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Manganese in PDB 4un9: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3), PDB code: 4un9 was solved by R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.860 / 2.73
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.025, 70.657, 107.259, 90.00, 119.58, 90.00
R / Rfree (%) 17.83 / 21.97

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) (pdb code 4un9). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3), PDB code: 4un9:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4un9

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Manganese binding site 1 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:46.6
occ:1.00
 O A:HOH2003 1.8 28.1 1.0
OP2 C:DC16 2.1 35.3 1.0
OD2 A:ASP21 2.1 35.5 1.0
OP1 B:DA14 2.2 41.5 1.0
O A:ALA116 2.3 36.1 1.0
O A:HOH2017 2.7 36.1 1.0
CG A:ASP21 3.0 37.6 1.0
OD1 A:ASP21 3.2 42.3 1.0
C A:ALA116 3.3 36.3 1.0
NZ A:LYS120 3.5 56.9 1.0
P C:DC16 3.5 43.9 1.0
MN A:MN1190 3.6 36.3 0.6
P B:DA14 3.6 40.4 1.0
CA A:ALA116 3.7 33.3 1.0
OE1 A:GLN42 4.1 39.0 1.0
O5' C:DC16 4.1 40.4 1.0
O3' B:DA13 4.2 39.6 1.0
C5' B:DA14 4.2 41.8 1.0
OP1 C:DC16 4.3 35.7 1.0
C4' B:DA14 4.3 37.8 1.0
O A:VAL115 4.4 33.9 1.0
C5' C:DC16 4.4 32.8 1.0
CB A:ASP21 4.4 28.6 1.0
O5' B:DA14 4.5 44.9 1.0
N A:GLU117 4.5 37.7 1.0
CB A:ALA116 4.5 30.1 1.0
O3' C:DC15 4.5 33.7 1.0
OP2 B:DA14 4.6 51.0 1.0
NE2 A:GLN42 4.6 41.3 1.0
CD A:GLN42 4.7 42.4 1.0
OE1 A:GLU117 4.8 36.4 1.0
O3' B:DA14 4.9 35.0 1.0
N A:ALA116 4.9 34.5 1.0
CA A:GLU117 4.9 35.5 1.0
CE A:LYS120 5.0 52.8 1.0

Manganese binding site 2 out of 10 in 4un9

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Manganese binding site 2 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:35.2
occ:1.00
 OP2 B:DG15 2.0 31.0 1.0
OP1 C:DC15 2.1 38.0 1.0
OE2 A:GLU117 2.2 35.7 1.0
O A:GLY20 2.3 26.9 1.0
O A:HOH2002 2.4 31.9 1.0
O A:HOH2001 2.5 26.1 1.0
CD A:GLU117 3.0 34.0 1.0
OE1 A:GLU117 3.2 36.4 1.0
P B:DG15 3.3 33.4 1.0
C A:GLY20 3.4 33.4 1.0
P C:DC15 3.5 35.7 1.0
MN A:MN1190 3.7 36.3 0.6
ND2 A:ASN129 3.8 31.0 1.0
O5' B:DG15 3.8 38.0 1.0
CA A:GLY20 3.9 29.3 1.0
C5' B:DG15 4.0 27.6 1.0
O3' C:DA14 4.1 29.6 1.0
OP1 B:DG15 4.1 36.1 1.0
C5' C:DC15 4.2 32.5 1.0
O A:ILE19 4.2 32.5 1.0
O A:HOH2023 4.2 20.0 1.0
OD1 A:ASP21 4.3 42.3 1.0
C4' C:DC15 4.3 31.1 1.0
O5' C:DC15 4.4 34.2 1.0
CG A:GLU117 4.4 37.0 1.0
O3' B:DA14 4.5 35.0 1.0
N A:ASP21 4.5 34.6 1.0
OP2 C:DC15 4.5 35.8 1.0
C4' B:DG15 4.8 34.5 1.0
CA A:ASP21 4.8 31.5 1.0
N A:GLY20 5.0 27.2 1.0
CG A:ASN129 5.0 31.1 1.0

Manganese binding site 3 out of 10 in 4un9

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Manganese binding site 3 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1190

b:36.3
occ:0.56
 OD1 A:ASP21 2.0 42.3 1.0
OE1 A:GLU117 2.2 36.4 1.0
OP2 B:DG15 2.5 31.0 1.0
OP2 C:DC16 2.5 35.3 1.0
O3' C:DC15 2.5 33.7 1.0
O3' B:DA14 2.7 35.0 1.0
P C:DC16 3.1 43.9 1.0
P B:DG15 3.1 33.4 1.0
CG A:ASP21 3.1 37.6 1.0
CD A:GLU117 3.3 34.0 1.0
C3' C:DC15 3.5 31.3 1.0
MN A:MN1188 3.6 46.6 1.0
OD2 A:ASP21 3.7 35.5 1.0
MN A:MN1189 3.7 35.2 1.0
O A:ALA116 3.7 36.1 1.0
C3' B:DA14 3.7 38.0 1.0
C4' C:DC15 3.9 31.1 1.0
OE2 A:GLU117 3.9 35.7 1.0
O5' C:DC16 4.0 40.4 1.0
O A:GLY20 4.0 26.9 1.0
O5' B:DG15 4.1 38.0 1.0
C4' B:DA14 4.1 37.8 1.0
C A:ALA116 4.3 36.3 1.0
OP1 C:DC16 4.3 35.7 1.0
OP1 B:DG15 4.3 36.1 1.0
CB A:ASP21 4.3 28.6 1.0
CA A:ASP21 4.4 31.5 1.0
C A:GLY20 4.4 33.4 1.0
CG A:GLU117 4.5 37.0 1.0
CA A:GLU117 4.6 35.5 1.0
C5' C:DC15 4.7 32.5 1.0
N A:ASP21 4.7 34.6 1.0
N A:GLU117 4.8 37.7 1.0
OP1 C:DC15 4.9 38.0 1.0
OP1 B:DA14 4.9 41.5 1.0
C2' C:DC15 4.9 32.5 1.0
C5' B:DA14 5.0 41.8 1.0
CB A:ALA116 5.0 30.1 1.0
CB A:GLU117 5.0 29.8 1.0

Manganese binding site 4 out of 10 in 4un9

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Manganese binding site 4 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1197

b:37.2
occ:1.00
 O D:HOH2003 2.0 30.1 1.0
OP1 E:DA14 2.0 35.6 1.0
OP2 F:DC16 2.2 29.9 1.0
OD2 D:ASP21 2.3 26.5 1.0
O D:ALA116 2.4 31.1 1.0
O D:HOH2018 2.5 39.6 1.0
CG D:ASP21 3.0 29.6 1.0
OD1 D:ASP21 3.1 28.2 1.0
C D:ALA116 3.4 29.8 1.0
P E:DA14 3.5 32.6 1.0
P F:DC16 3.6 41.9 1.0
MN D:MN1199 3.7 32.4 0.6
CA D:ALA116 3.8 29.2 1.0
OE1 D:GLN42 3.9 23.0 1.0
O3' E:DA13 4.1 36.7 1.0
C5' E:DA14 4.1 33.4 1.0
NE2 D:GLN42 4.2 23.3 1.0
C4' E:DA14 4.2 34.8 1.0
O5' F:DC16 4.3 37.0 1.0
O D:VAL115 4.3 34.8 1.0
O5' E:DA14 4.3 25.1 1.0
CD D:GLN42 4.4 30.5 1.0
CB D:ASP21 4.4 27.4 1.0
OP2 E:DA14 4.5 37.8 1.0
OP1 F:DC16 4.6 49.8 1.0
O3' F:DC15 4.6 38.7 1.0
C5' F:DC16 4.6 35.4 1.0
O D:HOH2013 4.6 42.8 1.0
N D:GLU117 4.6 34.0 1.0
CB D:ALA116 4.7 26.8 1.0
NZ D:LYS120 4.8 41.7 1.0
CE D:LYS120 4.9 61.3 1.0
OE1 D:GLU117 4.9 34.5 1.0
O3' E:DA14 4.9 30.5 1.0
N D:ALA116 4.9 34.5 1.0
C3' E:DA14 4.9 28.6 1.0

Manganese binding site 5 out of 10 in 4un9

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Manganese binding site 5 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1198

b:36.8
occ:1.00
 OE2 D:GLU117 1.9 29.9 1.0
OP1 F:DC15 2.1 33.6 1.0
OP2 E:DG15 2.2 25.1 1.0
O D:GLY20 2.3 29.8 1.0
O D:HOH2002 2.4 29.1 1.0
O D:HOH2001 2.8 26.2 1.0
CD D:GLU117 2.9 33.2 1.0
OE1 D:GLU117 3.2 34.5 1.0
C D:GLY20 3.4 31.8 1.0
P E:DG15 3.5 28.2 1.0
P F:DC15 3.6 36.0 1.0
ND2 D:ASN129 3.8 33.3 1.0
MN D:MN1199 3.8 32.4 0.6
C5' E:DG15 3.9 26.7 1.0
O5' E:DG15 3.9 31.6 1.0
CA D:GLY20 3.9 27.9 1.0
O D:ILE19 3.9 32.5 1.0
O3' F:DA14 4.1 34.8 1.0
CG D:GLU117 4.3 29.5 1.0
C5' F:DC15 4.4 35.4 1.0
C4' F:DC15 4.4 37.2 1.0
OP1 E:DG15 4.5 35.5 1.0
O5' F:DC15 4.5 41.1 1.0
N D:ASP21 4.5 30.8 1.0
OP2 F:DC15 4.5 28.3 1.0
O3' E:DA14 4.5 30.5 1.0
OD1 D:ASP21 4.6 28.2 1.0
C D:ILE19 4.8 28.5 1.0
O D:HOH2021 4.8 32.0 1.0
C4' E:DG15 4.8 24.5 1.0
CA D:ASP21 4.9 30.5 1.0
N D:GLY20 4.9 29.3 1.0
CG D:ASN129 4.9 41.3 1.0

Manganese binding site 6 out of 10 in 4un9

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Manganese binding site 6 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1199

b:32.4
occ:0.56
 OE1 D:GLU117 2.1 34.5 1.0
OD1 D:ASP21 2.4 28.2 1.0
O3' F:DC15 2.5 38.7 1.0
O3' E:DA14 2.6 30.5 1.0
OP2 E:DG15 2.7 25.1 1.0
OP2 F:DC16 2.7 29.9 1.0
P F:DC16 3.2 41.9 1.0
CD D:GLU117 3.2 33.2 1.0
P E:DG15 3.2 28.2 1.0
C3' F:DC15 3.4 36.4 1.0
CG D:ASP21 3.5 29.6 1.0
MN D:MN1197 3.7 37.2 1.0
C3' E:DA14 3.7 28.6 1.0
O D:ALA116 3.7 31.1 1.0
O D:GLY20 3.7 29.8 1.0
C4' F:DC15 3.7 37.2 1.0
MN D:MN1198 3.8 36.8 1.0
OE2 D:GLU117 3.8 29.9 1.0
O5' F:DC16 4.0 37.0 1.0
C4' E:DA14 4.1 34.8 1.0
O5' E:DG15 4.1 31.6 1.0
OD2 D:ASP21 4.2 26.5 1.0
CG D:GLU117 4.3 29.5 1.0
C D:GLY20 4.4 31.8 1.0
OP1 F:DC16 4.4 49.8 1.0
C D:ALA116 4.4 29.8 1.0
OP1 E:DG15 4.4 35.5 1.0
CA D:ASP21 4.5 30.5 1.0
CB D:ASP21 4.6 27.4 1.0
C5' F:DC15 4.6 35.4 1.0
CA D:GLU117 4.7 37.2 1.0
OP1 F:DC15 4.7 33.6 1.0
O4' F:DC15 4.8 35.1 1.0
CB D:GLU117 4.8 30.8 1.0
C2' F:DC15 4.8 36.8 1.0
N D:ASP21 4.8 30.8 1.0
OP1 E:DA14 4.9 35.6 1.0
N D:GLU117 4.9 34.0 1.0
O D:HOH2018 5.0 39.6 1.0
C5' E:DA14 5.0 33.4 1.0

Manganese binding site 7 out of 10 in 4un9

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Manganese binding site 7 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1182

b:38.0
occ:1.00
 OP1 I:DC15 2.0 28.9 1.0
OP2 H:DG15 2.1 29.0 1.0
OE2 G:GLU117 2.1 34.5 1.0
O G:GLY20 2.3 31.4 1.0
O G:HOH2001 2.5 24.7 1.0
O G:HOH2023 2.7 30.9 1.0
CD G:GLU117 2.9 38.9 1.0
OE1 G:GLU117 3.1 37.8 1.0
P H:DG15 3.3 38.1 1.0
C G:GLY20 3.4 32.9 1.0
P I:DC15 3.5 33.2 1.0
O5' H:DG15 3.8 43.4 1.0
MN G:MN1184 3.8 37.4 0.5
C5' I:DC15 3.8 37.3 1.0
C5' H:DG15 3.9 31.8 1.0
ND2 G:ASN129 3.9 31.8 1.0
CA G:GLY20 4.0 29.2 1.0
O G:ILE19 4.0 31.8 1.0
O3' I:DA14 4.1 25.7 1.0
O G:HOH2018 4.1 16.3 1.0
O5' I:DC15 4.2 40.2 1.0
C4' I:DC15 4.2 33.1 1.0
OP1 H:DG15 4.3 34.9 1.0
CG G:GLU117 4.3 34.5 1.0
O3' H:DA14 4.4 33.1 1.0
OP2 I:DC15 4.5 28.8 1.0
OD1 G:ASP21 4.5 36.0 1.0
N G:ASP21 4.5 28.1 1.0
C4' H:DG15 4.7 35.6 1.0
CA G:ASP21 4.8 31.2 1.0
C G:ILE19 4.9 31.1 1.0
N G:GLY20 5.0 25.3 1.0
CG G:ASN129 5.0 28.6 1.0

Manganese binding site 8 out of 10 in 4un9

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Manganese binding site 8 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


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 I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1183

b:39.8
occ:1.00
 OP2 I:DC16 1.7 41.8 1.0
O G:HOH2002 2.0 26.8 1.0
O G:ALA116 2.3 34.6 1.0
OD2 G:ASP21 2.4 38.4 1.0
OP1 H:DA14 2.5 40.4 1.0
O G:HOH2017 2.6 36.0 1.0
OD1 G:ASP21 3.1 36.0 1.0
CG G:ASP21 3.1 35.2 1.0
P I:DC16 3.2 46.4 1.0
C G:ALA116 3.3 36.0 1.0
MN G:MN1184 3.3 37.4 0.5
CA G:ALA116 3.8 30.2 1.0
OP1 I:DC16 3.8 42.0 1.0
P H:DA14 3.8 41.3 1.0
O5' I:DC16 4.0 35.8 1.0
C4' H:DA14 4.2 36.6 1.0
C5' H:DA14 4.2 37.2 1.0
O3' I:DC15 4.2 37.2 1.0
OE1 G:GLN42 4.3 38.6 1.0
NZ G:LYS120 4.3 38.4 1.0
O3' H:DA13 4.3 43.2 1.0
C5' I:DC16 4.4 38.5 1.0
O G:VAL115 4.4 34.9 1.0
N G:GLU117 4.4 31.2 1.0
NE2 G:GLN42 4.5 42.2 1.0
CB G:ASP21 4.5 34.5 1.0
O5' H:DA14 4.6 46.4 1.0
CB G:ALA116 4.6 27.0 1.0
O3' H:DA14 4.7 33.1 1.0
OE1 G:GLU117 4.7 37.8 1.0
CD G:GLN42 4.8 41.0 1.0
CA G:GLU117 4.8 36.0 1.0
C3' H:DA14 4.9 39.7 1.0
OP2 H:DA14 5.0 39.5 1.0
N G:ALA116 5.0 29.4 1.0

Manganese binding site 9 out of 10 in 4un9

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Manganese binding site 9 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1184

b:37.4
occ:0.54
 OD1 G:ASP21 2.1 36.0 1.0
OE1 G:GLU117 2.3 37.8 1.0
O3' H:DA14 2.5 33.1 1.0
OP2 I:DC16 2.5 41.8 1.0
O3' I:DC15 2.6 37.2 1.0
OP2 H:DG15 2.7 29.0 1.0
P I:DC16 3.1 46.4 1.0
P H:DG15 3.1 38.1 1.0
CG G:ASP21 3.2 35.2 1.0
MN G:MN1183 3.3 39.8 1.0
CD G:GLU117 3.4 38.9 1.0
C3' I:DC15 3.4 32.9 1.0
C3' H:DA14 3.5 39.7 1.0
C4' I:DC15 3.7 33.1 1.0
MN G:MN1182 3.8 38.0 1.0
OD2 G:ASP21 3.9 38.4 1.0
C4' H:DA14 3.9 36.6 1.0
O G:GLY20 3.9 31.4 1.0
O G:ALA116 4.0 34.6 1.0
O5' H:DG15 4.0 43.4 1.0
OE2 G:GLU117 4.1 34.5 1.0
O5' I:DC16 4.1 35.8 1.0
OP1 I:DC16 4.2 42.0 1.0
OP1 H:DG15 4.3 34.9 1.0
CB G:ASP21 4.4 34.5 1.0
CA G:ASP21 4.4 31.2 1.0
C5' I:DC15 4.4 37.3 1.0
C G:GLY20 4.4 32.9 1.0
C G:ALA116 4.5 36.0 1.0
CG G:GLU117 4.5 34.5 1.0
CA G:GLU117 4.7 36.0 1.0
N G:ASP21 4.7 28.1 1.0
OP1 I:DC15 4.8 28.9 1.0
C5' H:DA14 4.8 37.2 1.0
C2' I:DC15 4.9 34.8 1.0
C2' H:DA14 4.9 35.4 1.0
N G:GLU117 4.9 31.2 1.0
O4' I:DC15 4.9 27.7 1.0
O4' H:DA14 5.0 36.5 1.0
CB G:GLU117 5.0 32.3 1.0

Manganese binding site 10 out of 10 in 4un9

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Manganese binding site 10 out of 10 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 8H Incubation in 5MM Mn (State 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1185

b:79.9
occ:0.95
 NE2 G:HIS156 2.4 37.1 1.0
CE1 G:HIS156 3.2 39.5 1.0
CD2 G:HIS156 3.5 37.4 1.0
OP2 H:DC7 3.9 59.4 1.0
O G:LEU153 4.0 44.9 1.0
OP1 H:DC7 4.1 54.8 1.0
ND1 G:HIS156 4.3 43.2 1.0
P H:DC7 4.3 50.8 1.0
CG G:HIS156 4.5 33.9 1.0
OP2 H:DC8 4.5 45.3 1.0
O5' H:DC7 4.8 41.2 1.0

Reference:

R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya. Dissecting I-Dmoi Endonuclease Catalysis 'Live' To Be Published.
Page generated: Sat Oct 5 21:21:16 2024

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