Atomistry » Magnesium » PDB 7r41-7rax » 7r6v
Atomistry »
  Magnesium »
    PDB 7r41-7rax »
      7r6v »

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

Go back to Magnesium Binding Sites List in 7r6v
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

Go back to Magnesium Binding Sites List in 7r6v
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

Go back to Magnesium Binding Sites List in 7r6v
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

Go back to Magnesium Binding Sites List in 7r6v
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

Go back to Magnesium Binding Sites List in 7r6v
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

Go back to Magnesium Binding Sites List in 7r6v
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy