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Magnesium in PDB 3n4p: Human Cytomegalovirus Terminase Nuclease Domain

Protein crystallography data

The structure of Human Cytomegalovirus Terminase Nuclease Domain, PDB code: 3n4p was solved by M.Nadal, P.J.Mas, A.G.Blanco, C.Arnan, M.Sola, D.J.Hart, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.860, 87.960, 188.380, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 27.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Cytomegalovirus Terminase Nuclease Domain (pdb code 3n4p). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Human Cytomegalovirus Terminase Nuclease Domain, PDB code: 3n4p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 3n4p

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Magnesium binding site 1 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4

b:0.2
occ:1.00
 O B:ASN447 2.3 68.8 1.0
OD2 A:ASP439 2.4 67.3 1.0
OD1 A:ASP439 3.0 58.6 1.0
CG A:ASP439 3.0 57.7 1.0
OE1 A:GLU618 3.3 76.8 1.0
OE2 A:GLU618 3.4 80.0 1.0
C B:ASN447 3.5 66.4 1.0
CD A:GLU618 3.6 79.4 1.0
CA B:ASN447 4.2 63.8 1.0
CB B:ASN447 4.3 63.5 1.0
N B:THR448 4.5 65.9 1.0
CB A:ASP439 4.5 53.0 1.0
CA B:THR448 4.5 68.4 1.0
CG A:GLU618 4.9 74.7 1.0

Magnesium binding site 2 out of 7 in 3n4p

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Magnesium binding site 2 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1

b:0.8
occ:1.00
 OD1 B:ASP463 2.8 73.3 1.0
OE2 B:GLU534 2.9 91.7 1.0
OD2 B:ASP463 3.0 76.9 1.0
CG B:ASP463 3.3 70.0 1.0
CD B:GLU534 3.6 89.7 1.0
OE1 B:GLU534 3.6 94.2 1.0
CB B:ASP463 4.8 64.1 1.0
O B:PRO464 4.8 76.5 1.0
CB B:ASN536 4.9 90.1 1.0
CG B:GLU534 5.0 80.9 1.0

Magnesium binding site 3 out of 7 in 3n4p

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Magnesium binding site 3 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg5

b:96.2
occ:1.00
 O A:ASN447 2.3 85.1 1.0
OD2 B:ASP439 2.5 51.6 1.0
CG B:ASP439 3.3 48.0 1.0
OE2 B:GLU618 3.4 70.4 1.0
C A:ASN447 3.5 81.4 1.0
OD1 B:ASP439 3.5 55.4 1.0
O A:HOH79 3.6 22.4 1.0
CD B:GLU618 3.6 68.2 1.0
O A:HOH97 3.9 32.1 1.0
OE1 B:GLU618 4.1 69.0 1.0
CB B:GLU618 4.1 45.8 1.0
CG B:GLU618 4.2 54.0 1.0
CA A:ASN447 4.4 80.4 1.0
N A:THR448 4.4 78.8 1.0
CA A:THR448 4.5 80.2 1.0
CB A:ASN447 4.6 79.1 1.0
OD2 B:ASP615 4.8 51.6 1.0
CB B:ASP439 4.8 41.6 1.0
CA B:GLU618 4.8 43.3 1.0

Magnesium binding site 4 out of 7 in 3n4p

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Magnesium binding site 4 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2

b:0.1
occ:1.00
 CB C:ASN536 3.0 91.3 1.0
OE1 C:GLU534 3.1 78.1 1.0
N C:THR537 3.3 93.2 1.0
OD2 C:ASP463 3.3 68.0 1.0
N C:ASN536 3.7 85.7 1.0
CA C:ASN536 3.7 91.9 1.0
C C:ASN536 4.0 94.9 1.0
CG2 C:THR537 4.0 90.8 1.0
CB C:THR537 4.2 95.4 1.0
CG C:ASN536 4.3 97.5 1.0
CG C:ASP463 4.3 65.7 1.0
CA C:THR537 4.3 96.4 1.0
CD C:GLU534 4.3 74.8 1.0
OD1 C:ASP463 4.4 74.3 1.0
C C:GLY535 4.5 83.2 1.0
O C:PRO464 4.5 67.3 1.0
O C:GLU534 4.9 67.2 1.0
OD1 C:ASN536 4.9 0.4 1.0
OE2 C:GLU534 5.0 69.0 1.0

Magnesium binding site 5 out of 7 in 3n4p

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Magnesium binding site 5 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg7

b:0.7
occ:1.00
 O D:ASN447 2.5 0.5 1.0
OD2 C:ASP439 2.8 64.1 1.0
OE2 C:GLU618 3.1 73.6 1.0
OD1 C:ASP439 3.3 63.3 1.0
CG C:ASP439 3.5 60.1 1.0
CD C:GLU618 3.5 69.4 1.0
C D:ASN447 3.5 1.0 1.0
O C:HOH96 3.7 33.8 1.0
CG C:GLU618 3.9 59.3 1.0
OE1 C:GLU618 4.2 72.8 1.0
CB C:GLU618 4.2 47.4 1.0
ND2 D:ASN449 4.3 0.9 1.0
N D:THR448 4.4 98.1 1.0
CA D:ASN447 4.5 0.5 1.0
CA C:GLU618 4.5 48.4 1.0
CA D:THR448 4.5 99.0 1.0
CB D:ASN447 4.7 99.7 1.0
CB C:ASP439 5.0 60.8 1.0

Magnesium binding site 6 out of 7 in 3n4p

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Magnesium binding site 6 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3

b:0.3
occ:1.00
 ND2 D:ASN536 2.4 75.0 0.5
OD1 D:ASP463 2.5 83.0 1.0
OD2 D:ASP463 2.5 85.0 1.0
CG D:ASP463 2.8 79.5 1.0
OD1 D:ASN536 2.9 78.1 0.5
CG D:ASN536 3.0 76.8 0.5
CG D:GLU534 3.6 70.9 1.0
OD1 D:ASN536 4.1 75.7 0.5
CB D:ASN536 4.3 77.8 0.5
CB D:ASP463 4.3 73.6 1.0
CB D:ASN536 4.4 76.7 0.5
CD D:GLU534 4.6 74.3 1.0
CG D:ASN536 4.6 75.3 0.5
OE2 D:GLU534 4.7 75.4 1.0
CB D:GLU534 4.7 65.0 1.0
O D:PRO464 4.7 88.3 1.0

Magnesium binding site 7 out of 7 in 3n4p

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Magnesium binding site 7 out of 7 in the Human Cytomegalovirus Terminase Nuclease Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Cytomegalovirus Terminase Nuclease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg6

b:0.7
occ:1.00
 O C:ASN447 2.3 89.6 1.0
OD2 D:ASP439 2.5 87.4 1.0
OE2 D:GLU618 2.8 0.0 1.0
OE1 D:GLU618 3.0 97.2 1.0
OD1 D:ASP439 3.1 78.8 1.0
CG D:ASP439 3.1 79.0 1.0
CD D:GLU618 3.3 0.8 1.0
C C:ASN447 3.4 86.3 1.0
O D:HOH34 4.2 39.4 1.0
CA C:ASN447 4.2 82.8 1.0
N C:THR448 4.2 85.2 1.0
CA C:THR448 4.3 89.3 1.0
CB C:ASN447 4.4 85.4 1.0
CB D:ASP439 4.6 73.2 1.0
CG D:GLU618 4.8 95.6 1.0

Reference:

M.Nadal, P.J.Mas, A.G.Blanco, C.Arnan, M.Sola, D.J.Hart, M.Coll. Structure and Inhibition of Herpesvirus Dna Packaging Terminase Nuclease Domain. Proc.Natl.Acad.Sci.Usa V. 107 16078 2010.
ISSN: ISSN 0027-8424
PubMed: 20805464
DOI: 10.1073/PNAS.1007144107
Page generated: Thu Aug 15 07:50:44 2024

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