Atomistry » Manganese » PDB 4u87-4wiu » 4un8
Atomistry »
  Manganese »
    PDB 4u87-4wiu »
      4un8 »

Manganese in PDB 4un8: The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)

Protein crystallography data

The structure of The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2), PDB code: 4un8 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) 46.642 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 107.186, 70.851, 107.232, 90.00, 119.55, 90.00
R / Rfree (%) 17.84 / 22.31

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2) (pdb code 4un8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2), PDB code: 4un8:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 1 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1188

b:41.2
occ:1.00
 OP2 C:DC16 2.1 41.7 1.0
OD2 A:ASP21 2.2 35.5 1.0
OP1 B:DA14 2.2 46.0 1.0
O A:HOH2004 2.2 36.7 1.0
O A:ALA116 2.3 34.7 1.0
CG A:ASP21 2.9 38.6 1.0
OD1 A:ASP21 3.1 39.5 1.0
C A:ALA116 3.3 37.2 1.0
P C:DC16 3.5 35.7 1.0
NZ A:LYS120 3.5 65.0 1.0
O A:HOH2003 3.6 28.4 1.0
P B:DA14 3.6 46.6 1.0
CA A:ALA116 3.8 41.3 1.0
O5' C:DC16 4.1 37.1 1.0
OP1 C:DC16 4.2 37.2 1.0
C5' B:DA14 4.2 43.5 1.0
O3' B:DA13 4.3 47.0 1.0
C4' B:DA14 4.3 40.2 1.0
O A:VAL115 4.3 42.7 1.0
NE2 A:GLN42 4.3 46.9 1.0
OE1 A:GLN42 4.3 51.6 1.0
CB A:ASP21 4.4 37.1 1.0
C5' C:DC16 4.4 37.6 1.0
O5' B:DA14 4.5 46.1 1.0
N A:GLU117 4.5 37.0 1.0
OP2 B:DA14 4.5 50.0 1.0
O3' C:DC15 4.5 37.6 1.0
CB A:ALA116 4.6 37.8 1.0
CE A:LYS120 4.7 62.4 1.0
OE1 A:GLU117 4.7 41.6 1.0
CD A:GLN42 4.7 50.2 1.0
O3' B:DA14 4.8 37.1 1.0
N A:ALA116 4.9 40.6 1.0
CA A:GLU117 4.9 40.9 1.0
C3' B:DA14 5.0 38.5 1.0

Manganese binding site 2 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 2 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1189

b:39.9
occ:1.00
 OP1 C:DC15 2.1 44.5 1.0
OE2 A:GLU117 2.1 39.2 1.0
OP2 B:DG15 2.2 32.9 1.0
O A:GLY20 2.4 30.1 1.0
O A:HOH2001 2.5 38.7 1.0
O A:HOH2002 2.7 30.4 1.0
CD A:GLU117 3.1 40.1 1.0
P B:DG15 3.3 31.0 1.0
C A:GLY20 3.4 36.0 1.0
OE1 A:GLU117 3.5 41.6 1.0
P C:DC15 3.5 37.9 1.0
O5' B:DG15 3.7 43.7 1.0
O A:HOH2003 3.7 28.4 1.0
C5' B:DG15 3.8 36.1 1.0
CA A:GLY20 3.9 34.1 1.0
ND2 A:ASN129 3.9 35.0 1.0
O3' C:DA14 3.9 32.0 1.0
OP1 B:DG15 4.1 39.2 1.0
C5' C:DC15 4.2 36.4 1.0
O A:HOH2017 4.2 30.8 1.0
O A:ILE19 4.3 36.6 1.0
O5' C:DC15 4.4 41.2 1.0
C4' C:DC15 4.4 33.9 1.0
CG A:GLU117 4.5 36.3 1.0
OD1 A:ASP21 4.5 39.5 1.0
O3' B:DA14 4.5 37.1 1.0
N A:ASP21 4.5 38.8 1.0
OP2 C:DC15 4.6 38.0 1.0
C4' B:DG15 4.7 39.7 1.0
O B:HOH2009 4.8 43.3 1.0
CA A:ASP21 4.8 35.7 1.0
N A:GLY20 5.0 35.2 1.0

Manganese binding site 3 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 3 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1197

b:40.3
occ:1.00
 OP1 E:DA14 2.1 34.7 1.0
O D:HOH2005 2.2 41.2 1.0
OP2 F:DC16 2.2 39.0 1.0
OD2 D:ASP21 2.3 38.5 1.0
O D:ALA116 2.3 36.4 1.0
O D:HOH2027 2.5 48.0 1.0
CG D:ASP21 3.0 36.0 1.0
OD1 D:ASP21 3.1 32.8 1.0
C D:ALA116 3.4 34.8 1.0
P F:DC16 3.5 42.4 1.0
P E:DA14 3.6 40.4 1.0
O D:HOH2004 3.6 28.5 1.0
CA D:ALA116 3.9 39.3 1.0
O5' F:DC16 4.1 38.0 1.0
OE1 D:GLN42 4.1 35.2 1.0
C5' E:DA14 4.2 38.7 1.0
O3' E:DA13 4.2 42.4 1.0
C4' E:DA14 4.2 38.5 1.0
OP1 F:DC16 4.2 41.1 1.0
C5' F:DC16 4.3 40.1 1.0
O D:VAL115 4.3 37.8 1.0
O5' E:DA14 4.4 39.5 1.0
NE2 D:GLN42 4.4 36.7 1.0
CB D:ASP21 4.5 36.0 1.0
N D:GLU117 4.6 38.3 1.0
OP2 E:DA14 4.6 45.8 1.0
NZ D:LYS120 4.6 54.5 1.0
O3' F:DC15 4.6 39.2 1.0
CD D:GLN42 4.7 39.9 1.0
CE D:LYS120 4.7 66.7 1.0
CB D:ALA116 4.7 37.2 1.0
O3' E:DA14 4.9 34.4 1.0
O D:HOH2015 4.9 61.1 1.0
C3' E:DA14 4.9 33.5 1.0
OE1 D:GLU117 4.9 40.0 1.0
N D:ALA116 5.0 37.7 1.0
CA D:GLU117 5.0 37.1 1.0

Manganese binding site 4 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 4 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1198

b:39.1
occ:1.00
 OE2 D:GLU117 2.0 37.6 1.0
OP1 F:DC15 2.0 35.3 1.0
OP2 E:DG15 2.2 35.6 1.0
O D:GLY20 2.2 38.3 1.0
O D:HOH2001 2.6 42.8 1.0
O D:HOH2002 2.6 32.7 1.0
CD D:GLU117 3.0 35.8 1.0
OE1 D:GLU117 3.3 40.0 1.0
C D:GLY20 3.3 38.0 1.0
P E:DG15 3.5 34.2 1.0
P F:DC15 3.5 37.6 1.0
O D:HOH2004 3.7 28.5 1.0
ND2 D:ASN129 3.7 41.1 1.0
CA D:GLY20 3.8 34.8 1.0
O5' E:DG15 3.9 36.9 1.0
C5' E:DG15 4.0 30.7 1.0
O3' F:DA14 4.1 41.5 1.0
O D:ILE19 4.1 40.1 1.0
C5' F:DC15 4.3 37.4 1.0
CG D:GLU117 4.3 36.8 1.0
C4' F:DC15 4.4 37.7 1.0
OP2 F:DC15 4.4 40.6 1.0
OP1 E:DG15 4.4 36.6 1.0
O5' F:DC15 4.4 38.6 1.0
N D:ASP21 4.4 34.4 1.0
OD1 D:ASP21 4.5 32.8 1.0
O3' E:DA14 4.5 34.4 1.0
O D:HOH2028 4.6 39.9 1.0
CA D:ASP21 4.8 39.8 1.0
CG D:ASN129 4.8 40.3 1.0
N D:GLY20 4.9 34.7 1.0
C4' E:DG15 4.9 29.6 1.0
C D:ILE19 4.9 34.8 1.0

Manganese binding site 5 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 5 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1182

b:41.4
occ:1.00
 OP1 I:DC15 2.0 39.1 1.0
OP2 H:DG15 2.1 39.5 1.0
OE2 G:GLU117 2.1 45.9 1.0
O G:GLY20 2.3 35.4 1.0
O G:HOH2001 2.3 36.0 1.0
O G:HOH2002 2.6 39.9 1.0
CD G:GLU117 3.0 42.4 1.0
OE1 G:GLU117 3.3 51.1 1.0
C G:GLY20 3.3 41.5 1.0
P H:DG15 3.4 40.3 1.0
P I:DC15 3.5 39.6 1.0
ND2 G:ASN129 3.8 39.3 1.0
O G:HOH2003 3.8 31.5 1.0
O5' H:DG15 3.8 46.6 1.0
CA G:GLY20 3.9 36.5 1.0
C5' H:DG15 3.9 39.9 1.0
C5' I:DC15 4.0 44.6 1.0
O G:HOH2022 4.0 31.7 1.0
O G:ILE19 4.1 37.5 1.0
O3' I:DA14 4.1 37.1 1.0
O5' I:DC15 4.2 48.1 1.0
C4' I:DC15 4.3 43.8 1.0
OP1 H:DG15 4.3 39.0 1.0
CG G:GLU117 4.4 40.6 1.0
N G:ASP21 4.5 36.5 1.0
O3' H:DA14 4.5 40.3 1.0
OP2 I:DC15 4.5 40.6 1.0
OD1 G:ASP21 4.7 38.2 1.0
C4' H:DG15 4.8 41.5 1.0
CA G:ASP21 4.8 39.3 1.0
C G:ILE19 4.9 34.5 1.0
N G:GLY20 4.9 35.5 1.0
CG G:ASN129 4.9 40.9 1.0

Manganese binding site 6 out of 6 in 4un8

Go back to Manganese Binding Sites List in 4un8
Manganese binding site 6 out of 6 in the The Crystal Structure of I-Dmoi in Complex with Its Target Dna at 1H Incubation in 5MM Mn (State 2)


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 1H Incubation in 5MM Mn (State 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1183

b:45.7
occ:1.00
 O G:HOH2004 1.8 39.5 1.0
OP2 I:DC16 1.9 40.8 1.0
OP1 H:DA14 2.1 45.3 1.0
O G:ALA116 2.4 38.6 1.0
OD2 G:ASP21 2.5 42.0 1.0
O G:HOH2033 2.6 42.9 1.0
OD1 G:ASP21 3.1 38.2 1.0
CG G:ASP21 3.1 41.8 1.0
P I:DC16 3.3 36.2 1.0
C G:ALA116 3.4 43.2 1.0
P H:DA14 3.6 41.5 1.0
O G:HOH2003 3.6 31.5 1.0
OP1 I:DC16 3.9 48.6 1.0
CA G:ALA116 3.9 37.9 1.0
OE1 G:GLN42 4.0 43.4 1.0
O5' I:DC16 4.1 41.4 1.0
NE2 G:GLN42 4.1 39.6 1.0
C4' H:DA14 4.2 40.5 1.0
C5' H:DA14 4.2 41.7 1.0
O3' H:DA13 4.2 43.4 1.0
C5' I:DC16 4.4 46.2 1.0
O G:VAL115 4.4 40.0 1.0
O3' I:DC15 4.4 41.1 1.0
O5' H:DA14 4.4 46.6 1.0
CD G:GLN42 4.5 43.5 1.0
OP2 H:DA14 4.5 47.3 1.0
NZ G:LYS120 4.6 54.3 1.0
N G:GLU117 4.6 42.6 1.0
CB G:ASP21 4.6 39.3 1.0
OE1 G:GLU117 4.7 51.1 1.0
CB G:ALA116 4.8 35.0 1.0
O3' H:DA14 4.8 40.3 1.0
C3' H:DA14 4.9 43.0 1.0
CA G:GLU117 5.0 40.9 1.0

Reference:

R.Molina, S.Stella, P.Redondo, H.Gomez, M.J.Marcaida, M.Orozco, J.Prieto, G.Montoya. Visualizing Phosphodiester-Bond Hydrolysis By An Endonuclease. Nat.Struct.Mol.Biol. 2014.
ISSN: ESSN 1545-9985
PubMed: 25486305
DOI: 10.1038/NSMB.2932
Page generated: Sat Oct 5 21:21:12 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