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Magnesium in PDB 2br3: Cmci-D160 Mg

Protein crystallography data

The structure of Cmci-D160 Mg, PDB code: 2br3 was solved by L.M.Oster, D.R.Lester, A.Terwisscha Van Scheltinga, M.Svenda, C.Genereux, I.Andersson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.23 / 2.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.877, 145.515, 162.154, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 27.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cmci-D160 Mg (pdb code 2br3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cmci-D160 Mg, PDB code: 2br3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 2br3

Go back to Magnesium Binding Sites List in 2br3
Magnesium binding site 1 out of 5 in the Cmci-D160 Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cmci-D160 Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg300

b:0.5
occ:1.00
 NE2 B:GLN223 3.0 13.4 1.0
O B:LEU64 3.1 18.3 1.0
OE1 B:GLU186 3.5 21.3 1.0
CD B:GLN223 3.5 14.8 1.0
C B:LEU64 3.6 18.2 1.0
CG B:LYS65 3.8 19.3 1.0
OE1 B:GLN223 3.8 13.5 1.0
CA B:LYS65 3.8 19.0 1.0
N B:LYS65 3.9 18.5 1.0
O B:HOH2010 4.0 39.8 1.0
OD2 B:ASP187 4.0 22.5 1.0
O B:HOH2022 4.1 29.4 1.0
CB B:LEU64 4.3 18.3 1.0
CB B:LYS65 4.3 19.1 1.0
NZ B:LYS65 4.4 20.9 1.0
CG B:GLN223 4.4 16.9 1.0
CD B:GLU186 4.5 21.5 1.0
OD1 B:ASP160 4.6 16.7 1.0
CA B:LEU64 4.6 18.2 1.0
CB B:GLN223 4.7 18.1 1.0
OD1 B:ASP187 4.7 24.7 1.0
CD B:LYS65 4.8 19.4 1.0
CG B:ASP187 4.9 22.4 1.0

Magnesium binding site 2 out of 5 in 2br3

Go back to Magnesium Binding Sites List in 2br3
Magnesium binding site 2 out of 5 in the Cmci-D160 Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cmci-D160 Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg300

b:0.8
occ:1.00
 OD2 C:ASP187 2.6 24.7 1.0
OE1 C:GLU186 2.8 20.2 1.0
CD C:GLU186 3.6 22.0 1.0
CG C:ASP187 3.6 24.6 1.0
CB C:GLU186 3.7 22.0 1.0
CD C:GLN223 3.7 15.8 1.0
CB C:GLN223 3.7 18.7 1.0
CG C:GLN223 3.8 17.8 1.0
NE2 C:GLN223 3.8 12.8 1.0
OD1 C:ASP187 3.9 27.4 1.0
CG C:GLU186 4.2 21.9 1.0
OE1 C:GLN223 4.2 14.3 1.0
OD1 C:ASP160 4.2 21.5 1.0
OE2 C:GLU186 4.4 23.2 1.0
CG C:LYS65 4.6 21.9 1.0
NZ C:LYS65 4.7 22.7 1.0
CA C:GLN223 4.8 18.9 1.0
CB C:ASP187 4.8 23.3 1.0
CA C:GLU186 4.9 22.3 1.0
O C:GLN223 5.0 19.9 1.0

Magnesium binding site 3 out of 5 in 2br3

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Magnesium binding site 3 out of 5 in the Cmci-D160 Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cmci-D160 Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg300

b:0.1
occ:1.00
 O D:HOH2024 2.3 69.0 1.0
NZ D:LYS65 2.8 13.1 1.0
OD2 D:ASP160 3.4 13.6 1.0
OD1 D:ASP160 3.5 13.4 1.0
CG D:ASP160 3.6 14.8 1.0
CG D:LYS65 3.6 16.8 1.0
OG D:SER95 3.7 14.1 1.0
OE1 D:GLU186 3.7 19.1 1.0
CE D:LYS65 3.8 14.9 1.0
CB D:LEU64 4.0 17.3 1.0
CD D:LYS65 4.3 15.7 1.0
OE2 D:GLU87 4.4 18.2 1.0
N D:LYS65 4.5 17.0 1.0
CB D:ASP160 4.6 15.1 1.0
C D:LEU64 4.7 17.1 1.0
CD D:GLU186 4.7 17.9 1.0
CB D:SER95 4.7 14.3 1.0
CD1 D:LEU64 4.8 18.0 1.0
CG D:LEU64 4.9 18.0 1.0
CA D:LEU64 4.9 17.3 1.0
CB D:LYS65 4.9 17.1 1.0

Magnesium binding site 4 out of 5 in 2br3

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Magnesium binding site 4 out of 5 in the Cmci-D160 Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cmci-D160 Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg300

b:0.6
occ:1.00
 O E:LEU64 2.9 21.1 1.0
OE1 E:GLU186 3.3 21.0 1.0
C E:LEU64 3.3 20.9 1.0
NE2 E:GLN223 3.4 10.8 1.0
N E:LYS65 3.6 20.7 1.0
CG E:LYS65 3.7 21.2 1.0
CA E:LYS65 3.7 20.6 1.0
CB E:LEU64 3.8 21.0 1.0
CD E:GLN223 3.9 13.1 1.0
OD2 E:ASP187 4.0 21.8 1.0
OE1 E:GLN223 4.1 12.5 1.0
CB E:LYS65 4.2 20.6 1.0
CA E:LEU64 4.2 21.1 1.0
NZ E:LYS65 4.3 17.6 1.0
OD1 E:ASP160 4.4 11.2 1.0
O E:HOH2022 4.4 33.1 1.0
CD E:GLU186 4.5 21.4 1.0
CD E:LYS65 4.8 20.9 1.0
CG E:GLN223 4.9 14.4 1.0

Magnesium binding site 5 out of 5 in 2br3

Go back to Magnesium Binding Sites List in 2br3
Magnesium binding site 5 out of 5 in the Cmci-D160 Mg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cmci-D160 Mg within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg300

b:71.9
occ:1.00
 OE1 F:GLU186 3.0 16.6 1.0
OD2 F:ASP187 3.3 22.6 1.0
CD F:GLN223 3.3 16.7 1.0
NE2 F:GLN223 3.4 14.4 1.0
OE1 F:GLN223 3.7 18.0 1.0
CG F:GLN223 3.7 17.2 1.0
CB F:GLN223 3.7 18.0 1.0
CD F:GLU186 3.8 18.1 1.0
O F:LEU64 3.9 20.9 1.0
OD1 F:ASP187 4.0 21.1 1.0
CG F:ASP187 4.0 21.1 1.0
CB F:GLU186 4.1 19.7 1.0
OD1 F:ASP160 4.2 22.6 1.0
CG F:LYS65 4.3 20.3 1.0
OE2 F:GLU186 4.5 17.4 1.0
CG F:GLU186 4.6 19.1 1.0
CA F:LYS65 4.6 20.6 1.0
C F:LEU64 4.7 21.0 1.0
NZ F:LYS65 4.8 20.9 1.0
CA F:GLN223 5.0 18.4 1.0
CB F:LYS65 5.0 20.4 1.0
N F:LYS65 5.0 20.7 1.0

Reference:

L.M.Oster, D.R.Lester, A.Terwisscha Van Scheltinga, M.Svenda, M.Van Lun, C.Genereux, I.Andersson. Insights Into Cephamycin Biosynthesis: the Crystal Structure of Cmci From Streptomyces Clavuligerus. J.Mol.Biol. V. 358 546 2006.
ISSN: ISSN 0022-2836
PubMed: 16527306
DOI: 10.1016/J.JMB.2006.02.004
Page generated: Tue Aug 13 21:59:53 2024

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