Atomistry » Magnesium » PDB 3mv1-3n8b » 3n4p
Atomistry »
  Magnesium »
    PDB 3mv1-3n8b »
      3n4p »

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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Go back to Magnesium Binding Sites List in 3n4p
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy