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

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

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

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 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 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 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 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 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 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

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