Magnesium in PDB 7r6t: Human Exog Complexed with Drp-Containing Dna

Protein crystallography data

The structure of Human Exog Complexed with Drp-Containing Dna, PDB code: 7r6t 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) 37.97 / 2.90
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 73.252, 100.056, 174.902, 90, 90, 90
R / Rfree (%) 22.9 / 28.6

Other elements in 7r6t:

The structure of Human Exog Complexed with Drp-Containing Dna also contains other interesting chemical elements:

Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Exog Complexed with Drp-Containing Dna (pdb code 7r6t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Exog Complexed with Drp-Containing Dna, PDB code: 7r6t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7r6t

Go back to Magnesium Binding Sites List in 7r6t
Magnesium binding site 1 out of 4 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
F:Mg101

b:53.2
occ:1.00
 O D:HOH405 2.0 65.7 1.0
O3' F:DT2 2.0 59.0 1.0
OP1 F:DG3 2.0 51.9 1.0
ND2 D:ASN171 2.3 60.0 1.0
O D:HOH401 2.5 51.0 1.0
P F:DG3 2.5 48.0 1.0
CG D:ASN171 3.1 59.4 1.0
OD1 D:ASN171 3.1 64.8 1.0
O5' F:DG3 3.3 54.5 1.0
C3' F:DT2 3.3 70.6 1.0
N D:ALA140 3.6 48.4 1.0
OP2 F:DG3 3.8 57.2 1.0
C4' F:DT2 3.8 64.5 1.0
O D:ALA140 4.0 57.3 1.0
CA D:GLY139 4.1 52.1 1.0
C2' F:DT2 4.2 74.7 1.0
C5' F:DT2 4.2 70.9 1.0
C D:GLY139 4.3 44.8 1.0
OE2 D:GLU179 4.4 62.2 1.0
CA D:ALA140 4.5 46.1 1.0
OE1 D:GLN166 4.5 50.0 1.0
CB D:ASN171 4.5 43.2 1.0
CB D:ALA140 4.6 24.5 1.0
O D:ASN171 4.6 48.8 1.0
CD1 D:TRP175 4.6 53.0 1.0
C5' F:DG3 4.7 53.3 1.0
C D:ALA140 4.7 41.5 1.0
OE1 D:GLU179 4.8 62.0 1.0
O D:ARG138 4.8 50.7 1.0
O5' F:DT2 4.9 57.9 1.0
NE1 D:TRP175 5.0 50.8 1.0

Magnesium binding site 2 out of 4 in 7r6t

Go back to Magnesium Binding Sites List in 7r6t
Magnesium binding site 2 out of 4 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
A:Mg101

b:114.8
occ:1.00
 C5' A:DC5 3.0 161.3 1.0
C4' A:DC5 3.5 160.6 1.0
C3' A:DC5 3.6 159.9 1.0
OP1 A:DG6 3.9 170.6 1.0
O5' A:DC5 4.2 159.6 1.0
O3' A:DC5 4.4 168.3 1.0
P A:DG6 4.4 182.9 1.0
OP1 A:DC5 4.4 165.3 1.0
OP2 A:DG6 4.5 172.6 1.0
C2' A:DC5 4.7 159.2 1.0
P A:DC5 4.9 162.2 1.0
O4' A:DC5 4.9 157.5 1.0

Magnesium binding site 3 out of 4 in 7r6t

Go back to Magnesium Binding Sites List in 7r6t
Magnesium binding site 3 out of 4 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
E:Mg101

b:53.7
occ:1.00
 OP1 E:DG3 1.9 57.2 1.0
O C:HOH404 2.0 45.9 1.0
O C:HOH401 2.1 60.5 1.0
OD1 C:ASN171 2.1 57.8 1.0
O3' E:DT2 2.1 61.0 1.0
P E:DG3 2.4 49.3 1.0
CG C:ASN171 3.0 49.5 1.0
O5' E:DG3 3.1 47.1 1.0
ND2 C:ASN171 3.3 56.5 1.0
C3' E:DT2 3.5 64.9 1.0
OP2 E:DG3 3.8 57.5 1.0
N C:ALA140 3.8 51.9 1.0
C4' E:DT2 4.0 52.5 1.0
CA C:GLY139 4.1 39.2 1.0
O C:ALA140 4.2 47.9 1.0
C2' E:DT2 4.3 58.4 1.0
CB C:ASN171 4.3 43.4 1.0
OE1 C:GLN166 4.4 44.1 1.0
O C:ASN171 4.4 48.9 1.0
OE2 C:GLU179 4.4 51.2 1.0
C C:GLY139 4.4 49.0 1.0
C5' E:DG3 4.5 49.0 1.0
C5' E:DT2 4.6 45.3 1.0
CD1 C:TRP175 4.7 46.4 1.0
OE1 C:GLU179 4.7 57.7 1.0
CA C:ASN171 4.7 47.1 1.0
CA C:ALA140 4.8 43.5 1.0
O C:ARG138 4.8 71.2 1.0
C C:ASN171 4.8 57.8 1.0
CB C:ALA140 4.9 28.6 1.0
C C:ALA140 5.0 41.8 1.0

Magnesium binding site 4 out of 4 in 7r6t

Go back to Magnesium Binding Sites List in 7r6t
Magnesium binding site 4 out of 4 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
L:Mg401

b:95.9
occ:1.00
 OD1 L:ASN171 2.1 124.8 1.0
OP1 M:DG3 3.0 117.7 1.0
CG L:ASN171 3.2 131.9 1.0
O3' M:DT2 3.3 132.6 1.0
O L:ALA140 3.4 116.8 1.0
OE2 L:GLU179 3.5 126.0 1.0
N L:ALA140 3.6 107.1 1.0
P M:DG3 3.7 120.8 1.0
OE1 L:GLU179 3.9 133.7 1.0
ND2 L:ASN171 4.0 135.4 1.0
CD L:GLU179 4.1 131.3 1.0
C L:ALA140 4.2 97.4 1.0
CB L:ALA140 4.2 89.0 1.0
CA L:ALA140 4.2 103.6 1.0
CD1 L:TRP175 4.3 107.7 1.0
OE1 L:GLN166 4.4 98.1 1.0
CB L:ASN171 4.4 124.2 1.0
OP2 M:DG3 4.4 123.5 1.0
C5' M:DT2 4.4 112.6 1.0
C3' M:DT2 4.4 134.4 1.0
NE1 L:TRP175 4.4 100.2 1.0
C4' M:DT2 4.5 122.8 1.0
C L:GLY139 4.6 103.7 1.0
CA L:GLY139 4.6 110.7 1.0

Reference:

M.R.Szymanski, Y.W.Yin. Human Exog Possesses Strong Ap Hydrolysis Activity To Be Published.
Page generated: Thu Apr 6 21:32:54 2023

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