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Magnesium in PDB 1nzb: Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse

Protein crystallography data

The structure of Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse, PDB code: 1nzb was solved by E.Ennifar, J.E.W.Meyer, F.Buchholz, A.F.Stewart, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 108.890, 163.530, 195.790, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.7

Other elements in 1nzb:

The structure of Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse also contains other interesting chemical elements:

Iodine (I) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse (pdb code 1nzb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse, PDB code: 1nzb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1nzb

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Magnesium binding site 1 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg5308

b:49.3
occ:0.95
 N3 C:DG117 3.5 99.1 1.0
C2 C:DG117 3.5 89.3 1.0
N2 C:DG117 3.6 63.5 1.0
C4 C:DG117 4.1 0.2 1.0
N1 C:DG117 4.2 85.2 1.0
O2 C:DT116 4.3 45.8 1.0
O2 D:DC120 4.4 74.9 1.0
C2 D:DA121 4.4 55.2 1.0
O4' C:DG117 4.6 0.7 1.0
C2 C:DT116 4.7 37.2 1.0
C5 C:DG117 4.7 97.7 1.0
N3 D:DC120 4.8 69.5 1.0
N3 D:DA121 4.8 47.1 1.0
N9 C:DG117 4.8 0.4 1.0
C6 C:DG117 4.8 94.6 1.0
N1 D:DA121 4.9 50.6 1.0
N3 C:DT116 4.9 24.0 1.0
C2 D:DC120 4.9 69.5 1.0

Magnesium binding site 2 out of 10 in 1nzb

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Magnesium binding site 2 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5304

b:54.0
occ:0.98
 NE2 A:GLN156 3.2 56.8 1.0
OP2 D:DC106 3.5 35.0 1.0
NH2 A:ARG159 3.5 16.0 1.0
ND2 A:ASN160 3.6 32.6 1.0
CD A:GLN156 3.9 57.7 1.0
CG1 A:ILE264 4.2 21.9 1.0
CG A:GLN156 4.4 56.1 1.0
OD1 A:ASN160 4.4 42.4 1.0
CG A:ASN160 4.5 39.4 1.0
O A:GLY263 4.7 40.0 1.0
OE1 A:GLN156 4.7 57.0 1.0
CA A:ILE264 4.8 33.1 1.0
CZ A:ARG159 4.8 29.3 1.0
P D:DC106 4.8 37.7 1.0
CB A:ALA267 5.0 30.3 1.0

Magnesium binding site 3 out of 10 in 1nzb

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Magnesium binding site 3 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5305

b:42.6
occ:1.07
 C7 D:DT107 3.5 55.6 1.0
CA A:ALA260 3.9 37.8 1.0
CB A:ALA260 4.1 20.2 1.0
C6 D:DC106 4.2 26.3 1.0
C5 D:DC106 4.2 24.9 1.0
O A:ARG259 4.4 37.1 1.0
N A:ALA260 4.6 39.2 1.0
C5' D:DC106 4.6 23.1 1.0
CA A:GLY263 4.6 37.6 1.0
C A:ARG259 4.7 37.3 1.0
O5' D:DC106 4.8 33.6 1.0
O A:ALA260 4.9 44.6 1.0
C A:ALA260 4.9 39.4 1.0
C5 D:DT107 4.9 29.8 1.0

Magnesium binding site 4 out of 10 in 1nzb

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Magnesium binding site 4 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg5310

b:65.5
occ:1.06
 N7 D:DA105 2.8 35.7 1.0
N6 D:DA105 3.3 32.0 1.0
C5 D:DA105 3.7 32.4 1.0
C8 D:DA105 3.9 30.6 1.0
C6 D:DA105 3.9 23.9 1.0
N7 D:DA104 3.9 38.8 1.0
N4 D:DC106 4.0 39.4 1.0
C8 D:DA104 4.2 40.9 1.0
C5 D:DA104 4.8 39.5 1.0
C4 D:DC106 4.8 29.9 1.0
C4 D:DA105 4.9 35.3 1.0

Magnesium binding site 5 out of 10 in 1nzb

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Magnesium binding site 5 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg5306

b:69.1
occ:1.00
 C2 G:DG117 3.4 87.2 1.0
N3 G:DG117 3.5 91.3 1.0
N1 G:DG117 3.5 85.0 1.0
C4 G:DG117 3.6 91.4 1.0
C5 G:DG117 3.7 84.0 1.0
C6 G:DG117 3.8 79.0 1.0
N2 G:DG117 4.0 63.5 1.0
O2 G:DT116 4.1 56.2 1.0
N9 G:DG117 4.2 91.7 1.0
C2 H:DA121 4.4 54.1 1.0
C2 G:DT116 4.4 52.0 1.0
O6 G:DG117 4.5 65.4 1.0
N7 G:DG117 4.5 83.3 1.0
C8 G:DG117 4.7 87.0 1.0
N3 G:DT116 4.8 48.3 1.0
C1' G:DG117 4.9 90.7 1.0
O4' G:DG117 4.9 82.8 1.0
N1 H:DA121 4.9 50.5 1.0
O2 H:DC120 4.9 68.7 1.0
N1 G:DT116 4.9 53.4 1.0
N3 H:DA121 4.9 48.9 1.0

Magnesium binding site 6 out of 10 in 1nzb

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Magnesium binding site 6 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5301

b:70.3
occ:1.00
 ND1 A:HIS40 2.7 41.9 1.0
CE1 A:HIS40 3.5 36.8 1.0
O4 C:DT125 3.6 51.8 1.0
CG A:HIS40 3.6 43.8 1.0
C7 C:DT125 3.8 57.1 1.0
CB A:HIS40 3.9 43.4 1.0
CD A:LYS43 4.0 73.2 1.0
CA A:HIS40 4.1 40.6 1.0
CB A:LYS43 4.2 42.6 1.0
O A:HIS40 4.4 42.5 1.0
O4 D:DT111 4.4 38.5 1.0
C4 C:DT125 4.5 41.0 1.0
NE2 A:HIS40 4.6 35.8 1.0
CG A:LYS43 4.6 63.5 1.0
CD2 A:HIS40 4.7 33.5 1.0
C5 C:DT125 4.7 35.2 1.0
C A:HIS40 4.7 41.4 1.0
N6 C:DA126 4.8 44.5 1.0

Magnesium binding site 7 out of 10 in 1nzb

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Magnesium binding site 7 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5302

b:44.2
occ:1.00
 NE2 A:HIS269 3.3 19.9 1.0
CD2 A:LEU135 4.0 24.9 1.0
CE1 A:TYR273 4.1 30.5 1.0
CD2 A:HIS269 4.1 24.2 1.0
CD1 A:TYR273 4.1 32.8 1.0
CE1 A:HIS269 4.2 26.5 1.0
CZ A:TYR273 4.3 33.8 1.0
CG A:TYR273 4.4 34.8 1.0
CE2 A:TYR273 4.5 30.1 1.0
CD2 A:TYR273 4.5 30.5 1.0
CG A:LEU135 4.9 20.6 1.0
CD1 A:LEU135 4.9 4.3 1.0

Magnesium binding site 8 out of 10 in 1nzb

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Magnesium binding site 8 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg5303

b:44.4
occ:1.06
 OD2 A:ASP141 3.8 45.4 1.0
OE2 A:GLU138 4.3 64.8 1.0
OG1 A:THR140 4.7 38.1 1.0
CG A:ASP141 4.7 50.0 1.0
CD A:GLU138 4.9 62.8 1.0
OD1 A:ASP141 4.9 56.7 1.0

Magnesium binding site 9 out of 10 in 1nzb

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Magnesium binding site 9 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg5307

b:62.5
occ:0.65
 O F:GLN89 4.0 49.3 1.0
OP2 H:DC120 4.1 66.8 1.0
ND2 F:ASN96 4.3 26.1 1.0
CA F:GLY93 4.4 43.9 1.0
C6 H:DC120 4.5 67.5 1.0
N F:GLY93 4.7 41.8 1.0
C5 H:DC120 4.8 74.6 1.0
CD2 F:LEU92 4.8 28.7 1.0
N7 H:DA121 4.8 44.5 1.0
CG F:LEU92 4.8 26.9 1.0
C2' H:DA119 4.9 60.2 1.0

Magnesium binding site 10 out of 10 in 1nzb

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Magnesium binding site 10 out of 10 in the Crystal Structure of Wild Type Cre Recombinase-Loxp Synapse


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 Wild Type Cre Recombinase-Loxp Synapse within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg5309

b:44.4
occ:0.60
 NE2 F:HIS91 2.3 38.2 1.0
OP2 G:DA112 2.8 75.1 1.0
CE1 F:HIS91 3.0 38.5 1.0
CD2 F:HIS91 3.5 39.5 1.0
CG2 F:THR87 3.7 28.0 1.0
C7 G:DT113 3.8 71.9 1.0
C2' G:DT111 4.0 70.3 1.0
P G:DA112 4.0 76.6 1.0
O5' G:DA112 4.1 68.1 1.0
C8 G:DA112 4.1 47.6 1.0
ND1 F:HIS91 4.2 40.0 1.0
CG F:HIS91 4.5 34.8 1.0
C2' G:DA112 4.7 46.5 1.0
C3' G:DT111 4.7 73.7 1.0
N7 G:DA112 4.7 46.0 1.0
O3' G:DT111 4.9 71.6 1.0
CE F:MET44 5.0 16.4 1.0

Reference:

E.Ennifar, J.E.W.Meyer, F.Buchholz, A.F.Stewart, D.Suck. Crystal Structure of A Wild-Type Cre Recombinase-Loxp Synapse Reveals A Novel Spacer Conformation Suggesting An Alternative Mechanism For Dna Cleavage Activation Nucleic Acids Res. V. 31 5449 2003.
ISSN: ISSN 0305-1048
PubMed: 12954782
DOI: 10.1093/NAR/GKG732
Page generated: Tue Aug 13 10:28:12 2024

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