 1.0
O2G A:ATP1001 4.5 32.4 1.0
O3G A:ATP1001 4.6 32.4 1.0
PA A:ATP1001 4.7 32.4 1.0
O2B A:ATP1001 4.8 32.4 1.0

Magnesium binding site 6 out of 8 in 8s09

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Magnesium binding site 6 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg902

b:23.6
occ:1.00
 OG B:SER352 2.1 31.1 1.0
O1B B:ADP901 2.3 41.1 1.0
O3B B:ADP901 2.8 41.1 1.0
PB B:ADP901 3.0 41.1 1.0
OE1 D:GLU463 3.1 39.3 1.0
CB B:SER352 3.4 31.1 1.0
O2A B:ADP901 3.7 41.1 1.0
OD2 B:ASP409 4.1 30.8 1.0
O2B B:ADP901 4.1 41.1 1.0
N B:SER352 4.1 31.1 1.0
OD1 B:ASP409 4.1 30.8 1.0
O3A B:ADP901 4.2 41.1 1.0
CD D:GLU463 4.3 39.3 1.0
CA B:SER352 4.3 31.1 1.0
PA B:ADP901 4.4 41.1 1.0
NH2 D:ARG513 4.5 39.0 1.0
CG B:ASP409 4.6 30.8 1.0
OE2 D:GLU463 4.8 39.3 1.0
O1A B:ADP901 4.8 41.1 1.0
CE B:LYS351 4.8 32.3 1.0

Magnesium binding site 7 out of 8 in 8s09

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Magnesium binding site 7 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg901

b:36.5
occ:1.00
 OG E:SER403 2.1 37.0 1.0
O1B C:ADP902 2.3 42.2 1.0
O3B C:ADP902 2.3 42.2 1.0
PB C:ADP902 2.8 42.2 1.0
CB E:SER403 3.4 37.0 1.0
O2A C:ADP902 3.7 42.2 1.0
OD2 E:ASP460 3.7 35.8 1.0
O2B C:ADP902 3.9 42.2 1.0
O3A C:ADP902 4.0 42.2 1.0
OD1 E:ASP460 4.2 35.8 1.0
OE2 E:GLU461 4.3 38.4 1.0
N E:SER403 4.3 37.0 1.0
PA C:ADP902 4.3 42.2 1.0
CA E:SER403 4.4 37.0 1.0
CG E:ASP460 4.4 35.8 1.0
NH2 C:ARG643 4.5 32.7 1.0
O1A C:ADP902 4.8 42.2 1.0
CE E:LYS402 4.8 38.3 1.0

Magnesium binding site 8 out of 8 in 8s09

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Magnesium binding site 8 out of 8 in the H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of H. Sapiens MCM2-7 Double Hexamer Bound to Double Stranded Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg802

b:46.2
occ:1.00
 O3B F:ADP801 2.0 51.6 1.0
OG F:SER388 2.1 39.4 1.0
O1B F:ADP801 2.1 51.6 1.0
PB F:ADP801 2.4 51.6 1.0
OE2 F:GLU446 3.1 38.8 1.0
O2A F:ADP801 3.4 51.6 1.0
CB F:SER388 3.5 39.4 1.0
O3A F:ADP801 3.6 51.6 1.0
O2B F:ADP801 3.6 51.6 1.0
OD2 F:ASP445 3.7 35.2 1.0
PA F:ADP801 3.9 51.6 1.0
NE2 B:HIS423 4.0 40.3 1.0
OD1 F:ASP445 4.0 35.2 1.0
N F:SER388 4.3 39.4 1.0
CG F:ASP445 4.3 35.2 1.0
O1A F:ADP801 4.3 51.6 1.0
CD F:GLU446 4.4 38.8 1.0
CA F:SER388 4.4 39.4 1.0
CE1 B:HIS423 4.7 40.3 1.0

Reference:

F.Weissmann, J.F.Greiwe, T.Puehringer, E.L.Eastwood, E.C.Couves, T.C.R.Miller, J.F.X.Diffley, A.Costa. Mcm Double Hexamer Loading Visualised with Human Proteins Nature 2024.
ISSN: ESSN 1476-4687
Page generated: Thu Oct 31 22:10:34 2024

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