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Magnesium in PDB 7r6v: Human Exog Complexed with Drp-Containing Dna

Protein crystallography data

The structure of Human Exog Complexed with Drp-Containing Dna, PDB code: 7r6v was solved by M.R.Szymanski, Y.W.Yin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.16
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 73.749, 79.085, 79.635, 69.05, 65.02, 89.72
R / Rfree (%) 20 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Exog Complexed with Drp-Containing Dna (pdb code 7r6v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Human Exog Complexed with Drp-Containing Dna, PDB code: 7r6v:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7r6v

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Magnesium binding site 1 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:97.7
occ:1.00
 NH2 D:ARG291 1.9 74.4 1.0
NE D:ARG291 1.9 70.6 1.0
N D:ASN292 1.9 77.5 1.0
CZ D:ARG291 2.2 75.0 1.0
CB D:ARG291 2.6 59.5 1.0
C D:ARG291 2.7 48.1 1.0
CA D:ARG291 2.7 57.8 1.0
O D:HOH560 3.0 51.9 1.0
CA D:ASN292 3.0 42.8 1.0
O D:ASN292 3.0 48.3 1.0
CD D:ARG291 3.2 70.1 1.0
C D:ASN292 3.4 49.3 1.0
NH1 D:ARG291 3.4 62.2 1.0
CB D:ASN292 3.5 50.8 1.0
CG D:ARG291 3.5 55.7 1.0
O D:ARG291 3.8 48.5 1.0
CB D:SER295 3.9 54.9 1.0
N D:VAL296 4.1 43.6 1.0
N D:ARG291 4.2 46.5 1.0
CB D:VAL296 4.3 48.6 1.0
OG D:SER295 4.6 63.3 1.0
N D:ILE293 4.6 37.4 1.0
CG1 D:VAL296 4.7 50.0 1.0
CA D:SER295 4.8 48.3 1.0
C D:SER295 4.8 45.0 1.0
CA D:VAL296 4.8 50.4 1.0
CG D:ASN292 4.9 41.2 1.0
O D:ILE290 5.0 54.9 1.0
N D:SER295 5.0 47.8 1.0

Magnesium binding site 2 out of 6 in 7r6v

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Magnesium binding site 2 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:30.4
occ:1.00
 ND2 D:ASN171 1.9 27.0 1.0
O F:HOH203 2.1 28.7 1.0
O D:HOH528 2.1 27.5 1.0
O3' F:DT2 2.3 32.8 1.0
OP1 F:DG3 2.4 25.4 1.0
P F:DG3 2.8 32.4 1.0
CG D:ASN171 3.2 33.1 1.0
O5' F:DG3 3.3 27.8 1.0
C3' F:DT2 3.4 28.2 1.0
O D:ASN171 3.6 20.8 1.0
C2' F:DT2 3.8 32.7 1.0
C4' F:DT2 3.8 31.8 1.0
CA D:ASN171 3.9 28.4 1.0
OE1 D:GLN166 3.9 25.1 1.0
CB D:ASN171 4.0 27.0 1.0
OD1 D:ASN171 4.0 50.8 1.0
C D:ASN171 4.0 27.4 1.0
OP2 F:DG3 4.2 30.6 1.0
N D:HIS140 4.4 26.5 1.0
OE1 D:GLU179 4.4 27.4 1.0
CA D:GLY139 4.4 27.6 1.0
CD D:GLN166 4.5 24.9 1.0
CD1 D:TRP175 4.6 24.6 1.0
OE2 D:GLU179 4.6 33.8 1.0
C5' F:DT2 4.7 26.8 1.0
C5' F:DG3 4.7 28.5 1.0
O D:HIS140 4.7 30.3 1.0
NE2 D:GLN166 4.7 24.5 1.0
O F:HOH206 4.8 35.8 1.0
C D:GLY139 4.9 25.1 1.0
CD D:GLU179 4.9 33.8 1.0
C1' F:DT2 5.0 33.6 1.0
O4' F:DT2 5.0 28.0 1.0

Magnesium binding site 3 out of 6 in 7r6v

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Magnesium binding site 3 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg101

b:30.1
occ:1.00
 ND2 E:ASN171 1.9 41.6 1.0
OD1 E:ASN171 2.0 55.0 1.0
CG E:ASN171 2.2 28.1 1.0
OP1 H:DG3 2.2 31.0 1.0
O3' H:DT2 2.3 36.1 1.0
O E:HOH410 2.4 25.1 1.0
O E:HOH418 2.4 28.0 1.0
O E:HOH428 2.4 29.3 1.0
P H:DG3 2.8 30.9 1.0
O5' H:DG3 3.4 34.9 1.0
CB E:ASN171 3.6 29.5 1.0
C3' H:DT2 3.6 34.8 1.0
N E:HIS140 4.0 24.2 1.0
O E:ASN171 4.0 29.2 1.0
OE1 E:GLN166 4.0 30.9 1.0
C4' H:DT2 4.1 35.0 1.0
OP2 H:DG3 4.1 34.1 1.0
CA E:ASN171 4.2 33.9 1.0
CA E:GLY139 4.2 26.0 1.0
C2' H:DT2 4.2 32.8 1.0
O E:HIS140 4.3 32.0 1.0
OE2 E:GLU179 4.4 33.7 1.0
C E:ASN171 4.4 32.1 1.0
OE1 E:GLU179 4.4 29.2 1.0
CD1 E:TRP175 4.5 27.6 1.0
C E:GLY139 4.5 29.4 1.0
O H:HOH206 4.6 32.4 1.0
CD E:GLN166 4.7 34.1 1.0
C5' H:DT2 4.7 29.7 1.0
C5' H:DG3 4.8 36.8 1.0
CD E:GLU179 4.8 32.9 1.0
NE2 E:GLN166 4.9 30.7 1.0
CA E:HIS140 4.9 27.3 1.0
O E:ARG138 4.9 30.9 1.0
CB E:HIS140 5.0 25.1 1.0

Magnesium binding site 4 out of 6 in 7r6v

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Magnesium binding site 4 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg401

b:31.8
occ:1.00
 ND2 I:ASN171 1.9 31.7 1.0
O K:HOH101 2.2 27.1 1.0
OP1 K:DG3 2.4 27.5 1.0
O3' K:DT2 2.4 34.2 1.0
O I:HOH538 2.4 26.5 1.0
CB I:ASN171 2.5 36.8 1.0
CG I:ASN171 2.5 35.4 1.0
P K:DG3 2.8 33.5 1.0
O I:HOH506 2.9 43.8 1.0
O5' K:DG3 3.0 33.2 1.0
O I:ASN171 3.5 31.9 1.0
C3' K:DT2 3.6 34.5 1.0
CA I:ASN171 3.7 36.3 1.0
OD1 I:ASN171 3.7 43.1 1.0
C I:ASN171 3.8 31.3 1.0
OE1 I:GLN166 3.8 30.9 1.0
C2' K:DT2 3.9 37.6 1.0
C4' K:DT2 4.1 32.8 1.0
CA I:GLY139 4.1 26.3 1.0
OP2 K:DG3 4.3 38.2 1.0
N I:HIS140 4.4 27.3 1.0
C5' K:DG3 4.5 34.4 1.0
CD I:GLN166 4.5 36.4 1.0
O I:ARG138 4.7 27.6 1.0
N I:SER172 4.7 28.5 1.0
C I:GLY139 4.7 26.5 1.0
CD1 I:TRP175 4.8 28.4 1.0
N I:ASN171 4.9 29.5 1.0
NE2 I:GLN166 4.9 31.7 1.0
O I:HIS140 4.9 30.6 1.0
OE1 I:GLU179 5.0 28.5 1.0

Magnesium binding site 5 out of 6 in 7r6v

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Magnesium binding site 5 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg402

b:71.0
occ:1.00
 N I:GLY71 1.9 37.7 1.0
CA I:GLY71 2.4 33.0 1.0
OE1 I:GLU73 2.4 43.8 1.0
C I:THR70 3.1 37.3 1.0
C I:GLY71 3.3 36.1 1.0
N I:THR72 3.3 33.8 1.0
N I:THR70 3.4 36.9 1.0
CD I:GLU73 3.5 50.7 1.0
OG1 I:THR70 3.6 40.0 1.0
CA I:THR70 3.7 36.7 1.0
OE2 I:GLU73 3.8 58.9 1.0
O I:THR70 4.1 32.2 1.0
C I:LEU69 4.2 31.0 1.0
CB I:THR70 4.3 40.8 1.0
O I:GLY71 4.4 30.6 1.0
CB I:LEU69 4.5 31.5 1.0
N I:GLU73 4.5 36.0 1.0
CA I:LEU69 4.5 29.8 1.0
CA I:THR72 4.6 32.8 1.0
CG I:GLU73 4.8 46.8 1.0
OG1 I:THR72 4.9 38.9 1.0
CD2 I:LEU69 5.0 38.6 1.0

Magnesium binding site 6 out of 6 in 7r6v

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Magnesium binding site 6 out of 6 in the Human Exog Complexed with Drp-Containing Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Exog Complexed with Drp-Containing Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg101

b:33.2
occ:1.00
 ND2 G:ASN171 1.9 39.5 1.0
OD1 G:ASN171 2.0 53.3 1.0
OP1 J:DG3 2.0 30.6 1.0
O3' J:DT2 2.1 35.7 1.0
CG G:ASN171 2.2 35.1 1.0
P J:DG3 2.5 27.3 1.0
O G:HOH514 2.6 28.7 1.0
O G:HOH503 2.6 32.6 1.0
O G:HOH518 2.7 31.0 1.0
O5' J:DG3 3.1 30.4 1.0
C3' J:DT2 3.4 36.6 1.0
CB G:ASN171 3.7 29.9 1.0
N G:HIS140 3.9 24.6 1.0
OP2 J:DG3 3.9 35.1 1.0
C4' J:DT2 3.9 36.0 1.0
C2' J:DT2 4.0 37.1 1.0
O G:ASN171 4.1 32.8 1.0
OE1 G:GLN166 4.2 31.5 1.0
CA G:GLY139 4.2 27.1 1.0
O J:HOH206 4.2 27.5 1.0
O G:HIS140 4.3 31.5 1.0
CA G:ASN171 4.5 36.2 1.0
C G:GLY139 4.5 27.6 1.0
OE2 G:GLU179 4.5 33.6 1.0
C5' J:DG3 4.5 30.6 1.0
C G:ASN171 4.5 32.3 1.0
C5' J:DT2 4.6 30.4 1.0
OE1 G:GLU179 4.7 34.4 1.0
O G:ARG138 4.7 28.6 1.0
CA G:HIS140 4.8 26.2 1.0
CB G:HIS140 4.8 21.7 1.0
CD G:GLN166 4.9 33.0 1.0
CD1 G:TRP175 4.9 30.4 1.0

Reference:

M.R.Szymanski, Y.W.Yin. Human Exog Possesses Strong Ap Hydrolysis Activity To Be Published.
Page generated: Thu Oct 3 07:29:10 2024

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