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Magnesium in PDB 4kft: Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas

Protein crystallography data

The structure of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas, PDB code: 4kft 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) 46.61 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.726, 65.185, 71.620, 90.55, 93.65, 91.59
R / Rfree (%) 18.1 / 24.6

Other elements in 4kft:

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

Chlorine (Cl) 2 atoms
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 Atp-Gammas (pdb code 4kft). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas, PDB code: 4kft:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4kft

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Magnesium binding site 1 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:28.3
occ:1.00
 OG A:SER18 2.0 28.0 1.0
O A:HOH447 2.1 28.8 1.0
O A:HOH401 2.1 24.1 1.0
O A:HOH420 2.1 30.8 1.0
O A:HOH446 2.1 22.7 1.0
O3B A:AGS302 2.1 19.2 1.0
CB A:SER18 3.0 28.9 1.0
PB A:AGS302 3.5 27.1 1.0
OD2 A:ASP103 3.6 38.4 0.6
OE2 A:GLU49 3.7 37.8 1.0
O2B A:AGS302 3.8 27.0 1.0
OE1 A:GLU49 4.0 33.4 1.0
N A:SER18 4.0 23.5 1.0
CA A:SER18 4.1 25.0 1.0
O A:HOH424 4.1 39.0 1.0
O2A A:AGS302 4.2 28.0 1.0
CD A:GLU49 4.2 36.3 1.0
OD1 A:ASP103 4.3 30.8 0.6
CG A:ASP103 4.3 37.0 0.6
O3A A:AGS302 4.5 24.7 1.0
O1B A:AGS302 4.5 24.6 1.0
O1A A:AGS302 4.6 27.2 1.0
O A:HOH434 4.6 29.1 1.0
PA A:AGS302 4.7 22.9 1.0
OH A:TYR50 4.7 34.6 1.0
O A:HOH416 4.8 34.2 1.0
OD2 A:ASP103 5.0 39.2 0.4

Magnesium binding site 2 out of 8 in 4kft

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Magnesium binding site 2 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:51.9
occ:1.00
 O B:HOH460 2.1 30.8 1.0
O B:HOH461 2.1 35.6 1.0
O B:HOH462 2.2 41.6 1.0
OG2 B:FLC304 2.2 45.8 1.0
OHB B:FLC304 2.3 52.8 1.0
OB2 B:FLC304 2.5 51.7 1.0
CB B:FLC304 3.0 54.6 1.0
CBC B:FLC304 3.0 54.9 1.0
CGC B:FLC304 3.1 52.2 1.0
O B:HOH473 3.3 48.9 1.0
ND2 B:ASN194 3.3 36.9 1.0
CG B:FLC304 3.4 49.9 1.0
OD1 B:ASP192 3.8 35.2 1.0
OD2 B:ASP192 3.9 44.4 1.0
OB1 B:FLC304 4.1 58.3 1.0
NH1 C:ARG160 4.1 41.6 1.0
CG B:ASP192 4.3 37.7 1.0
ND2 B:ASN2 4.3 44.7 1.0
OG1 B:FLC304 4.3 55.4 1.0
CG B:ASN194 4.3 36.2 1.0
CB B:ASN194 4.4 35.2 1.0
CA B:FLC304 4.4 57.0 1.0
OD2 B:ASP5 4.4 34.5 1.0
NH2 C:ARG160 4.5 47.2 1.0
CZ C:ARG160 4.6 46.4 1.0
OA1 B:FLC304 4.6 55.9 1.0
OD1 B:ASP5 4.7 30.6 1.0
CB B:ASP152 4.7 26.5 1.0
O B:ASP152 4.8 25.8 1.0
CG B:ASP5 5.0 30.1 1.0

Magnesium binding site 3 out of 8 in 4kft

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Magnesium binding site 3 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:34.4
occ:1.00
 OB2 B:FLC303 2.0 32.4 1.0
OA2 B:FLC303 2.0 41.9 1.0
O B:HOH459 2.0 30.8 1.0
O B:HOH457 2.1 27.8 1.0
O B:HOH458 2.1 30.9 1.0
OHB B:FLC303 2.2 32.5 1.0
CBC B:FLC303 2.8 37.0 1.0
CB B:FLC303 2.9 34.4 1.0
CAC B:FLC303 3.0 36.2 1.0
CA B:FLC303 3.5 35.6 1.0
OD1 B:ASN126 3.7 30.6 1.0
O B:GLN150 3.9 22.3 1.0
OB1 B:FLC303 4.0 35.6 1.0
OA1 B:FLC303 4.1 34.0 1.0
OG2 B:FLC303 4.1 30.1 1.0
CG B:FLC303 4.2 32.5 1.0
O B:LEU123 4.3 28.6 1.0
OD1 B:ASP152 4.4 27.0 1.0
NE2 B:GLN150 4.5 26.8 1.0
OD2 B:ASP152 4.5 29.9 1.0
CGC B:FLC303 4.7 32.0 1.0
CD1 B:ILE6 4.7 17.4 1.0
NH2 B:ARG127 4.7 36.4 1.0
NE B:ARG127 4.8 37.4 1.0
CG B:ASP152 4.9 33.1 1.0
CG B:ASN126 4.9 24.9 1.0
O B:HIS124 4.9 31.0 1.0
C B:GLN150 5.0 22.1 1.0

Magnesium binding site 4 out of 8 in 4kft

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Magnesium binding site 4 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:33.0
occ:1.00
 O B:HOH450 2.0 34.2 1.0
O1B B:AGS301 2.0 30.3 1.0
O B:HOH401 2.0 24.0 1.0
O B:HOH451 2.1 28.8 1.0
O B:HOH436 2.1 26.5 1.0
OG B:SER18 2.2 30.4 1.0
PB B:AGS301 3.2 25.7 1.0
CB B:SER18 3.2 31.7 1.0
O3B B:AGS301 3.3 29.1 1.0
N B:SER18 3.9 26.5 1.0
O B:HOH452 4.1 33.0 1.0
O2A B:AGS301 4.1 25.8 1.0
CA B:SER18 4.1 27.4 1.0
OE1 B:GLU49 4.1 36.5 1.0
O B:HOH435 4.2 35.3 1.0
O2B B:AGS301 4.3 23.4 1.0
O3A B:AGS301 4.3 27.0 1.0
PA B:AGS301 4.6 29.2 1.0
OD1 B:ASP103 4.6 43.4 1.0
O1A B:AGS301 4.7 26.1 1.0
CE B:LYS17 4.7 28.6 1.0
OE2 B:GLU49 4.8 44.5 1.0
NZ B:LYS17 4.8 29.8 1.0
CD B:GLU49 4.9 44.0 1.0
OD2 B:ASP103 4.9 54.1 1.0
CB B:LYS17 4.9 21.4 1.0

Magnesium binding site 5 out of 8 in 4kft

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Magnesium binding site 5 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:26.3
occ:1.00
 O C:HOH412 2.1 23.8 1.0
O1B C:AGS301 2.1 23.0 1.0
O C:HOH439 2.1 27.6 1.0
O C:HOH406 2.1 24.2 1.0
O C:HOH415 2.1 24.2 1.0
OG C:SER18 2.1 27.2 1.0
CB C:SER18 3.2 25.0 1.0
PB C:AGS301 3.3 22.7 1.0
O2B C:AGS301 3.5 21.9 1.0
OD2 C:ASP103 3.9 36.9 1.0
O1A C:AGS301 3.9 24.1 1.0
N C:SER18 4.0 22.8 1.0
OE1 C:GLU49 4.0 35.0 1.0
CA C:SER18 4.2 28.2 1.0
OE2 C:GLU49 4.2 35.7 1.0
O C:HOH405 4.3 31.4 1.0
O3A C:AGS301 4.3 26.8 1.0
O3B C:AGS301 4.3 25.3 1.0
O C:HOH430 4.5 36.6 1.0
PA C:AGS301 4.5 28.0 1.0
CD C:GLU49 4.6 34.4 1.0
OD1 C:ASP103 4.6 42.0 1.0
O2A C:AGS301 4.6 25.1 1.0
CG C:ASP103 4.6 32.2 1.0
O C:HOH402 4.9 39.3 1.0
NZ C:LYS17 4.9 23.8 1.0
CE C:LYS17 5.0 25.0 1.0

Magnesium binding site 6 out of 8 in 4kft

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Magnesium binding site 6 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


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 Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:36.8
occ:1.00
 OB1 D:FLC303 1.8 36.6 1.0
O D:HOH425 2.0 28.1 1.0
OHB D:FLC303 2.0 37.6 1.0
O D:HOH427 2.1 33.1 1.0
O D:HOH426 2.1 33.2 1.0
OA1 D:FLC303 2.1 33.3 1.0
CBC D:FLC303 2.5 37.3 1.0
CB D:FLC303 2.7 41.0 1.0
CAC D:FLC303 3.0 38.5 1.0
CA D:FLC303 3.3 43.5 1.0
OB2 D:FLC303 3.7 41.6 1.0
OG1 D:FLC303 4.0 32.5 1.0
CG D:FLC303 4.1 34.7 1.0
OD1 D:ASN126 4.1 31.0 1.0
O D:GLN150 4.2 28.1 1.0
OA2 D:FLC303 4.2 43.7 1.0
NH1 D:ARG127 4.3 28.2 1.0
O D:HOH436 4.3 40.6 1.0
OD1 D:ASP152 4.4 31.1 1.0
CGC D:FLC303 4.5 37.8 1.0
OD2 D:ASP152 4.6 32.8 1.0
O D:LEU123 4.6 33.1 1.0
NE2 D:GLN150 4.6 28.1 1.0
CG D:ASP152 4.9 30.9 1.0
O D:HOH437 4.9 30.3 1.0

Magnesium binding site 7 out of 8 in 4kft

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Magnesium binding site 7 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:49.7
occ:1.00
 O2B D:AGS301 2.0 38.5 1.0
O D:HOH414 2.1 39.8 1.0
O D:HOH419 2.1 40.1 1.0
O D:HOH417 2.1 42.6 1.0
O D:HOH418 2.1 43.8 1.0
OG D:SER18 2.2 44.4 1.0
CB D:SER18 3.2 45.4 1.0
PB D:AGS301 3.2 41.0 1.0
O1B D:AGS301 3.3 43.8 1.0
O2A D:AGS301 3.5 48.1 1.0
O D:HOH416 3.8 43.7 1.0
N D:SER18 4.0 44.6 1.0
CA D:SER18 4.1 42.6 1.0
OE1 D:GLU49 4.2 55.0 1.0
O3A D:AGS301 4.2 48.3 1.0
O3B D:AGS301 4.2 42.1 1.0
OD2 D:ASP103 4.3 51.9 1.0
PA D:AGS301 4.4 46.2 1.0
OD1 D:ASP103 4.5 45.0 1.0
CG D:ASP103 4.7 45.1 1.0
CG D:LYS17 4.8 43.9 1.0
NZ D:LYS17 4.8 39.9 1.0

Magnesium binding site 8 out of 8 in 4kft

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Magnesium binding site 8 out of 8 in the Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Genome Packaging Ntpase B204 From Sulfolobus Turreted Icosahedral Virus 2 in Complex with Atp-Gammas within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg306

b:46.8
occ:1.00
 O D:HOH423 2.1 39.0 1.0
O D:HOH424 2.1 44.0 1.0
O D:HOH422 2.1 38.3 1.0
OHB D:FLC302 2.2 42.1 1.0
OG1 D:FLC302 2.3 45.1 1.0
OB2 D:FLC302 2.5 43.0 1.0
CB D:FLC302 3.0 49.5 1.0
CBC D:FLC302 3.1 50.6 1.0
CGC D:FLC302 3.2 46.3 1.0
CG D:FLC302 3.5 43.7 1.0
ND2 D:ASN194 3.7 37.5 1.0
O D:HOH435 3.9 41.1 1.0
ND2 D:ASN2 3.9 38.1 1.0
OD2 D:ASP192 4.0 38.9 1.0
OD1 D:ASP192 4.1 42.7 1.0
OD2 D:ASP5 4.2 34.7 1.0
OB1 D:FLC302 4.2 59.3 1.0
CA D:FLC302 4.3 49.5 1.0
OG2 D:FLC302 4.3 50.3 1.0
OD1 D:ASP5 4.4 34.2 1.0
CG D:ASP192 4.4 39.5 1.0
OA2 D:FLC302 4.5 55.5 1.0
CG D:ASP5 4.6 33.8 1.0
CB D:ASP152 4.7 28.4 1.0
O D:ASP152 4.8 28.9 1.0
CG D:ASN194 4.8 43.3 1.0
CAC D:FLC302 4.9 53.6 1.0
CB D:ASN194 4.9 41.6 1.0
CD2 D:LEU153 4.9 30.1 1.0
CG D:ASN2 5.0 42.6 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: Sat Aug 17 03:35:13 2024

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