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Manganese in PDB 7m0n: The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir

Protein crystallography data

The structure of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir, PDB code: 7m0n was solved by M.G.Cuypers, P.J.Slavish, M.K.Yun, R.Dubois, Z.Rankovic, S.W.White, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.44 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 126.702, 135.126, 126.751, 90, 90, 90
R / Rfree (%) 19.2 / 23.1

Other elements in 7m0n:

The structure of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir (pdb code 7m0n). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir, PDB code: 7m0n:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 7m0n

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Manganese binding site 1 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:64.6
occ:1.00
 O A:ILE120 2.1 59.3 1.0
OE2 A:GLU119 2.3 71.5 1.0
OD2 A:ASP108 2.3 55.5 1.0
NE2 A:HIS41 2.3 54.7 1.0
OAH A:RLT301 2.3 105.5 1.0
OAG A:RLT301 2.4 98.8 1.0
CE1 A:HIS41 3.0 40.1 1.0
CG A:ASP108 3.1 58.2 1.0
CBD A:RLT301 3.1 111.3 1.0
CAZ A:RLT301 3.1 109.9 1.0
OD1 A:ASP108 3.2 49.7 1.0
C A:ILE120 3.3 62.2 1.0
CD2 A:HIS41 3.3 54.7 1.0
CD A:GLU119 3.3 68.2 1.0
N A:ILE120 3.7 56.7 1.0
O A:HOH401 3.8 76.2 1.0
MN A:MN303 3.8 81.4 1.0
OE1 A:GLU119 3.8 81.0 1.0
CA A:ILE120 4.0 48.2 1.0
ND1 A:HIS41 4.2 61.9 1.0
NZ A:LYS134 4.3 80.1 0.3
N A:GLY121 4.3 53.5 1.0
CG A:HIS41 4.3 58.8 1.0
CBB A:RLT301 4.4 131.8 1.0
NBE A:RLT301 4.5 134.7 1.0
CB A:ASP108 4.5 52.5 1.0
CB A:ILE120 4.5 65.3 1.0
CG A:GLU119 4.5 61.1 1.0
CA A:GLY121 4.6 47.3 1.0
C A:GLU119 4.7 54.8 1.0
OAE A:RLT301 4.8 125.0 1.0
CG2 A:ILE120 4.9 56.5 1.0

Manganese binding site 2 out of 8 in 7m0n

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Manganese binding site 2 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:81.4
occ:1.00
 OAE A:RLT301 2.0 125.0 1.0
OD1 A:ASP108 2.3 49.7 1.0
O A:HOH401 2.3 76.2 1.0
OAH A:RLT301 2.3 105.5 1.0
O A:HOH405 2.4 60.3 1.0
OE1 A:GLU80 2.6 66.4 1.0
CAU A:RLT301 3.1 131.7 1.0
CG A:ASP108 3.3 58.2 1.0
CAZ A:RLT301 3.4 109.9 1.0
CD A:GLU80 3.7 65.7 1.0
CBB A:RLT301 3.7 131.8 1.0
OD2 A:ASP108 3.8 55.5 1.0
MN A:MN302 3.8 64.6 1.0
CE1 A:HIS41 3.9 40.1 1.0
O A:PRO107 4.1 59.8 1.0
O A:LEU106 4.2 74.0 1.0
NAR A:RLT301 4.2 140.1 1.0
CG A:GLU80 4.3 61.8 1.0
OE1 A:GLU119 4.4 81.0 1.0
C A:PRO107 4.4 72.4 1.0
CB A:ASP108 4.4 52.5 1.0
CB A:GLU80 4.5 59.7 1.0
NE2 A:HIS41 4.5 54.7 1.0
CA A:ASP108 4.5 55.8 1.0
CBD A:RLT301 4.6 111.3 1.0
OE2 A:GLU80 4.6 80.5 1.0
N A:ASP108 4.6 55.8 1.0
CAN A:RLT301 4.6 149.6 1.0
OE2 A:GLU119 4.7 71.5 1.0
ND1 A:HIS41 4.9 61.9 1.0
OAG A:RLT301 4.9 98.8 1.0
CD A:GLU119 5.0 68.2 1.0

Manganese binding site 3 out of 8 in 7m0n

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Manganese binding site 3 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn304

b:79.8
occ:1.00
 OAE B:RLT301 2.1 91.5 1.0
OD1 B:ASP108 2.2 57.5 1.0
OAH B:RLT301 2.3 77.8 1.0
O B:HOH403 2.3 75.0 1.0
O B:HOH406 2.4 58.5 1.0
OE1 B:GLU80 2.5 60.1 1.0
CG B:ASP108 3.2 53.3 1.0
CAU B:RLT301 3.2 100.1 1.0
CAZ B:RLT301 3.4 97.3 1.0
CD B:GLU80 3.6 64.6 1.0
OD2 B:ASP108 3.7 57.1 1.0
MN B:MN305 3.7 62.0 1.0
CBB B:RLT301 3.7 111.2 1.0
CE1 B:HIS41 3.9 47.6 1.0
O B:PRO107 4.0 47.8 1.0
O B:LEU106 4.1 60.8 1.0
CG B:GLU80 4.3 52.2 1.0
NE2 B:HIS41 4.3 50.5 1.0
C B:PRO107 4.4 52.8 1.0
NAR B:RLT301 4.4 119.3 1.0
CB B:GLU80 4.4 46.6 1.0
CB B:ASP108 4.4 54.4 1.0
CA B:ASP108 4.4 40.4 1.0
OE2 B:GLU119 4.4 63.5 1.0
OE1 B:GLU119 4.5 73.4 1.0
N B:ASP108 4.5 41.2 1.0
CBD B:RLT301 4.6 101.9 1.0
OE2 B:GLU80 4.6 67.7 1.0
CAN B:RLT301 4.8 119.1 1.0
OAG B:RLT301 4.9 77.1 1.0
CD B:GLU119 4.9 63.1 1.0
ND1 B:HIS41 5.0 64.2 1.0

Manganese binding site 4 out of 8 in 7m0n

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Manganese binding site 4 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn305

b:62.0
occ:1.00
 OD2 B:ASP108 2.1 57.1 1.0
O B:ILE120 2.2 54.7 1.0
OAH B:RLT301 2.3 77.8 1.0
NE2 B:HIS41 2.3 50.5 1.0
OE2 B:GLU119 2.4 63.5 1.0
OAG B:RLT301 2.5 77.1 1.0
CG B:ASP108 3.1 53.3 1.0
CAZ B:RLT301 3.2 97.3 1.0
CBD B:RLT301 3.2 101.9 1.0
CE1 B:HIS41 3.2 47.6 1.0
CD2 B:HIS41 3.3 54.9 1.0
OD1 B:ASP108 3.3 57.5 1.0
C B:ILE120 3.4 54.1 1.0
CD B:GLU119 3.5 63.1 1.0
MN B:MN304 3.7 79.8 1.0
O B:HOH403 3.8 75.0 1.0
N B:ILE120 3.9 44.8 1.0
CA B:ILE120 4.1 50.5 1.0
OE1 B:GLU119 4.2 73.4 1.0
ND1 B:HIS41 4.3 64.2 1.0
CG B:HIS41 4.4 62.4 1.0
NZ B:LYS134 4.4 87.9 1.0
N B:GLY121 4.4 56.6 1.0
CB B:ASP108 4.5 54.4 1.0
CBB B:RLT301 4.5 111.2 1.0
O B:HOH412 4.5 61.9 1.0
NBE B:RLT301 4.5 115.9 1.0
CB B:ILE120 4.5 63.4 1.0
CG B:GLU119 4.6 56.4 1.0
CA B:GLY121 4.7 56.8 1.0
C B:GLU119 4.8 46.1 1.0
OAE B:RLT301 4.8 91.5 1.0
CG2 B:ILE120 4.9 50.7 1.0
CE B:LYS134 5.0 101.2 1.0

Manganese binding site 5 out of 8 in 7m0n

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Manganese binding site 5 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:60.4
occ:1.00
 OD2 C:ASP108 2.2 51.4 1.0
O C:ILE120 2.3 52.2 1.0
NE2 C:HIS41 2.3 50.7 1.0
OAH C:RLT301 2.3 76.6 1.0
OAG C:RLT301 2.4 72.4 1.0
OE2 C:GLU119 2.6 55.1 1.0
CG C:ASP108 2.9 54.6 1.0
OD1 C:ASP108 3.0 50.0 1.0
CBD C:RLT301 3.1 97.2 1.0
CE1 C:HIS41 3.1 39.2 1.0
CAZ C:RLT301 3.1 100.2 1.0
CD2 C:HIS41 3.3 51.8 1.0
C C:ILE120 3.5 53.5 1.0
MN C:MN303 3.7 77.5 1.0
CD C:GLU119 3.7 76.7 1.0
O C:HOH403 3.8 65.7 1.0
N C:ILE120 3.9 53.7 1.0
NZ C:LYS134 4.1 82.8 1.0
CA C:ILE120 4.2 58.1 1.0
ND1 C:HIS41 4.2 62.2 1.0
CG C:HIS41 4.4 53.1 1.0
OE1 C:GLU119 4.4 77.2 1.0
CB C:ASP108 4.4 49.9 1.0
NBE C:RLT301 4.4 108.3 1.0
CBB C:RLT301 4.5 113.6 1.0
N C:GLY121 4.5 50.1 1.0
CG C:GLU119 4.6 61.5 1.0
CB C:ILE120 4.7 54.7 1.0
O C:HOH423 4.7 64.7 1.0
CA C:GLY121 4.7 47.5 1.0
OE1 C:GLU80 4.8 71.0 1.0
C C:GLU119 4.8 45.9 1.0
OAE C:RLT301 4.9 90.8 1.0
CAB C:RLT301 4.9 101.3 1.0

Manganese binding site 6 out of 8 in 7m0n

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Manganese binding site 6 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:77.5
occ:1.00
 OAE C:RLT301 2.2 90.8 1.0
OAH C:RLT301 2.2 76.6 1.0
OD1 C:ASP108 2.3 50.0 1.0
O C:HOH408 2.4 69.5 1.0
O C:HOH403 2.5 65.7 1.0
OE1 C:GLU80 2.5 71.0 1.0
CAU C:RLT301 3.3 106.1 1.0
CAZ C:RLT301 3.4 100.2 1.0
CG C:ASP108 3.4 54.6 1.0
CD C:GLU80 3.6 67.5 1.0
MN C:MN302 3.7 60.4 1.0
CBB C:RLT301 3.8 113.6 1.0
CE1 C:HIS41 3.9 39.2 1.0
OD2 C:ASP108 4.0 51.4 1.0
O C:LEU106 4.0 67.8 1.0
O C:PRO107 4.1 57.3 1.0
C C:PRO107 4.3 59.6 1.0
OE2 C:GLU80 4.3 68.9 1.0
CG C:GLU80 4.3 58.8 1.0
CB C:GLU80 4.4 48.7 1.0
CA C:ASP108 4.4 52.6 1.0
NE2 C:HIS41 4.4 50.7 1.0
NAR C:RLT301 4.4 115.1 1.0
N C:ASP108 4.5 53.3 1.0
CB C:ASP108 4.5 49.9 1.0
CBD C:RLT301 4.5 97.2 1.0
OE2 C:GLU119 4.6 55.1 1.0
OAG C:RLT301 4.8 72.4 1.0
CAN C:RLT301 4.9 120.5 1.0
OE1 C:GLU119 4.9 77.2 1.0
C C:LEU106 5.0 62.6 1.0

Manganese binding site 7 out of 8 in 7m0n

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Manganese binding site 7 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn305

b:82.5
occ:1.00
 OAE D:RLT301 2.3 114.3 1.0
OAH D:RLT301 2.3 92.6 1.0
OD1 D:ASP108 2.3 49.8 1.0
O D:HOH404 2.4 65.6 1.0
OE1 D:GLU80 2.5 74.2 1.0
O D:HOH402 2.7 71.2 1.0
CAU D:RLT301 3.3 122.7 1.0
CAZ D:RLT301 3.4 103.0 1.0
CG D:ASP108 3.5 48.4 1.0
CD D:GLU80 3.6 69.3 1.0
MN D:MN306 3.8 62.7 1.0
CBB D:RLT301 3.8 125.4 1.0
CE1 D:HIS41 4.1 47.1 1.0
OD2 D:ASP108 4.1 54.5 1.0
O D:LEU106 4.1 65.7 1.0
O D:PRO107 4.2 49.2 1.0
OE2 D:GLU80 4.3 67.2 1.0
CG D:GLU80 4.4 60.2 1.0
CB D:GLU80 4.4 49.4 1.0
C D:PRO107 4.5 67.0 1.0
OE2 D:GLU119 4.5 68.0 1.0
NAR D:RLT301 4.5 134.4 1.0
NE2 D:HIS41 4.6 51.4 1.0
CBD D:RLT301 4.6 101.8 1.0
CB D:ASP108 4.6 51.9 1.0
CA D:ASP108 4.6 48.3 1.0
N D:ASP108 4.7 45.8 1.0
OAG D:RLT301 4.9 88.9 1.0
OE1 D:GLU119 4.9 72.5 1.0
CAN D:RLT301 5.0 135.8 1.0

Manganese binding site 8 out of 8 in 7m0n

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Manganese binding site 8 out of 8 in the The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn306

b:62.7
occ:1.00
 OD2 D:ASP108 2.2 54.5 1.0
O D:ILE120 2.3 60.1 1.0
NE2 D:HIS41 2.3 51.4 1.0
OE2 D:GLU119 2.3 68.0 1.0
OAH D:RLT301 2.5 92.6 1.0
OAG D:RLT301 2.5 88.9 1.0
CG D:ASP108 3.0 48.4 1.0
OD1 D:ASP108 3.1 49.8 1.0
CE1 D:HIS41 3.1 47.1 1.0
CBD D:RLT301 3.3 101.8 1.0
CAZ D:RLT301 3.3 103.0 1.0
CD2 D:HIS41 3.3 58.3 1.0
C D:ILE120 3.4 59.3 1.0
CD D:GLU119 3.5 74.4 1.0
N D:ILE120 3.8 49.8 1.0
O D:HOH404 3.8 65.6 1.0
MN D:MN305 3.8 82.5 1.0
CA D:ILE120 4.1 50.9 1.0
ND1 D:HIS41 4.2 54.7 1.0
OE1 D:GLU119 4.3 72.5 1.0
NZ D:LYS134 4.3 80.5 1.0
CG D:HIS41 4.4 59.5 1.0
CB D:ASP108 4.4 51.9 1.0
CG D:GLU119 4.5 66.4 1.0
N D:GLY121 4.5 55.0 1.0
CB D:ILE120 4.5 53.4 1.0
NBE D:RLT301 4.6 117.6 1.0
CBB D:RLT301 4.6 125.4 1.0
C D:GLU119 4.7 42.1 1.0
CA D:GLY121 4.8 51.7 1.0
OE1 D:GLU80 4.9 74.2 1.0
OAE D:RLT301 5.0 114.3 1.0

Reference:

M.G.Cuypers, P.J.Slavish, R.Dubois, Z.Rankovic, S.W.White. The Crystal Structure of Wild Type Pa Endonuclease (2009/H1N1/California) in Complex with Raltegravir To Be Published.
Page generated: Sun Oct 6 10:01:36 2024

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