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Manganese in PDB 6ey7: Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound

Protein crystallography data

The structure of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound, PDB code: 6ey7 was solved by S.Bongarzone, M.Nadal, Z.Kaczmarska, C.Machon, M.Alvarez, F.Albericio, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.87 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 81.650, 87.650, 186.580, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.8

Other elements in 6ey7:

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

Fluorine (F) 4 atoms
Chlorine (Cl) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound (pdb code 6ey7). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound, PDB code: 6ey7:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 6ey7

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Manganese binding site 1 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:96.6
occ:1.00
 O A:C3W704 2.1 0.7 1.0
O A:HOH801 2.2 69.5 1.0
OD1 A:ASP463 2.2 1.0 1.0
OE1 A:GLU534 2.3 0.3 1.0
O1 A:C3W704 2.6 0.5 1.0
OE2 A:GLU534 2.7 75.8 1.0
CD A:GLU534 2.8 0.9 1.0
CG A:ASP463 3.2 98.2 1.0
C8 A:C3W704 3.2 0.9 1.0
O A:HOH805 3.4 97.7 1.0
C10 A:C3W704 3.6 0.5 1.0
MN A:MN702 3.7 93.8 1.0
OD2 A:ASP463 3.7 0.7 1.0
C9 A:C3W704 4.0 0.4 1.0
CG A:GLU534 4.3 86.2 1.0
N A:C3W704 4.3 0.3 1.0
CB A:ASP463 4.3 83.9 1.0
O A:PRO464 4.4 97.5 1.0
C1 A:C3W704 4.5 0.8 1.0
O A:HOH802 4.6 82.9 1.0
CA A:ASP463 4.7 82.5 1.0
OG1 A:THR537 4.7 0.5 1.0
O A:HOH803 4.7 91.2 1.0
CB A:GLU534 4.8 77.3 1.0
CE A:MET579 4.9 0.9 1.0
C A:ASP463 4.9 90.4 1.0
C11 A:C3W704 5.0 0.9 1.0

Manganese binding site 2 out of 10 in 6ey7

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Manganese binding site 2 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:93.8
occ:1.00
 O1 A:C3W704 2.0 0.5 1.0
O A:HOH802 2.3 82.9 1.0
OD1 A:ASP651 2.3 99.8 1.0
O3 A:C3W704 2.3 0.6 1.0
O A:HOH803 2.5 91.2 1.0
OD2 A:ASP463 2.5 0.7 1.0
C10 A:C3W704 2.8 0.5 1.0
C11 A:C3W704 3.0 0.9 1.0
OD1 A:ASP463 3.1 1.0 1.0
CG A:ASP463 3.1 98.2 1.0
CG A:ASP651 3.4 98.3 1.0
MN A:MN701 3.7 96.6 1.0
CB A:ASP651 3.9 89.6 1.0
CA A:ASP651 4.1 86.5 1.0
O A:HOH805 4.1 97.7 1.0
O2 A:C3W704 4.2 0.5 1.0
CB A:SER473 4.3 0.6 1.0
C9 A:C3W704 4.3 0.4 1.0
O A:C3W704 4.5 0.7 1.0
OD2 A:ASP651 4.5 0.4 1.0
O A:GLY474 4.5 89.7 1.0
CB A:ASP463 4.5 83.9 1.0
O A:HOH801 4.5 69.5 1.0
O A:PRO464 4.6 97.5 1.0
N A:ASP651 4.6 89.4 1.0
O A:ASP463 4.9 90.4 1.0
C8 A:C3W704 4.9 0.9 1.0
OD1 A:ASP650 5.0 0.2 1.0

Manganese binding site 3 out of 10 in 6ey7

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Manganese binding site 3 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:0.2
occ:1.00
 O B:ASN447 2.2 0.4 1.0
OD2 A:ASP439 2.8 0.8 1.0
OE2 A:GLU618 3.3 0.8 1.0
C B:ASN447 3.4 0.0 1.0
OD1 A:ASP439 3.4 0.7 1.0
CG A:ASP439 3.5 0.5 1.0
CA B:ASN447 4.1 94.6 1.0
CD A:GLU618 4.3 0.0 1.0
CB B:ASN447 4.3 91.5 1.0
N B:THR448 4.4 98.3 1.0
CG A:GLU618 4.4 0.7 1.0
CA B:THR448 4.6 0.9 1.0
CG B:ASN447 4.9 0.0 1.0
ND2 B:ASN447 4.9 100.0 1.0
CB A:ASP439 5.0 81.3 1.0

Manganese binding site 4 out of 10 in 6ey7

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Manganese binding site 4 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:80.5
occ:1.00
 O B:C3W703 2.1 0.0 1.0
OD1 B:ASP463 2.3 88.2 1.0
O1 B:C3W703 2.3 0.7 1.0
O B:HOH801 2.4 64.1 1.0
OE2 B:GLU534 2.5 79.8 0.0
O B:HOH802 2.6 60.5 1.0
OE1 B:GLU534 2.6 80.9 1.0
CD B:GLU534 2.9 83.7 1.0
C8 B:C3W703 3.2 0.1 1.0
CG B:ASP463 3.3 84.3 1.0
C10 B:C3W703 3.3 0.5 1.0
C9 B:C3W703 3.8 0.4 1.0
OD2 B:ASP463 3.8 90.2 1.0
MN B:MN702 4.0 81.3 1.0
CG B:GLU534 4.3 76.8 1.0
O B:HOH805 4.3 73.8 1.0
N B:C3W703 4.3 0.8 1.0
CB B:ASP463 4.4 69.2 1.0
O B:PRO464 4.4 87.2 1.0
O B:HOH803 4.6 72.0 1.0
C11 B:C3W703 4.7 0.8 1.0
C1 B:C3W703 4.7 0.1 1.0
CG2 B:THR537 4.7 0.9 1.0
CA B:ASP463 4.8 68.0 1.0
CB B:GLU534 4.8 71.0 1.0
O2 B:C3W703 4.9 0.1 1.0
C B:ASP463 4.9 74.1 1.0

Manganese binding site 5 out of 10 in 6ey7

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Manganese binding site 5 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:81.3
occ:1.00
 O2 B:C3W703 2.0 0.1 1.0
OD2 B:ASP651 2.1 0.2 1.0
O B:HOH805 2.2 73.8 1.0
O1 B:C3W703 2.3 0.7 1.0
O B:HOH803 2.5 72.0 1.0
OD2 B:ASP463 2.6 90.2 1.0
C11 B:C3W703 2.9 0.8 1.0
C10 B:C3W703 2.9 0.5 1.0
CG B:ASP651 3.2 92.8 1.0
CG B:ASP463 3.2 84.3 1.0
OD1 B:ASP463 3.2 88.2 1.0
CB B:ASP651 3.7 77.5 1.0
MN B:MN701 4.0 80.5 1.0
CA B:ASP651 4.0 74.8 1.0
O3 B:C3W703 4.1 0.1 1.0
OG B:SER473 4.2 0.3 1.0
OD1 B:ASP651 4.3 92.9 1.0
OD2 B:ASP650 4.3 0.3 1.0
O B:HOH802 4.3 60.5 1.0
O B:GLY474 4.3 84.5 1.0
O B:HOH801 4.4 64.1 1.0
N B:ASP651 4.5 78.2 1.0
C9 B:C3W703 4.5 0.4 1.0
O B:PRO464 4.6 87.2 1.0
CB B:ASP463 4.6 69.2 1.0
O B:ASP463 4.9 73.5 1.0
O B:C3W703 4.9 0.0 1.0

Manganese binding site 6 out of 10 in 6ey7

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Manganese binding site 6 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn701

b:87.2
occ:1.00
 O C:HOH803 2.1 64.1 1.0
OD1 C:ASP463 2.1 0.3 1.0
O C:C3W704 2.2 0.9 1.0
O1 C:C3W704 2.5 0.2 1.0
OE1 C:GLU534 2.6 0.3 1.0
OE2 C:GLU534 3.0 95.4 1.0
CD C:GLU534 3.1 0.8 1.0
CG C:ASP463 3.1 0.8 1.0
C8 C:C3W704 3.2 0.8 1.0
C10 C:C3W704 3.4 0.7 1.0
OD2 C:ASP463 3.6 0.7 1.0
MN C:MN702 3.7 94.2 1.0
C9 C:C3W704 3.8 0.3 1.0
O C:HOH802 4.2 61.2 1.0
N C:C3W704 4.3 0.9 1.0
CB C:ASP463 4.4 88.9 1.0
O C:PRO464 4.4 0.4 1.0
C1 C:C3W704 4.5 0.6 1.0
CG C:GLU534 4.6 92.9 1.0
C11 C:C3W704 4.7 0.9 1.0
CA C:ASP463 4.8 87.1 1.0
C3 C:C3W704 4.9 0.5 1.0
CG2 C:THR537 4.9 0.4 1.0
C C:ASP463 4.9 95.0 1.0

Manganese binding site 7 out of 10 in 6ey7

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Manganese binding site 7 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn702

b:94.2
occ:1.00
 OD1 C:ASP651 2.1 0.6 1.0
O1 C:C3W704 2.3 0.2 1.0
O3 C:C3W704 2.4 0.8 1.0
O C:HOH802 2.6 61.2 1.0
OD2 C:ASP463 2.6 0.7 1.0
C10 C:C3W704 3.1 0.7 1.0
CG C:ASP651 3.1 0.1 1.0
C11 C:C3W704 3.2 0.9 1.0
OD1 C:ASP463 3.2 0.3 1.0
CG C:ASP463 3.2 0.8 1.0
CB C:ASP651 3.6 88.0 1.0
MN C:MN701 3.7 87.2 1.0
O C:HOH803 3.9 64.1 1.0
O C:GLY474 4.0 92.7 1.0
CA C:ASP651 4.1 83.9 1.0
OD2 C:ASP651 4.2 0.7 1.0
O C:PRO464 4.3 0.4 1.0
OG C:SER473 4.3 0.5 1.0
O2 C:C3W704 4.3 0.7 1.0
C9 C:C3W704 4.6 0.3 1.0
CB C:ASP463 4.6 88.9 1.0
O C:ASP463 4.6 95.3 1.0
N C:ASP651 4.6 85.1 1.0
O C:C3W704 4.8 0.9 1.0

Manganese binding site 8 out of 10 in 6ey7

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Manganese binding site 8 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


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, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn703

b:0.4
occ:1.00
 O C:ASN447 2.3 0.4 1.0
OD2 D:ASP439 2.6 0.3 1.0
C C:ASN447 3.3 0.1 1.0
CG D:ASP439 3.4 94.4 1.0
OD1 D:ASP439 3.5 93.1 1.0
CA C:ASN447 4.0 99.2 1.0
CB C:ASN447 4.2 0.2 1.0
ND2 C:ASN447 4.3 0.4 1.0
N C:THR448 4.3 0.2 1.0
CA C:THR448 4.7 0.6 1.0
CG C:ASN447 4.8 0.5 1.0
CB D:ASP439 4.9 78.9 1.0

Manganese binding site 9 out of 10 in 6ey7

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Manganese binding site 9 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn701

b:0.9
occ:1.00
 O1 D:C3W703 2.0 0.9 1.0
OD1 D:ASP463 2.1 91.2 1.0
O D:C3W703 2.3 0.9 1.0
OE1 D:GLU534 2.5 0.4 1.0
O D:HOH801 2.6 88.6 1.0
O D:HOH802 2.7 0.7 1.0
OE2 D:GLU534 2.9 88.9 1.0
CD D:GLU534 3.0 0.9 1.0
C10 D:C3W703 3.1 0.6 1.0
CG D:ASP463 3.1 90.8 1.0
C8 D:C3W703 3.3 0.9 1.0
OD2 D:ASP463 3.6 0.9 1.0
MN D:MN702 3.7 91.2 1.0
C9 D:C3W703 3.7 0.2 1.0
O D:HOH803 3.8 69.7 1.0
O D:PRO464 4.1 98.1 1.0
CB D:ASP463 4.3 80.1 1.0
C11 D:C3W703 4.4 0.2 1.0
CG D:GLU534 4.4 89.0 1.0
N D:C3W703 4.5 0.2 1.0
OG1 D:THR537 4.6 0.8 1.0
O2 D:C3W703 4.6 0.3 1.0
CA D:ASP463 4.6 79.4 1.0
O D:HOH804 4.7 83.3 1.0
C D:ASP463 4.8 87.2 1.0
N D:PRO464 4.9 87.1 1.0
CB D:GLU534 4.9 78.2 1.0
C1 D:C3W703 5.0 0.4 1.0

Manganese binding site 10 out of 10 in 6ey7

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Manganese binding site 10 out of 10 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn702

b:91.2
occ:1.00
 O2 D:C3W703 2.1 0.3 1.0
OD1 D:ASP651 2.3 0.2 1.0
O D:HOH803 2.3 69.7 1.0
OD2 D:ASP463 2.5 0.9 1.0
O1 D:C3W703 2.5 0.9 1.0
C11 D:C3W703 2.8 0.2 1.0
C10 D:C3W703 3.0 0.6 1.0
CG D:ASP463 3.3 90.8 1.0
OD1 D:ASP463 3.4 91.2 1.0
CG D:ASP651 3.4 0.5 1.0
MN D:MN701 3.7 0.9 1.0
O D:HOH801 3.8 88.6 1.0
CB D:ASP651 3.8 88.2 1.0
CA D:ASP651 3.9 83.9 1.0
O3 D:C3W703 4.0 0.8 1.0
N D:ASP651 4.3 86.7 1.0
C9 D:C3W703 4.4 0.2 1.0
OD2 D:ASP651 4.5 0.6 1.0
O D:GLY474 4.5 98.3 1.0
N D:SER473 4.6 0.3 1.0
CB D:ASP463 4.7 80.1 1.0
O D:HOH804 4.9 83.3 1.0

Reference:

S.Bongarzone, M.Nadal, Z.Kaczmarska, C.Machon, M.Alvarez, F.Albericio, M.Coll. Structure-Driven Discovery of Alpha , Gamma-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. Acs Omega V. 3 8497 2018.
ISSN: ESSN 2470-1343
PubMed: 31458978
DOI: 10.1021/ACSOMEGA.8B01472
Page generated: Sun Oct 6 04:21:51 2024

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