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Manganese in PDB 4n83: X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf

Enzymatic activity of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf

All present enzymatic activity of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf:
1.17.4.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf, PDB code: 4n83 was solved by A.K.Boal, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 117.657, 80.224, 166.374, 90.00, 105.91, 90.00
R / Rfree (%) 23.5 / 27.8

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf (pdb code 4n83). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf, PDB code: 4n83:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 4n83

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Manganese binding site 1 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:72.8
occ:1.00
 OE1 A:GLU157 2.0 0.3 1.0
OE2 A:GLU97 2.2 72.3 1.0
OE1 A:GLU191 2.4 72.3 1.0
CD A:GLU157 3.0 1.0 1.0
ND1 A:HIS194 3.0 69.8 1.0
CD A:GLU191 3.3 72.1 1.0
OE2 A:GLU157 3.3 0.7 1.0
CB A:HIS194 3.4 70.7 1.0
OE2 A:GLU191 3.4 71.3 1.0
CD A:GLU97 3.4 72.8 1.0
CG A:HIS194 3.4 69.8 1.0
CE1 A:HIS194 3.9 69.2 1.0
OE1 A:GLU97 4.1 73.4 1.0
OE1 A:GLN69 4.1 95.2 1.0
CG A:GLU157 4.2 1.0 1.0
CG2 A:ILE93 4.4 71.5 1.0
CG A:GLU97 4.4 72.8 1.0
CD2 A:HIS194 4.5 68.8 1.0
CB A:GLU157 4.5 0.6 1.0
OG A:SER153 4.7 0.8 1.0
CD1 A:ILE198 4.7 79.2 1.0
CG A:GLU191 4.7 71.8 1.0
NE2 A:HIS194 4.7 69.0 1.0
MN A:MN402 4.7 91.4 1.0
CA A:HIS194 4.8 70.5 1.0

Manganese binding site 2 out of 16 in 4n83

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Manganese binding site 2 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:91.4
occ:1.00
 OD1 A:ASP66 2.1 96.6 1.0
OE2 A:GLU191 2.2 71.3 1.0
OE1 A:GLU97 2.2 73.4 1.0
OE2 A:GLU157 2.4 0.7 1.0
ND1 A:HIS100 2.9 76.1 1.0
CD A:GLU191 3.1 72.1 1.0
CG A:ASP66 3.3 97.5 1.0
CD A:GLU97 3.3 72.8 1.0
CD A:GLU157 3.5 1.0 1.0
CG A:GLU191 3.7 71.8 1.0
OE2 A:GLU97 3.7 72.3 1.0
OD2 A:ASP66 3.8 97.7 1.0
CE1 A:HIS100 3.8 75.3 1.0
CG A:HIS100 3.9 76.3 1.0
OE1 A:GLU191 3.9 72.3 1.0
CB A:HIS100 4.1 77.1 1.0
CE1 A:PHE161 4.1 0.6 1.0
OE1 A:GLU157 4.3 0.3 1.0
CZ A:PHE161 4.3 0.4 1.0
CG A:GLU157 4.4 1.0 1.0
CB A:ASP66 4.5 98.8 1.0
CG A:GLU97 4.6 72.8 1.0
CA A:GLU97 4.7 72.9 1.0
MN A:MN401 4.7 72.8 1.0
CG2 A:ILE187 4.7 79.7 1.0
CA A:ASP66 4.8 99.7 1.0
CB A:GLU97 4.8 73.2 1.0
NE2 A:HIS100 5.0 74.9 1.0
CD1 A:PHE161 5.0 1.0 1.0

Manganese binding site 3 out of 16 in 4n83

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Manganese binding site 3 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:5.5
occ:1.00
 OE1 B:GLU97 2.0 11.4 1.0
OD1 B:ASP66 2.0 11.5 1.0
OE2 B:GLU191 2.3 11.7 1.0
OE2 B:GLU157 2.3 11.7 1.0
ND1 B:HIS100 2.4 11.5 1.0
O B:HOH521 2.5 3.1 1.0
CG B:ASP66 3.0 11.5 1.0
CD B:GLU97 3.0 11.4 1.0
CD B:GLU191 3.2 11.8 1.0
CE1 B:HIS100 3.2 11.6 1.0
OD2 B:ASP66 3.3 11.6 1.0
CG B:HIS100 3.4 11.5 1.0
OE2 B:GLU97 3.4 11.5 1.0
CD B:GLU157 3.5 11.8 1.0
CB B:HIS100 3.7 11.5 1.0
MN B:MN402 3.8 9.5 1.0
CG B:GLU191 3.9 12.0 1.0
OE1 B:GLU191 4.0 11.9 1.0
OE1 B:GLU157 4.1 11.8 1.0
CB B:ASP66 4.3 11.5 1.0
NE2 B:HIS100 4.3 11.7 1.0
CG B:GLU97 4.4 11.4 1.0
CD2 B:HIS100 4.4 11.6 1.0
CA B:GLU97 4.5 11.3 1.0
CG2 B:ILE187 4.5 12.0 1.0
CG B:GLU157 4.6 12.0 1.0
CB B:GLU97 4.7 11.3 1.0
CA B:ASP66 4.8 11.5 1.0
CE1 B:PHE161 4.9 12.1 1.0

Manganese binding site 4 out of 16 in 4n83

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Manganese binding site 4 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:9.5
occ:1.00
 OE2 B:GLU97 1.9 11.5 1.0
OE1 B:GLU191 2.2 11.9 1.0
OE1 B:GLU157 2.3 11.8 1.0
O B:HOH509 2.3 4.8 1.0
ND1 B:HIS194 2.5 11.8 1.0
OE2 B:GLU191 2.6 11.7 1.0
CD B:GLU191 2.7 11.8 1.0
CD B:GLU157 2.9 11.8 1.0
CD B:GLU97 3.0 11.4 1.0
OE2 B:GLU157 3.1 11.7 1.0
CE1 B:HIS194 3.4 11.7 1.0
CG B:HIS194 3.5 11.9 1.0
OE1 B:GLU97 3.5 11.4 1.0
CB B:HIS194 3.8 12.1 1.0
MN B:MN401 3.8 5.5 1.0
O B:HOH511 4.1 7.7 1.0
CG B:GLU97 4.2 11.4 1.0
CG B:GLU191 4.2 12.0 1.0
CG B:GLU157 4.2 12.0 1.0
NE2 B:GLN69 4.5 11.9 1.0
CB B:GLU157 4.5 12.1 1.0
CG2 B:ILE93 4.5 11.6 1.0
NE2 B:HIS194 4.5 11.8 1.0
CD2 B:HIS194 4.6 11.9 1.0
O B:HOH522 4.8 12.1 1.0
CA B:GLU191 4.9 12.2 1.0
O B:HOH510 4.9 16.2 1.0
CB B:GLU191 4.9 12.2 1.0

Manganese binding site 5 out of 16 in 4n83

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Manganese binding site 5 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:16.0
occ:1.00
 OE2 C:GLU191 1.8 17.1 1.0
OD1 C:ASP66 2.0 13.5 1.0
OE1 C:GLU97 2.2 13.5 1.0
OE1 C:GLU157 2.4 15.0 1.0
ND1 C:HIS100 2.5 12.6 1.0
CD C:GLU191 2.9 17.3 1.0
CG C:ASP66 3.1 13.3 1.0
CD C:GLU97 3.2 13.7 1.0
CD C:GLU157 3.3 15.2 1.0
CE1 C:HIS100 3.4 12.9 1.0
OD2 C:ASP66 3.5 13.3 1.0
OE2 C:GLU157 3.5 15.4 1.0
OE2 C:GLU97 3.5 13.8 1.0
CG C:HIS100 3.5 12.6 1.0
CG C:GLU191 3.7 17.3 1.0
OE1 C:GLU191 3.8 17.4 1.0
MN C:MN402 3.8 25.9 1.0
CB C:HIS100 3.9 12.3 1.0
CB C:ASP66 4.4 13.3 1.0
NE2 C:HIS100 4.5 13.0 1.0
CG C:GLU97 4.5 13.9 1.0
CE1 C:PHE161 4.6 12.7 1.0
CD2 C:HIS100 4.6 12.8 1.0
CG2 C:ILE187 4.6 14.8 1.0
CA C:GLU97 4.6 13.8 1.0
CG C:GLU157 4.7 15.0 1.0
CB C:GLU97 4.8 13.8 1.0
CA C:ASP66 4.8 13.4 1.0
CZ C:PHE161 5.0 12.7 1.0

Manganese binding site 6 out of 16 in 4n83

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Manganese binding site 6 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:25.9
occ:1.00
 OE1 C:GLU191 2.0 17.4 1.0
OE2 C:GLU157 2.1 15.4 1.0
OE2 C:GLU97 2.1 13.8 1.0
ND1 C:HIS194 2.5 20.2 1.0
CD C:GLU191 2.6 17.3 1.0
OE2 C:GLU191 2.6 17.1 1.0
CD C:GLU97 3.1 13.7 1.0
CD C:GLU157 3.1 15.2 1.0
CE1 C:HIS194 3.4 20.4 1.0
CG C:HIS194 3.5 20.5 1.0
OE1 C:GLU97 3.5 13.5 1.0
CB C:HIS194 3.7 20.5 1.0
OE1 C:GLU157 3.8 15.0 1.0
MN C:MN401 3.8 16.0 1.0
CG C:GLU191 4.1 17.3 1.0
CG C:GLU157 4.2 15.0 1.0
CG C:GLU97 4.4 13.9 1.0
CB C:GLU157 4.4 15.0 1.0
NE2 C:HIS194 4.5 20.8 1.0
CG2 C:ILE93 4.6 18.4 1.0
CD2 C:HIS194 4.6 20.8 1.0
OE1 C:GLN69 4.6 16.5 1.0
CA C:GLU191 4.7 17.8 1.0
CB C:GLU191 4.7 17.4 1.0

Manganese binding site 7 out of 16 in 4n83

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Manganese binding site 7 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:37.5
occ:1.00
 OE1 D:GLU97 2.0 28.8 1.0
OD1 D:ASP66 2.0 41.8 1.0
OE2 D:GLU191 2.1 29.6 1.0
OE1 D:GLU157 2.3 38.8 1.0
ND1 D:HIS100 2.4 31.4 1.0
CD D:GLU191 3.1 29.6 1.0
CD D:GLU97 3.1 28.1 1.0
CG D:ASP66 3.2 42.0 1.0
CE1 D:HIS100 3.2 31.2 1.0
CD D:GLU157 3.4 39.4 1.0
CG D:HIS100 3.4 31.8 1.0
OE2 D:GLU97 3.5 28.1 1.0
OD2 D:ASP66 3.6 42.5 1.0
CG D:GLU191 3.7 29.9 1.0
CB D:HIS100 3.8 32.2 1.0
OE2 D:GLU157 3.9 38.9 1.0
OE1 D:GLU191 4.0 29.6 1.0
MN D:MN402 4.1 33.4 1.0
NE2 D:HIS100 4.3 31.2 1.0
CG D:GLU97 4.4 27.6 1.0
CB D:ASP66 4.4 41.9 1.0
CA D:GLU97 4.4 27.6 1.0
CD2 D:HIS100 4.4 31.6 1.0
CG D:GLU157 4.6 40.3 1.0
CB D:GLU97 4.6 27.6 1.0
CG2 D:ILE187 4.7 35.8 1.0
CE1 D:PHE161 4.8 50.2 1.0
CA D:ASP66 4.8 41.6 1.0
CZ D:PHE161 5.0 50.2 1.0

Manganese binding site 8 out of 16 in 4n83

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Manganese binding site 8 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:33.4
occ:1.00
 OE2 D:GLU97 1.9 28.1 1.0
OE2 D:GLU157 2.0 38.9 1.0
OE1 D:GLU191 2.2 29.6 1.0
ND1 D:HIS194 2.4 23.8 1.0
OE2 D:GLU191 2.7 29.6 1.0
CD D:GLU191 2.8 29.6 1.0
CD D:GLU157 3.0 39.4 1.0
CD D:GLU97 3.1 28.1 1.0
CG D:HIS194 3.3 23.7 1.0
CE1 D:HIS194 3.4 23.6 1.0
CB D:HIS194 3.5 23.9 1.0
OE1 D:GLU157 3.5 38.8 1.0
OE1 D:GLU97 3.6 28.8 1.0
MN D:MN401 4.1 37.5 1.0
CG D:GLU157 4.2 40.3 1.0
CG D:GLU191 4.3 29.9 1.0
CG D:GLU97 4.3 27.6 1.0
CD2 D:HIS194 4.4 23.4 1.0
OE1 D:GLN69 4.4 35.6 1.0
CB D:GLU157 4.4 40.4 1.0
NE2 D:HIS194 4.5 23.4 1.0
CG2 D:ILE93 4.6 20.9 1.0
CA D:GLU191 4.9 29.3 1.0
CB D:GLU191 4.9 29.9 1.0

Manganese binding site 9 out of 16 in 4n83

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Manganese binding site 9 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:41.1
occ:1.00
 OE2 E:GLU97 1.9 40.9 1.0
OE1 E:GLU157 2.0 49.1 1.0
OE1 E:GLU191 2.4 44.4 1.0
ND1 E:HIS194 2.5 37.9 1.0
OE2 E:GLU191 2.8 43.9 1.0
CD E:GLU191 3.0 44.3 1.0
CD E:GLU157 3.1 50.5 1.0
CD E:GLU97 3.1 41.2 1.0
CG E:HIS194 3.4 37.8 1.0
CE1 E:HIS194 3.5 37.8 1.0
OE2 E:GLU157 3.6 50.6 1.0
CB E:HIS194 3.7 37.9 1.0
OE1 E:GLU97 3.7 41.8 1.0
OE1 E:GLN69 4.0 46.0 1.0
MN E:MN402 4.2 51.0 1.0
CG E:GLU157 4.3 51.5 1.0
CG E:GLU97 4.3 40.9 1.0
CG2 E:ILE93 4.4 32.4 1.0
CB E:GLU157 4.5 51.8 1.0
CG E:GLU191 4.5 44.8 1.0
NE2 E:HIS194 4.6 37.8 1.0
CD2 E:HIS194 4.6 37.7 1.0
CD E:GLN69 4.9 46.4 1.0
CG E:GLN69 5.0 46.5 1.0
CD1 E:ILE198 5.0 33.3 1.0

Manganese binding site 10 out of 16 in 4n83

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Manganese binding site 10 out of 16 in the X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of X-Ray Crystal Structure of Streptococcus Sanguinis Dimanganese(II)- Nrdf within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn402

b:51.0
occ:1.00
 OE2 E:GLU157 2.0 50.6 1.0
OE1 E:GLU97 2.1 41.8 1.0
OD1 E:ASP66 2.2 53.2 1.0
OE2 E:GLU191 2.3 43.9 1.0
ND1 E:HIS100 2.5 47.1 1.0
CD E:GLU157 3.1 50.5 1.0
CD E:GLU97 3.1 41.2 1.0
CD E:GLU191 3.1 44.3 1.0
CG E:ASP66 3.2 53.8 1.0
CE1 E:HIS100 3.2 47.0 1.0
OE2 E:GLU97 3.5 40.9 1.0
CG E:HIS100 3.6 47.9 1.0
OE1 E:GLU157 3.6 49.1 1.0
OD2 E:ASP66 3.6 55.2 1.0
CG E:GLU191 3.7 44.8 1.0
CB E:HIS100 4.0 48.7 1.0
OE1 E:GLU191 4.0 44.4 1.0
MN E:MN401 4.2 41.1 1.0
CG E:GLU157 4.4 51.5 1.0
NE2 E:HIS100 4.4 47.1 1.0
CG E:GLU97 4.5 40.9 1.0
CB E:ASP66 4.5 53.4 1.0
CD2 E:HIS100 4.6 47.6 1.0
CG2 E:ILE187 4.6 52.1 1.0
CA E:GLU97 4.7 41.4 1.0
CE1 E:PHE161 4.7 66.2 1.0
CB E:GLU97 4.7 41.0 1.0
CZ E:PHE161 4.8 66.1 1.0
CA E:ASP66 4.9 53.0 1.0
CG E:GLN69 5.0 46.5 1.0

Reference:

O.Makhlynets, A.K.Boal, D.V.Rhodes, T.Kitten, A.C.Rosenzweig, J.Stubbe. Streptococcus Sanguinis Class Ib Ribonucleotide Reductase: High Activity with Both Iron and Manganese Cofactors and Structural Insights. J.Biol.Chem. V. 289 6259 2014.
ISSN: ISSN 0021-9258
PubMed: 24381172
DOI: 10.1074/JBC.M113.533554
Page generated: Sat Oct 5 20:30:13 2024

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