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Magnesium in PDB 3cmx: Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures

Protein crystallography data

The structure of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures, PDB code: 3cmx was solved by N.P.Pavletich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 3.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.000, 300.500, 80.100, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 25.6

Other elements in 3cmx:

The structure of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures also contains other interesting chemical elements:

Fluorine (F) 40 atoms
Aluminium (Al) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures (pdb code 3cmx). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures, PDB code: 3cmx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3cmx

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Magnesium binding site 1 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg500

b:24.3
occ:1.00
 F2 A:ALF501 2.0 23.0 1.0
O1B A:ADP502 2.2 25.2 1.0
OG1 A:THR73 2.2 24.2 1.0
OD1 A:ASP144 3.1 29.3 1.0
F4 A:ALF501 3.1 17.6 1.0
OE1 A:GLU96 3.3 39.3 1.0
PB A:ADP502 3.4 28.4 1.0
AL A:ALF501 3.4 22.5 1.0
N A:THR73 3.4 22.8 1.0
CB A:THR73 3.5 23.7 1.0
O3B A:ADP502 3.7 26.5 1.0
OD2 A:ASP144 3.8 31.0 1.0
CA A:THR73 3.8 22.9 1.0
CG A:ASP144 3.9 29.4 1.0
CB A:LYS72 4.1 21.8 1.0
CE A:LYS72 4.1 18.5 1.0
CG2 A:ILE192 4.1 26.9 1.0
CD A:GLU96 4.2 35.4 1.0
O2B A:ADP502 4.2 29.5 1.0
OE2 A:GLU96 4.3 37.7 1.0
CG2 A:THR73 4.3 23.3 1.0
O2A A:ADP502 4.4 26.0 1.0
C A:LYS72 4.4 22.3 1.0
CD1 A:ILE192 4.5 26.9 1.0
F3 A:ALF501 4.5 21.5 1.0
NZ A:LYS1250 4.5 32.0 1.0
O3A A:ADP502 4.6 26.5 1.0
NZ A:LYS72 4.6 15.7 1.0
CA A:LYS72 4.7 22.1 1.0
CE A:LYS1250 4.7 30.4 1.0
PA A:ADP502 4.8 27.2 1.0
O1A A:ADP502 4.8 24.2 1.0

Magnesium binding site 2 out of 10 in 3cmx

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Magnesium binding site 2 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1500

b:3.5
occ:1.00
 F2 A:ALF1501 2.0 5.7 1.0
OG1 A:THR1073 2.1 13.4 1.0
O1B A:ADP1502 2.2 2.2 1.0
OE1 A:GLU1096 2.7 38.0 1.0
OD1 A:ASP1144 3.1 33.6 1.0
F4 A:ALF1501 3.1 4.3 1.0
AL A:ALF1501 3.4 3.0 1.0
OD2 A:ASP1144 3.4 34.7 1.0
CB A:THR1073 3.5 20.0 1.0
PB A:ADP1502 3.5 2.0 1.0
CG A:ASP1144 3.6 32.1 1.0
CD A:GLU1096 3.7 34.7 1.0
O3B A:ADP1502 3.9 2.0 1.0
N A:THR1073 3.9 21.3 1.0
OE2 A:GLU1096 4.0 37.1 1.0
NZ A:LYS2250 4.0 27.7 1.0
CG2 A:THR1073 4.1 19.9 1.0
CA A:THR1073 4.1 20.5 1.0
CE A:LYS2250 4.2 27.8 1.0
O2A A:ADP1502 4.4 2.0 1.0
F3 A:ALF1501 4.5 2.0 1.0
O2B A:ADP1502 4.5 3.9 1.0
O3A A:ADP1502 4.7 2.4 1.0
CE A:LYS1072 4.7 19.9 1.0
CG2 A:ILE1192 4.8 24.7 1.0
CB A:LYS1072 4.8 19.8 1.0
CD1 A:ILE1192 4.9 26.0 1.0
PA A:ADP1502 5.0 2.0 1.0

Magnesium binding site 3 out of 10 in 3cmx

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Magnesium binding site 3 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2500

b:2.0
occ:1.00
 F2 A:ALF2501 2.0 2.0 1.0
OG1 A:THR2073 2.1 13.8 1.0
O1B A:ADP2502 2.2 2.0 1.0
OE1 A:GLU2096 2.7 40.6 1.0
F4 A:ALF2501 3.1 2.0 1.0
OD1 A:ASP2144 3.2 34.2 1.0
AL A:ALF2501 3.4 2.0 1.0
PB A:ADP2502 3.5 2.0 1.0
CB A:THR2073 3.5 20.2 1.0
OD2 A:ASP2144 3.5 33.0 1.0
CD A:GLU2096 3.7 35.8 1.0
CG A:ASP2144 3.8 32.1 1.0
O3B A:ADP2502 3.8 2.0 1.0
OE2 A:GLU2096 4.0 36.7 1.0
NZ A:LYS3250 4.0 27.9 1.0
N A:THR2073 4.0 20.6 1.0
CG2 A:THR2073 4.1 20.8 1.0
CA A:THR2073 4.2 19.9 1.0
O2A A:ADP2502 4.2 2.0 1.0
CE A:LYS3250 4.2 27.3 1.0
O2B A:ADP2502 4.4 2.0 1.0
F3 A:ALF2501 4.5 2.0 1.0
O3A A:ADP2502 4.7 2.0 1.0
CE A:LYS2072 4.7 19.3 1.0
CG2 A:ILE2192 4.9 26.7 1.0
PA A:ADP2502 4.9 2.0 1.0
CB A:LYS2072 4.9 18.7 1.0

Magnesium binding site 4 out of 10 in 3cmx

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Magnesium binding site 4 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3500

b:2.0
occ:1.00
 F2 A:ALF3501 2.0 2.0 1.0
OG1 A:THR3073 2.1 15.2 1.0
O1B A:ADP3502 2.2 2.0 1.0
OE1 A:GLU3096 2.9 38.5 1.0
F4 A:ALF3501 3.1 2.0 1.0
OD1 A:ASP3144 3.1 28.3 1.0
AL A:ALF3501 3.3 2.0 1.0
PB A:ADP3502 3.4 2.0 1.0
CB A:THR3073 3.5 21.3 1.0
OD2 A:ASP3144 3.5 33.3 1.0
CG A:ASP3144 3.7 29.7 1.0
O3B A:ADP3502 3.8 2.0 1.0
N A:THR3073 3.8 21.2 1.0
CD A:GLU3096 3.8 34.7 1.0
OE2 A:GLU3096 4.0 33.9 1.0
NZ A:LYS4250 4.1 30.4 1.0
CA A:THR3073 4.1 21.2 1.0
CG2 A:THR3073 4.1 20.1 1.0
O2B A:ADP3502 4.3 2.0 1.0
O2A A:ADP3502 4.3 2.0 1.0
F3 A:ALF3501 4.4 2.0 1.0
CE A:LYS4250 4.4 30.8 1.0
CE A:LYS3072 4.5 19.3 1.0
O3A A:ADP3502 4.6 2.0 1.0
CG2 A:ILE3192 4.7 26.0 1.0
CB A:LYS3072 4.7 18.7 1.0
CD1 A:ILE3192 4.9 27.0 1.0
C A:LYS3072 4.9 20.2 1.0
PA A:ADP3502 4.9 2.0 1.0
F1 A:ALF3501 4.9 2.0 1.0
NZ A:LYS3072 5.0 17.8 1.0

Magnesium binding site 5 out of 10 in 3cmx

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Magnesium binding site 5 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg4500

b:2.0
occ:1.00
 F2 A:ALF4501 1.7 36.4 1.0
OG1 A:THR4073 1.8 24.4 1.0
O1B A:ADP4502 2.7 11.1 1.0
OE1 A:GLU4096 3.0 40.6 1.0
OD1 A:ASP4144 3.0 28.4 1.0
F4 A:ALF4501 3.0 38.9 1.0
CB A:THR4073 3.2 23.2 1.0
AL A:ALF4501 3.2 40.5 1.0
OD2 A:ASP4144 3.3 29.2 1.0
CG A:ASP4144 3.6 28.4 1.0
N A:THR4073 3.7 22.9 1.0
CG2 A:THR4073 3.8 21.5 1.0
CA A:THR4073 3.8 23.0 1.0
PB A:ADP4502 3.9 12.3 1.0
CD A:GLU4096 4.0 35.5 1.0
O3B A:ADP4502 4.1 12.9 1.0
F3 A:ALF4501 4.2 39.7 1.0
OE2 A:GLU4096 4.3 38.5 1.0
O2A A:ADP4502 4.4 12.4 1.0
CD1 A:ILE4192 4.7 26.1 1.0
CG2 A:ILE4192 4.7 25.5 1.0
CB A:LYS4072 4.7 19.9 1.0
C A:LYS4072 4.8 22.5 1.0
CE A:LYS4072 4.8 18.4 1.0
F1 A:ALF4501 4.9 40.7 1.0
O2B A:ADP4502 5.0 13.7 1.0

Magnesium binding site 6 out of 10 in 3cmx

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Magnesium binding site 6 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg500

b:5.9
occ:1.00
 F2 D:ALF501 2.0 2.0 1.0
OG1 D:THR73 2.1 20.1 1.0
O1B D:ADP502 2.2 5.0 1.0
F4 D:ALF501 2.8 2.0 1.0
OE1 D:GLU96 3.0 40.3 1.0
AL D:ALF501 3.2 2.0 1.0
OD1 D:ASP144 3.2 32.0 1.0
PB D:ADP502 3.4 5.5 1.0
CB D:THR73 3.5 23.8 1.0
O3B D:ADP502 3.6 5.5 1.0
OD2 D:ASP144 3.7 34.8 1.0
N D:THR73 3.7 24.0 1.0
CG D:ASP144 3.9 30.4 1.0
CD D:GLU96 3.9 37.3 1.0
CA D:THR73 4.0 23.4 1.0
OE2 D:GLU96 4.1 40.7 1.0
NZ D:LYS1250 4.1 30.3 1.0
CG2 D:THR73 4.2 23.0 1.0
O2B D:ADP502 4.4 4.7 1.0
CE D:LYS72 4.4 20.6 1.0
F3 D:ALF501 4.4 2.0 1.0
CE D:LYS1250 4.4 29.7 1.0
O2A D:ADP502 4.4 3.4 1.0
CB D:LYS72 4.5 23.4 1.0
CG2 D:ILE192 4.5 27.3 1.0
O3A D:ADP502 4.6 4.5 1.0
C D:LYS72 4.7 23.9 1.0
F1 D:ALF501 4.8 2.0 1.0
CD1 D:ILE192 4.8 25.4 1.0
NZ D:LYS72 4.8 20.3 1.0
PA D:ADP502 5.0 2.8 1.0

Magnesium binding site 7 out of 10 in 3cmx

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Magnesium binding site 7 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1500

b:2.0
occ:1.00
 F2 D:ALF1501 1.9 2.0 1.0
OG1 D:THR1073 2.1 18.1 1.0
O1B D:ADP1502 2.2 2.0 1.0
OE1 D:GLU1096 2.7 36.9 1.0
F4 D:ALF1501 3.1 2.0 1.0
OD1 D:ASP1144 3.3 28.8 1.0
AL D:ALF1501 3.3 2.0 1.0
CB D:THR1073 3.5 22.6 1.0
OD2 D:ASP1144 3.5 29.8 1.0
PB D:ADP1502 3.5 2.0 1.0
CD D:GLU1096 3.7 31.9 1.0
NZ D:LYS2250 3.7 33.7 1.0
O3B D:ADP1502 3.8 2.0 1.0
CG D:ASP1144 3.8 29.4 1.0
CE D:LYS2250 3.9 30.3 1.0
OE2 D:GLU1096 4.0 33.1 1.0
N D:THR1073 4.1 22.6 1.0
CG2 D:THR1073 4.1 21.8 1.0
O2A D:ADP1502 4.2 5.0 1.0
CA D:THR1073 4.2 22.7 1.0
F3 D:ALF1501 4.3 2.0 1.0
O2B D:ADP1502 4.6 2.0 1.0
O3A D:ADP1502 4.6 2.1 1.0
PA D:ADP1502 4.8 4.0 1.0
CE D:LYS1072 4.8 20.2 1.0
F1 D:ALF1501 5.0 2.0 1.0

Magnesium binding site 8 out of 10 in 3cmx

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Magnesium binding site 8 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2500

b:2.0
occ:1.00
 F2 D:ALF2501 1.9 2.0 1.0
OG1 D:THR2073 2.1 16.5 1.0
O1B D:ADP2502 2.2 2.0 1.0
F4 D:ALF2501 2.9 2.0 1.0
OE1 D:GLU2096 3.0 39.7 1.0
OD1 D:ASP2144 3.0 28.9 1.0
AL D:ALF2501 3.3 2.0 1.0
CB D:THR2073 3.4 22.7 1.0
PB D:ADP2502 3.5 2.0 1.0
OD2 D:ASP2144 3.5 33.0 1.0
N D:THR2073 3.7 23.8 1.0
CG D:ASP2144 3.7 29.2 1.0
O3B D:ADP2502 3.8 2.0 1.0
CD D:GLU2096 3.9 35.7 1.0
CA D:THR2073 4.0 22.1 1.0
OE2 D:GLU2096 4.1 36.9 1.0
CG2 D:THR2073 4.1 25.2 1.0
NZ D:LYS3250 4.3 27.6 1.0
F3 D:ALF2501 4.4 2.0 1.0
O2B D:ADP2502 4.4 2.0 1.0
CE D:LYS2072 4.5 25.5 1.0
CG2 D:ILE2192 4.5 26.3 1.0
O2A D:ADP2502 4.5 2.0 1.0
CB D:LYS2072 4.5 22.2 1.0
CE D:LYS3250 4.6 25.9 1.0
CD1 D:ILE2192 4.7 27.1 1.0
O3A D:ADP2502 4.7 2.0 1.0
C D:LYS2072 4.7 23.8 1.0
F1 D:ALF2501 4.9 2.0 1.0
NZ D:LYS2072 4.9 25.5 1.0

Magnesium binding site 9 out of 10 in 3cmx

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Magnesium binding site 9 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3500

b:6.3
occ:1.00
 F2 D:ALF3501 2.0 6.2 1.0
OG1 D:THR3073 2.1 16.4 1.0
O1B D:ADP3502 2.2 2.0 1.0
OE1 D:GLU3096 2.7 39.7 1.0
F4 D:ALF3501 3.2 2.0 1.0
OD1 D:ASP3144 3.2 29.5 1.0
AL D:ALF3501 3.4 2.0 1.0
PB D:ADP3502 3.5 2.0 1.0
CB D:THR3073 3.5 21.5 1.0
OD2 D:ASP3144 3.5 30.0 1.0
NZ D:LYS4250 3.6 27.3 1.0
CD D:GLU3096 3.8 35.2 1.0
CG D:ASP3144 3.8 29.7 1.0
O3B D:ADP3502 3.8 2.0 1.0
CE D:LYS4250 3.9 26.5 1.0
OE2 D:GLU3096 4.0 36.0 1.0
N D:THR3073 4.0 23.0 1.0
CG2 D:THR3073 4.1 21.9 1.0
CA D:THR3073 4.2 22.2 1.0
O2A D:ADP3502 4.2 2.0 1.0
O2B D:ADP3502 4.4 2.7 1.0
F3 D:ALF3501 4.5 3.6 1.0
O3A D:ADP3502 4.7 2.0 1.0
CE D:LYS3072 4.8 17.9 1.0
PA D:ADP3502 4.9 2.0 1.0
CG2 D:ILE3192 4.9 26.5 1.0
CB D:LYS3072 4.9 21.3 1.0

Magnesium binding site 10 out of 10 in 3cmx

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Magnesium binding site 10 out of 10 in the Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4500

b:17.4
occ:1.00
 F2 D:ALF4501 2.0 26.7 1.0
OG1 D:THR4073 2.2 20.5 1.0
O1B D:ADP4502 2.2 18.7 1.0
OE1 D:GLU4096 3.0 38.9 1.0
F4 D:ALF4501 3.2 32.5 1.0
OD1 D:ASP4144 3.4 32.8 1.0
PB D:ADP4502 3.4 19.7 1.0
AL D:ALF4501 3.4 32.4 1.0
CB D:THR4073 3.6 21.9 1.0
O3B D:ADP4502 3.6 24.9 1.0
OD2 D:ASP4144 3.8 32.4 1.0
N D:THR4073 3.8 20.4 1.0
CD D:GLU4096 3.9 35.2 1.0
CG D:ASP4144 4.0 31.6 1.0
OE2 D:GLU4096 4.0 38.9 1.0
CA D:THR4073 4.2 21.4 1.0
CG2 D:THR4073 4.3 23.1 1.0
O2A D:ADP4502 4.3 17.6 1.0
O2B D:ADP4502 4.4 21.0 1.0
CE D:LYS4072 4.4 15.2 1.0
F3 D:ALF4501 4.5 30.9 1.0
O3A D:ADP4502 4.6 18.1 1.0
CB D:LYS4072 4.6 18.2 1.0
CG2 D:ILE4192 4.7 24.3 1.0
NZ D:LYS4072 4.8 14.9 1.0
PA D:ADP4502 4.8 19.1 1.0
C D:LYS4072 4.9 19.4 1.0

Reference:

Z.Chen, H.Yang, N.P.Pavletich. Mechanism of Homologous Recombination From the Reca-Ssdna/Dsdna Structures. Nature V. 453 489 2008.
ISSN: ISSN 0028-0836
PubMed: 18497818
DOI: 10.1038/NATURE06971
Page generated: Wed Aug 14 11:31:39 2024

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