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Manganese in PDB 3n4q: Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked

Protein crystallography data

The structure of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, PDB code: 3n4q 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) 44.05 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.700, 88.100, 190.700, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 28.3

Other elements in 3n4q:

The structure of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked (pdb code 3n4q). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, PDB code: 3n4q:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3n4q

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Manganese binding site 1 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1

b:58.0
occ:1.00
 OD2 A:ASP651 1.9 0.5 1.0
OD1 A:ASP463 1.9 0.0 1.0
O A:HOH23 2.6 84.9 1.0
CG A:ASP463 2.8 90.1 1.0
CG A:ASP651 3.0 97.2 1.0
OD2 A:ASP463 3.2 0.9 1.0
MN A:MN2 3.4 55.5 1.0
CB A:ASP651 3.8 88.8 1.0
OD1 A:ASP651 4.0 1.0 1.0
O A:PRO464 4.1 93.9 1.0
CB A:ASP463 4.2 80.4 1.0
O A:GLY474 4.2 91.8 1.0
CA A:ASP651 4.3 84.7 1.0
O A:HOH49 4.7 81.2 1.0
OD1 A:ASP650 4.8 93.0 1.0
N A:ASP651 5.0 87.5 1.0

Manganese binding site 2 out of 8 in 3n4q

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Manganese binding site 2 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn2

b:55.5
occ:1.00
 OD2 A:ASP463 1.9 0.9 1.0
OE1 A:GLU534 2.1 92.7 1.0
O A:HOH49 2.5 81.2 1.0
CG A:ASP463 2.9 90.1 1.0
CD A:GLU534 3.2 87.0 1.0
OD1 A:ASP463 3.3 0.0 1.0
MN A:MN1 3.4 58.0 1.0
O A:PRO464 3.4 93.9 1.0
O A:HOH23 3.6 84.9 1.0
OE2 A:GLU534 3.7 85.9 1.0
CB A:ASP463 4.2 80.4 1.0
CG A:GLU534 4.5 82.2 1.0
C A:PRO464 4.6 94.5 1.0
CA A:ASP463 4.6 78.5 1.0
N A:PRO464 4.7 85.3 1.0
C A:ASP463 4.8 82.3 1.0
CD A:PRO464 4.9 84.0 1.0

Manganese binding site 3 out of 8 in 3n4q

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Manganese binding site 3 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:55.9
occ:1.00
 OD1 B:ASP651 1.9 97.9 1.0
OD1 B:ASP463 1.9 98.4 1.0
O B:HOH31 2.7 77.0 1.0
CG B:ASP463 2.9 86.0 1.0
CG B:ASP651 3.1 84.5 1.0
OD2 B:ASP463 3.3 97.9 1.0
MN B:MN4 3.6 52.0 1.0
OD2 B:ASP651 3.9 88.6 1.0
OD1 B:ASP650 4.0 87.4 1.0
CB B:ASP651 4.0 76.5 1.0
CB B:ASP463 4.2 77.3 1.0
CA B:ASP651 4.3 74.4 1.0
O B:HOH51 4.5 60.1 1.0
O B:HOH50 4.5 72.9 1.0
O B:GLY474 4.7 76.5 1.0
N B:ASP651 4.7 76.7 1.0
OG B:SER473 4.9 93.3 1.0

Manganese binding site 4 out of 8 in 3n4q

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Manganese binding site 4 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn4

b:52.0
occ:1.00
 OD2 B:ASP463 1.9 97.9 1.0
OE1 B:GLU534 1.9 98.6 1.0
O B:HOH50 2.4 72.9 1.0
CD B:GLU534 2.9 87.2 1.0
CG B:ASP463 2.9 86.0 1.0
O B:HOH51 2.9 60.1 1.0
OE2 B:GLU534 3.2 84.7 1.0
OD1 B:ASP463 3.3 98.4 1.0
MN B:MN3 3.6 55.9 1.0
CD B:PRO464 4.2 82.1 1.0
CB B:ASP463 4.2 77.3 1.0
CG B:GLU534 4.2 84.4 1.0
CA B:ASP463 4.6 76.0 1.0
N B:PRO464 4.8 79.5 1.0
O B:HOH31 4.9 77.0 1.0
C B:ASP463 4.9 76.9 1.0

Manganese binding site 5 out of 8 in 3n4q

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Manganese binding site 5 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn5

b:58.9
occ:1.00
 OD2 C:ASP463 1.9 0.8 1.0
OE2 C:GLU534 1.9 0.5 1.0
O C:HOH52 2.2 87.9 1.0
CD C:GLU534 2.7 0.1 1.0
OE1 C:GLU534 2.9 0.1 1.0
CG C:ASP463 2.9 91.2 1.0
O C:HOH53 3.0 90.9 1.0
O C:HOH24 3.3 86.2 1.0
OD1 C:ASP463 3.4 0.5 1.0
MN C:MN6 3.5 58.4 1.0
O C:PRO464 4.1 89.1 1.0
CG C:GLU534 4.2 98.6 1.0
O C:HOH54 4.2 77.4 1.0
CB C:ASP463 4.2 81.7 1.0
O C:HOH55 4.3 77.9 1.0
O C:HOH37 4.4 83.7 1.0
CA C:ASP463 4.8 79.1 1.0
C C:ASP463 4.9 79.4 1.0
CB C:GLU534 5.0 89.9 1.0

Manganese binding site 6 out of 8 in 3n4q

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Manganese binding site 6 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn6

b:58.4
occ:1.00
 OD1 C:ASP651 1.9 0.2 1.0
OD1 C:ASP463 1.9 0.5 1.0
O C:HOH55 2.3 77.9 1.0
O C:HOH54 2.4 77.4 1.0
CG C:ASP463 3.0 91.2 1.0
CG C:ASP651 3.1 87.4 1.0
O C:HOH24 3.3 86.2 1.0
OD2 C:ASP463 3.3 0.8 1.0
MN C:MN5 3.5 58.9 1.0
OD2 C:ASP651 3.8 91.0 1.0
CB C:ASP651 4.1 79.7 1.0
CA C:ASP651 4.3 78.8 1.0
CB C:ASP463 4.3 81.7 1.0
O C:GLY474 4.4 80.1 1.0
OD1 C:ASP650 4.5 89.0 1.0
O C:HOH52 4.7 87.9 1.0
O C:HOH37 4.8 83.7 1.0
N C:ASP651 4.8 80.8 1.0
O C:ASP463 4.8 79.3 1.0
CD1 C:ILE654 4.9 82.5 1.0
O C:HOH53 5.0 90.9 1.0

Manganese binding site 7 out of 8 in 3n4q

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Manganese binding site 7 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn7

b:60.5
occ:1.00
 OD2 D:ASP651 1.9 0.7 1.0
OD1 D:ASP463 1.9 0.0 1.0
CG D:ASP651 2.6 96.2 1.0
CG D:ASP463 2.9 97.0 1.0
O D:HOH56 2.9 80.9 1.0
OD1 D:ASP651 3.0 0.4 1.0
OD2 D:ASP463 3.2 0.3 1.0
MN D:MN8 3.6 64.2 1.0
OD2 D:ASP650 3.7 92.2 1.0
CB D:ASP651 3.9 90.8 1.0
O D:ASP463 4.1 93.9 1.0
O D:HOH35 4.1 78.1 1.0
CA D:ASP651 4.2 87.1 1.0
CB D:ASP463 4.2 88.7 1.0
O D:GLY474 4.4 95.5 1.0
CG D:ASP650 4.5 94.7 1.0
OD1 D:ASP650 4.6 98.1 1.0
O D:PRO464 4.7 0.8 1.0
N D:ASP651 4.8 89.7 1.0
OG D:SER473 4.8 0.6 1.0
CG2 D:ILE654 4.8 74.6 1.0
C D:ASP463 4.9 91.5 1.0

Manganese binding site 8 out of 8 in 3n4q

Go back to Manganese Binding Sites List in 3n4q
Manganese binding site 8 out of 8 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn8

b:64.2
occ:1.00
 OD2 D:ASP463 1.9 0.3 1.0
O D:HOH35 2.6 78.1 1.0
OE1 D:GLU534 2.6 82.1 1.0
CG D:ASP463 2.9 97.0 1.0
OD1 D:ASP463 3.4 0.0 1.0
CD D:GLU534 3.6 77.4 1.0
MN D:MN7 3.6 60.5 1.0
O D:HOH56 3.8 80.9 1.0
OE2 D:GLU534 3.8 76.3 1.0
O D:PRO464 4.1 0.8 1.0
CB D:ASP463 4.1 88.7 1.0
CA D:ASP463 4.7 87.7 1.0
C D:ASP463 4.8 91.5 1.0
O D:ASP463 4.8 93.9 1.0
OD2 D:ASP651 4.9 0.7 1.0
CG D:GLU534 5.0 74.5 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: Sat Oct 5 17:17:04 2024

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