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Magnesium in PDB 4kfu: Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp

Protein crystallography data

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp, PDB code: 4kfu was solved by L.J.Happonen, E.Oksanen, T.Kajander, A.Goldman, S.Butcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.558, 65.227, 72.118, 90.85, 93.77, 91.56
R / Rfree (%) 18.8 / 23.4

Other elements in 4kfu:

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp (pdb code 4kfu). 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 the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp, PDB code: 4kfu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4kfu

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Magnesium binding site 1 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:36.1
occ:1.00
O A:HOH507 2.9 33.4 1.0
OHB A:FLC304 3.0 34.0 1.0
OB1 A:FLC304 3.0 31.3 1.0
O A:HOH506 3.0 27.0 1.0
O A:HOH508 3.0 26.2 1.0
OA1 A:FLC304 3.7 41.0 1.0
CBC A:FLC304 3.9 40.0 1.0
OG2 A:FLC304 3.9 32.7 1.0
CB A:FLC304 4.0 35.2 1.0
CAC A:FLC304 4.7 44.5 1.0
CGC A:FLC304 4.9 36.0 1.0
NH1 A:ARG160 4.9 35.6 1.0
CG A:FLC304 5.0 31.6 1.0
CA A:FLC304 5.0 36.9 1.0

Magnesium binding site 2 out of 6 in 4kfu

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Magnesium binding site 2 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:29.9
occ:1.00
O A:HOH504 2.7 33.1 1.0
O A:HOH503 2.9 25.3 1.0
OB2 A:FLC303 2.9 28.5 1.0
O A:HOH505 3.0 29.7 1.0
OHB A:FLC303 3.3 27.1 1.0
CBC A:FLC303 3.8 29.1 1.0
OA2 A:FLC303 4.0 25.7 1.0
OG2 A:FLC303 4.1 20.2 1.0
CB A:FLC303 4.1 25.1 1.0
CAC A:FLC303 4.9 30.3 1.0
OB1 A:FLC303 4.9 31.6 1.0

Magnesium binding site 3 out of 6 in 4kfu

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Magnesium binding site 3 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg307

b:30.2
occ:1.00
O2G A:ACP301 1.7 34.9 1.0
O1B A:ACP301 1.9 27.8 1.0
O A:HOH429 2.1 26.3 1.0
O A:HOH484 2.1 33.7 1.0
O A:HOH403 2.1 28.7 1.0
OG A:SER18 2.2 27.4 1.0
CB A:SER18 3.0 27.0 1.0
PG A:ACP301 3.1 41.2 1.0
PB A:ACP301 3.2 29.2 1.0
C3B A:ACP301 3.6 31.5 1.0
OE2 A:GLU49 4.0 34.6 1.0
O2B A:ACP301 4.0 31.5 1.0
OD2 A:ASP103 4.0 31.4 1.0
O1A A:ACP301 4.0 33.5 1.0
O1G A:ACP301 4.1 35.1 1.0
O3G A:ACP301 4.1 41.8 1.0
OE1 A:GLU49 4.1 32.9 1.0
CA A:SER18 4.2 29.0 1.0
OD1 A:ASP103 4.2 31.5 1.0
N A:SER18 4.3 24.5 1.0
O3A A:ACP301 4.4 28.4 1.0
CG A:ASP103 4.5 36.1 1.0
CD A:GLU49 4.5 34.4 1.0
PA A:ACP301 4.7 30.4 1.0
NZ A:LYS17 4.7 24.3 1.0
CE A:LYS17 4.7 20.4 1.0
CG A:LYS17 4.7 23.9 1.0
OE2 A:GLU104 4.7 37.3 1.0
O2A A:ACP301 5.0 27.5 1.0

Magnesium binding site 4 out of 6 in 4kfu

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Magnesium binding site 4 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:35.3
occ:1.00
OG1 B:FLC304 2.9 29.9 1.0
O B:HOH518 3.0 23.7 1.0
O B:HOH516 3.0 47.0 1.0
O B:HOH517 3.0 26.0 1.0
O B:HOH422 3.0 30.5 1.0
OB2 B:FLC304 3.3 31.9 1.0
NH1 B:ARG160 3.5 29.2 1.0
CGC B:FLC304 4.1 32.4 1.0
OHB B:FLC304 4.2 28.3 1.0
CBC B:FLC304 4.3 34.8 1.0
CZ B:ARG160 4.5 27.5 1.0
CB B:FLC304 4.7 30.2 1.0
OG2 B:FLC304 4.9 33.7 1.0

Magnesium binding site 5 out of 6 in 4kfu

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Magnesium binding site 5 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:34.4
occ:1.00
O B:HOH515 2.6 20.9 1.0
OA1 B:FLC303 2.9 22.4 1.0
OB1 B:FLC303 3.1 24.7 1.0
O B:HOH514 3.2 19.3 1.0
O B:HOH513 3.4 36.4 1.0
O B:HOH516 3.6 47.0 1.0
CBC B:FLC303 4.1 26.5 1.0
CAC B:FLC303 4.2 26.6 1.0
OHB B:FLC303 4.4 22.1 1.0
CB B:FLC303 4.8 20.5 1.0
OA2 B:FLC303 5.0 27.1 1.0
OB2 B:FLC303 5.0 24.7 1.0

Magnesium binding site 6 out of 6 in 4kfu

Go back to Magnesium Binding Sites List in 4kfu
Magnesium binding site 6 out of 6 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Amppcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:24.7
occ:1.00
O3G B:ACP301 2.0 29.8 1.0
OG B:SER18 2.0 23.1 1.0
O2B B:ACP301 2.0 24.4 1.0
O B:HOH409 2.1 26.4 1.0
O B:HOH414 2.1 26.0 1.0
O B:HOH412 2.1 30.9 1.0
CB B:SER18 2.9 25.3 1.0
PB B:ACP301 3.3 23.6 1.0
PG B:ACP301 3.3 34.5 1.0
C3B B:ACP301 3.7 27.2 1.0
OD2 B:ASP103 4.0 27.1 1.0
OE2 B:GLU49 4.1 34.2 1.0
O B:HOH449 4.1 40.7 1.0
CA B:SER18 4.1 20.7 1.0
O2A B:ACP301 4.1 27.2 1.0
N B:SER18 4.1 22.3 1.0
O1G B:ACP301 4.2 32.4 1.0
OE1 B:GLU49 4.2 36.8 1.0
OD1 B:ASP103 4.2 33.1 1.0
O1B B:ACP301 4.3 26.6 1.0
O3A B:ACP301 4.4 20.2 1.0
O2G B:ACP301 4.4 27.7 1.0
CG B:ASP103 4.5 27.9 1.0
PA B:ACP301 4.6 23.9 1.0
CD B:GLU49 4.6 39.8 1.0
O1A B:ACP301 4.8 25.9 1.0
CG B:LYS17 4.8 24.8 1.0
NZ B:LYS17 5.0 20.8 1.0

Reference:

L.J.Happonen, E.Oksanen, L.Liljeroos, A.Goldman, T.Kajander, S.J.Butcher. The Structure of the Ntpase That Powers Dna Packaging Into Sulfolobus Turreted Icosahedral Virus 2. J.Virol. V. 87 8388 2013.
ISSN: ISSN 0022-538X
PubMed: 23698307
DOI: 10.1128/JVI.00831-13
Page generated: Mon Dec 14 19:02:38 2020

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