Magnesium in PDB 4tug: Crystal Structure of MJMRE11-DNA2 Complex

The structure of Crystal Structure of MJMRE11-DNA2 Complex, PDB code: 4tug was solved by S.Sung, Y.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.42 / 3.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	91.530, 185.624, 106.212, 90.00, 99.86, 90.00
R / Rfree (%)	18.4 / 23.6

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>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of MJMRE11-DNA2 Complex (pdb code 4tug). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Crystal Structure of MJMRE11-DNA2 Complex, PDB code: 4tug:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg401 b:50.9 occ:1.00 ND1 C:HIS186 1.9 0.1 1.0 OD1 C:ASP49 2.1 85.9 1.0 OD1 C:ASN84 2.3 89.8 1.0 NE2 C:HIS158 2.4 99.9 1.0 CE1 C:HIS186 2.6 1.0 1.0 CE1 C:HIS158 2.8 99.9 1.0 MG C:MG402 2.9 77.6 1.0 CG C:HIS186 3.0 0.6 1.0 CG C:ASN84 3.2 93.4 1.0 CG C:ASP49 3.2 86.3 1.0 ND2 C:ASN84 3.4 0.3 1.0 CA C:HIS186 3.5 0.4 1.0 CD2 C:HIS158 3.6 99.7 1.0 CB C:HIS186 3.6 0.6 1.0 O C:HOH501 3.7 65.7 1.0 OD2 C:ASP8 3.8 86.4 1.0 O C:HIS186 3.8 0.8 1.0 NE2 C:HIS186 3.8 0.5 1.0 OD1 C:ASP8 3.8 96.7 1.0 OD2 C:ASP49 3.9 86.0 1.0 ND1 C:HIS158 4.0 0.7 1.0 CD2 C:HIS186 4.0 0.5 1.0 C C:HIS186 4.1 0.2 1.0 CG C:ASP8 4.2 93.1 1.0 CB C:ASP49 4.3 88.4 1.0 CG C:HIS158 4.4 0.8 1.0 N C:HIS186 4.5 0.9 1.0 NE2 C:HIS188 4.5 0.3 1.0 CB C:ASN84 4.6 94.9 1.0 N C:ASN84 4.7 0.6 1.0 NE2 C:HIS10 4.7 0.6 1.0 O C:GLY185 4.9 0.5 1.0

Magnesium binding site 2 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:77.6 occ:1.00 OD2 C:ASP8 1.7 86.4 1.0 NE2 C:HIS188 2.0 0.3 1.0 NE2 C:HIS10 2.1 0.6 1.0 OD1 C:ASP49 2.5 85.9 1.0 CE1 C:HIS10 2.7 0.5 1.0 CE1 C:HIS188 2.8 0.6 1.0 CG C:ASP8 2.9 93.1 1.0 MG C:MG401 2.9 50.9 1.0 CD2 C:HIS188 3.2 0.6 1.0 O C:HOH501 3.2 65.7 1.0 CD2 C:HIS10 3.4 0.1 1.0 OD1 C:ASP8 3.4 96.7 1.0 CG C:ASP49 3.5 86.3 1.0 CB C:ASP49 3.8 88.4 1.0 ND1 C:HIS10 4.0 0.5 1.0 ND1 C:HIS188 4.0 0.5 1.0 CB C:ASP8 4.1 93.0 1.0 CG C:HIS188 4.2 0.2 1.0 ND1 C:HIS186 4.3 0.1 1.0 CG C:HIS10 4.3 94.7 1.0 O C:HIS186 4.4 0.8 1.0 CD2 C:HIS85 4.5 0.0 1.0 OD2 C:ASP49 4.5 86.0 1.0 NE2 C:HIS85 4.6 0.6 1.0 CE1 C:HIS186 4.6 1.0 1.0 CE1 C:HIS158 4.7 99.9 1.0 ND2 C:ASN84 4.8 0.3 1.0 OD1 C:ASN84 4.8 89.8 1.0 CA C:ASP8 4.8 89.4 1.0 NE2 C:HIS158 4.9 99.9 1.0 C C:HIS186 5.0 0.2 1.0

Magnesium binding site 3 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:54.9 occ:1.00 ND1 A:HIS186 1.8 0.4 1.0 OD1 A:ASN84 1.9 0.8 1.0 NE2 A:HIS158 2.1 87.0 1.0 OD1 A:ASP49 2.1 0.7 1.0 CE1 A:HIS186 2.6 0.1 1.0 CG A:ASN84 2.7 0.2 1.0 CE1 A:HIS158 2.7 90.2 1.0 ND2 A:ASN84 2.9 0.9 1.0 CG A:HIS186 2.9 0.3 1.0 MG A:MG402 3.0 55.0 1.0 CG A:ASP49 3.2 0.3 1.0 CD2 A:HIS158 3.3 92.2 1.0 CB A:HIS186 3.5 0.6 1.0 O A:HOH506 3.5 58.9 1.0 CA A:HIS186 3.6 0.3 1.0 OD2 A:ASP49 3.6 0.3 1.0 NE2 A:HIS186 3.8 0.5 1.0 CD2 A:HIS186 3.9 0.6 1.0 OD2 A:ASP8 3.9 82.0 1.0 ND1 A:HIS158 4.0 97.3 1.0 CB A:ASN84 4.2 0.5 1.0 CG A:HIS158 4.3 0.9 1.0 O A:HIS186 4.3 0.8 1.0 N A:ASN84 4.3 0.1 1.0 C A:HIS186 4.4 0.4 1.0 CB A:ASP49 4.5 97.1 1.0 N A:HIS186 4.5 0.8 1.0 NE2 A:HIS188 4.6 0.5 1.0 CG A:ASP8 4.9 95.4 1.0 NE2 A:HIS10 4.9 95.2 1.0 CA A:ASN84 4.9 0.2 1.0 OD1 A:ASP8 4.9 0.1 1.0 CE1 A:HIS10 5.0 93.1 1.0

Magnesium binding site 4 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:55.0 occ:1.00 OD2 A:ASP8 1.9 82.0 1.0 NE2 A:HIS188 2.1 0.5 1.0 NE2 A:HIS10 2.2 95.2 1.0 OD1 A:ASP49 2.3 0.7 1.0 CE1 A:HIS10 2.7 93.1 1.0 CE1 A:HIS188 2.9 0.3 1.0 MG A:MG401 3.0 54.9 1.0 CG A:ASP8 3.0 95.4 1.0 CD2 A:HIS188 3.2 0.7 1.0 CG A:ASP49 3.3 0.3 1.0 O A:HOH506 3.3 58.9 1.0 CD2 A:HIS10 3.4 93.0 1.0 CB A:ASP49 3.7 97.1 1.0 OD1 A:ASP8 3.7 0.1 1.0 ND1 A:HIS10 3.9 88.6 1.0 CB A:ASP8 4.1 96.8 1.0 ND1 A:HIS188 4.1 0.1 1.0 ND1 A:HIS186 4.1 0.4 1.0 CE1 A:HIS158 4.2 90.2 1.0 CG A:HIS188 4.3 0.5 1.0 CG A:HIS10 4.3 86.2 1.0 OD2 A:ASP49 4.3 0.3 1.0 CA A:HIS186 4.4 0.3 1.0 NE2 A:HIS85 4.4 0.6 1.0 NE2 A:HIS158 4.4 87.0 1.0 CD2 A:HIS85 4.5 0.5 1.0 ND2 A:ASN84 4.6 0.9 1.0 OD1 A:ASN84 4.7 0.8 1.0 O A:HIS186 4.7 0.8 1.0 CA A:ASP8 4.8 92.8 1.0 C A:HIS186 4.8 0.4 1.0 CE1 A:HIS186 4.9 0.1 1.0 N A:HIS186 5.0 0.8 1.0

Magnesium binding site 5 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:57.2 occ:1.00 ND1 B:HIS186 1.8 0.7 1.0 OD1 B:ASP49 1.9 0.8 1.0 OD1 B:ASN84 2.0 0.6 1.0 NE2 B:HIS158 2.1 86.3 1.0 CE1 B:HIS186 2.5 0.3 1.0 CG B:ASN84 2.8 0.3 1.0 CE1 B:HIS158 2.8 88.0 1.0 CG B:ASP49 2.8 0.2 1.0 CG B:HIS186 3.0 0.0 1.0 ND2 B:ASN84 3.0 0.5 1.0 MG B:MG402 3.1 77.6 1.0 OD2 B:ASP49 3.2 92.5 1.0 CD2 B:HIS158 3.2 89.7 1.0 NE2 B:HIS186 3.6 0.1 1.0 CB B:HIS186 3.6 1.0 1.0 CA B:HIS186 3.8 0.4 1.0 CD2 B:HIS186 3.9 0.9 1.0 ND1 B:HIS158 4.0 92.6 1.0 CB B:ASP49 4.2 0.3 1.0 CG B:HIS158 4.2 93.5 1.0 N B:ASN84 4.3 0.9 1.0 OD2 B:ASP8 4.3 74.6 1.0 CB B:ASN84 4.3 0.9 1.0 ND1 B:HIS85 4.4 0.5 1.0 OD1 B:ASP8 4.6 93.8 1.0 O B:HIS186 4.6 0.1 1.0 CE1 B:HIS85 4.7 0.6 1.0 C B:HIS186 4.7 0.7 1.0 N B:HIS186 4.7 0.6 1.0 CG B:ASP8 4.9 82.4 1.0 CA B:ASN84 4.9 0.9 1.0

Magnesium binding site 6 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:77.6 occ:1.00 OD2 B:ASP8 1.8 74.6 1.0 OD1 B:ASP49 2.0 0.8 1.0 NE2 B:HIS10 2.0 87.9 1.0 CE1 B:HIS10 2.4 93.3 1.0 NE2 B:HIS188 2.6 0.8 1.0 CG B:ASP49 2.8 0.2 1.0 CG B:ASP8 3.0 82.4 1.0 MG B:MG401 3.1 57.2 1.0 CB B:ASP49 3.3 0.3 1.0 CD2 B:HIS10 3.3 88.9 1.0 CE1 B:HIS188 3.5 0.1 1.0 OD1 B:ASP8 3.6 93.8 1.0 ND1 B:HIS10 3.6 94.7 1.0 CD2 B:HIS188 3.7 0.1 1.0 OD2 B:ASP49 3.8 92.5 1.0 ND1 B:HIS85 4.1 0.5 1.0 CG B:HIS10 4.1 89.9 1.0 CB B:ASP8 4.1 81.1 1.0 ND1 B:HIS186 4.1 0.7 1.0 CE1 B:HIS85 4.2 0.6 1.0 CE1 B:HIS158 4.3 88.0 1.0 NE2 B:HIS158 4.5 86.3 1.0 ND1 B:HIS188 4.7 1.0 1.0 CA B:ASP8 4.7 80.8 1.0 CE1 B:HIS186 4.7 0.3 1.0 CA B:ASP49 4.7 95.4 1.0 CG B:HIS188 4.8 0.1 1.0 CA B:HIS186 4.8 0.4 1.0 ND2 B:ASN84 4.8 0.5 1.0 OD1 B:ASN84 4.9 0.6 1.0

Magnesium binding site 7 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg401 b:45.8 occ:1.00 OD1 D:ASP49 2.0 97.9 1.0 ND1 D:HIS186 2.0 0.7 1.0 NE2 D:HIS158 2.2 91.8 1.0 OD1 D:ASN84 2.2 84.6 1.0 CE1 D:HIS158 2.8 90.8 1.0 MG D:MG402 2.9 61.2 1.0 O D:HOH501 2.9 52.1 1.0 CE1 D:HIS186 2.9 0.6 1.0 CG D:ASN84 3.0 90.1 1.0 CG D:HIS186 3.1 0.3 1.0 CG D:ASP49 3.1 97.5 1.0 ND2 D:ASN84 3.2 85.2 1.0 CA D:HIS186 3.3 0.3 1.0 CD2 D:HIS158 3.4 94.6 1.0 CB D:HIS186 3.5 0.1 1.0 OD2 D:ASP49 3.7 95.4 1.0 OD2 D:ASP8 3.8 81.6 1.0 ND1 D:HIS158 4.0 94.3 1.0 O D:HIS186 4.0 0.3 1.0 NE2 D:HIS186 4.1 0.8 1.0 C D:HIS186 4.1 0.7 1.0 CD2 D:HIS186 4.1 0.2 1.0 CB D:ASP49 4.2 95.5 1.0 N D:HIS186 4.2 0.1 1.0 CG D:HIS158 4.3 97.7 1.0 OD1 D:ASP8 4.4 0.0 1.0 NE2 D:HIS188 4.4 95.7 1.0 CB D:ASN84 4.5 0.0 1.0 CG D:ASP8 4.5 95.9 1.0 N D:ASN84 4.5 0.9 1.0 NE2 D:HIS10 4.8 98.2 1.0 CE1 D:HIS10 5.0 98.9 1.0

Magnesium binding site 8 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:61.2 occ:1.00 OD2 D:ASP8 1.7 81.6 1.0 NE2 D:HIS188 2.0 95.7 1.0 NE2 D:HIS10 2.2 98.2 1.0 OD1 D:ASP49 2.2 97.9 1.0 CE1 D:HIS10 2.7 98.9 1.0 MG D:MG401 2.9 45.8 1.0 CE1 D:HIS188 2.9 95.0 1.0 CG D:ASP8 2.9 95.9 1.0 O D:HOH501 3.0 52.1 1.0 CD2 D:HIS188 3.1 98.2 1.0 CG D:ASP49 3.2 97.5 1.0 CD2 D:HIS10 3.4 97.8 1.0 CB D:ASP49 3.5 95.5 1.0 OD1 D:ASP8 3.6 0.0 1.0 ND1 D:HIS10 3.9 93.7 1.0 CB D:ASP8 4.0 0.6 1.0 ND1 D:HIS188 4.1 96.5 1.0 CG D:HIS188 4.2 98.6 1.0 CE1 D:HIS158 4.3 90.8 1.0 OD2 D:ASP49 4.3 95.4 1.0 CG D:HIS10 4.3 92.3 1.0 ND1 D:HIS186 4.4 0.7 1.0 NE2 D:HIS158 4.5 91.8 1.0 CD2 D:HIS85 4.5 0.3 1.0 CA D:HIS186 4.5 0.3 1.0 O D:HIS186 4.6 0.3 1.0 CA D:ASP8 4.7 0.3 1.0 ND2 D:ASN84 4.8 85.2 1.0 NE2 D:HIS85 4.8 0.3 1.0 C D:HIS186 4.8 0.7 1.0 OD1 D:ASN84 4.8 84.6 1.0 CA D:ASP49 5.0 89.7 1.0

Magnesium binding site 9 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg401 b:70.6 occ:1.00 ND1 E:HIS186 2.0 0.1 1.0 OD1 E:ASN84 2.0 0.8 1.0 NE2 E:HIS158 2.0 0.0 1.0 OD1 E:ASP49 2.2 0.3 1.0 CE1 E:HIS158 2.7 0.5 1.0 CE1 E:HIS186 2.8 0.6 1.0 MG E:MG402 2.8 0.0 1.0 CG E:ASN84 3.0 0.8 1.0 CG E:HIS186 3.1 0.8 1.0 CG E:ASP49 3.1 0.6 1.0 CD2 E:HIS158 3.1 0.4 1.0 O E:HOH503 3.3 65.3 1.0 ND2 E:ASN84 3.4 0.4 1.0 CA E:HIS186 3.5 0.5 1.0 OD2 E:ASP49 3.5 0.6 1.0 CB E:HIS186 3.6 0.0 1.0 ND1 E:HIS158 3.8 0.6 1.0 NE2 E:HIS186 4.0 0.9 1.0 O E:HIS186 4.0 0.7 1.0 CG E:HIS158 4.1 0.2 1.0 CD2 E:HIS186 4.1 0.2 1.0 OD2 E:ASP8 4.2 85.8 1.0 C E:HIS186 4.2 0.2 1.0 OD1 E:ASP8 4.3 0.3 1.0 N E:ASN84 4.3 0.5 1.0 CB E:ASN84 4.3 0.9 1.0 CB E:ASP49 4.4 0.3 1.0 N E:HIS186 4.5 0.8 1.0 CG E:ASP8 4.7 0.0 1.0 CA E:ASN84 5.0 0.2 1.0

Magnesium binding site 10 out of 12 in the Crystal Structure of MJMRE11-DNA2 Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of MJMRE11-DNA2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg402 b:0.0 occ:1.00 OD2 E:ASP8 2.1 85.8 1.0 OD1 E:ASP49 2.2 0.3 1.0 NE2 E:HIS188 2.5 1.0 1.0 O E:HOH503 2.7 65.3 1.0 NE2 E:HIS10 2.8 0.7 1.0 MG E:MG401 2.8 70.6 1.0 CG E:ASP8 3.1 0.0 1.0 CE1 E:HIS10 3.2 0.6 1.0 CD2 E:HIS188 3.3 0.4 1.0 CG E:ASP49 3.3 0.6 1.0 OD1 E:ASP8 3.5 0.3 1.0 CE1 E:HIS188 3.5 0.6 1.0 CB E:ASP49 4.0 0.3 1.0 ND1 E:HIS186 4.0 0.1 1.0 CD2 E:HIS10 4.1 0.1 1.0 O E:HIS186 4.1 0.7 1.0 OD2 E:ASP49 4.3 0.6 1.0 CE1 E:HIS158 4.3 0.5 1.0 OD1 E:ASN84 4.3 0.8 1.0 NE2 E:HIS158 4.4 0.0 1.0 CB E:ASP8 4.4 0.3 1.0 ND1 E:HIS10 4.5 0.8 1.0 CE1 E:HIS186 4.5 0.6 1.0 CG E:HIS188 4.5 0.9 1.0 ND2 E:ASN84 4.5 0.4 1.0 C E:HIS186 4.5 0.2 1.0 ND1 E:HIS188 4.6 0.2 1.0 CA E:HIS186 4.6 0.5 1.0 NE2 E:HIS85 4.7 0.5 1.0 CD2 E:HIS85 4.8 0.9 1.0 CG E:ASN84 4.9 0.8 1.0 CG E:HIS10 4.9 0.8 1.0 O E:GLY185 5.0 0.4 1.0

S.Sung, F.Li, Y.B.Park, J.S.Kim, A.K.Kim, O.K.Song, J.Kim, J.Che, S.E.Lee, Y.Cho. Dna End Recognition By the MRE11 Nuclease Dimer: Insights Into Resection and Repair of Damaged Dna. Embo J. V. 33 2422 2014.
ISSN: ESSN 1460-2075
PubMed: 25107472
DOI: 10.15252/EMBJ.201488299