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Magnesium in PDB 8ili: The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex

Enzymatic activity of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex

All present enzymatic activity of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex, PDB code: 8ili was solved by T.Qin, J.H.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.42, 87.344, 87.48, 90, 91.16, 90
R / Rfree (%) 21.5 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex (pdb code 8ili). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex, PDB code: 8ili:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8ili

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Magnesium binding site 1 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg101

b:27.9
occ:1.00
 OP1 F:7S88 1.7 22.1 1.0
OD2 B:ASP100 2.1 16.8 1.0
OD1 B:ASP51 2.1 16.3 1.0
OD1 B:ASP49 2.3 22.0 1.0
MG B:MG204 2.6 10.2 1.0
P F:7S88 2.9 20.9 1.0
CG B:ASP49 3.0 22.3 1.0
CG B:ASP51 3.0 16.4 1.0
CG B:ASP100 3.1 16.9 1.0
O3' F:DC7 3.1 20.4 1.0
OD2 B:ASP51 3.2 16.4 1.0
OD2 B:ASP49 3.4 22.8 1.0
CB B:ASP100 3.5 16.7 1.0
O B:HOH351 3.7 22.9 1.0
O5' F:7S88 4.0 19.7 1.0
CB B:ASP49 4.1 22.0 1.0
C5' F:7S88 4.1 18.2 1.0
OD1 B:ASP100 4.2 16.4 1.0
SE1 F:7S88 4.3 27.6 1.0
O B:HOH380 4.3 21.3 1.0
CB B:ASP51 4.4 16.2 1.0
C3' F:DC7 4.5 20.0 1.0
O B:HOH301 4.6 30.0 1.0
NE2 B:GLN98 4.8 26.1 1.0
CZ B:PHE102 4.8 13.0 1.0
O B:VAL50 4.8 16.7 1.0
CA B:ASP100 4.9 16.9 1.0
CA B:ASP51 4.9 16.2 1.0
CE2 B:PHE102 4.9 12.9 1.0
C B:VAL50 5.0 17.2 1.0

Magnesium binding site 2 out of 8 in 8ili

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Magnesium binding site 2 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:6.5
occ:1.00
 OD2 A:ASP51 2.0 9.9 1.0
O A:HOH378 2.1 26.7 1.0
OP1 E:7S88 2.2 13.9 1.0
OD1 A:ASP49 2.4 14.2 1.0
O A:HOH301 2.4 29.0 1.0
O A:HOH302 2.6 23.3 1.0
MG A:MG204 2.8 6.3 1.0
CG A:ASP51 3.0 9.5 1.0
OD1 A:ASP51 3.3 9.5 1.0
CG A:ASP49 3.3 14.3 1.0
P E:7S88 3.5 13.7 1.0
OD2 A:ASP49 3.5 14.8 1.0
O A:HOH331 3.7 41.0 1.0
O A:HOH418 4.0 13.4 1.0
O5' E:7S88 4.1 13.1 1.0
C5' E:7S88 4.1 12.0 1.0
OG A:SER39 4.2 14.3 1.0
N A:SER39 4.3 12.2 1.0
O A:ASP49 4.3 11.3 1.0
CB A:ASP51 4.3 9.3 1.0
SE1 E:7S88 4.5 19.2 1.0
CA A:GLY38 4.6 10.5 1.0
O A:HOH326 4.6 32.8 1.0
O3' E:DC7 4.6 13.0 1.0
CB A:ASP49 4.6 13.6 1.0
C A:ASP49 4.7 11.9 1.0
OD2 A:ASP100 4.8 9.7 1.0
CB A:SER39 4.9 13.6 1.0
N A:ASP49 4.9 14.0 1.0

Magnesium binding site 3 out of 8 in 8ili

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Magnesium binding site 3 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:6.3
occ:1.00
 OP1 E:7S88 2.0 13.9 1.0
OD1 A:ASP51 2.1 9.5 1.0
OD2 A:ASP100 2.1 9.7 1.0
OD1 A:ASP49 2.2 14.2 1.0
MG A:MG203 2.8 6.5 1.0
CG A:ASP49 2.9 14.3 1.0
CG A:ASP51 3.0 9.5 1.0
O3' E:DC7 3.1 13.0 1.0
P E:7S88 3.1 13.7 1.0
CG A:ASP100 3.1 9.3 1.0
OD2 A:ASP51 3.2 9.9 1.0
OD2 A:ASP49 3.3 14.8 1.0
CB A:ASP100 3.4 8.9 1.0
O A:HOH302 3.9 23.3 1.0
CB A:ASP49 4.0 13.6 1.0
O5' E:7S88 4.1 13.1 1.0
C5' E:7S88 4.2 12.0 1.0
OD1 A:ASP100 4.2 9.9 1.0
CB A:ASP51 4.4 9.3 1.0
C3' E:DC7 4.4 13.3 1.0
SE1 E:7S88 4.5 19.2 1.0
O A:HOH378 4.6 26.7 1.0
CZ A:PHE102 4.7 6.9 1.0
NE2 A:GLN98 4.7 12.4 1.0
O A:VAL50 4.8 9.6 1.0
CA A:ASP100 4.8 8.5 1.0
O A:HOH301 4.8 29.0 1.0
CE2 A:PHE102 4.8 6.9 1.0
CA A:ASP51 4.9 9.2 1.0
C4' E:DC7 5.0 14.1 1.0
C A:VAL50 5.0 9.9 1.0

Magnesium binding site 4 out of 8 in 8ili

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Magnesium binding site 4 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg204

b:10.2
occ:1.00
 O B:HOH380 2.1 21.3 1.0
OD2 B:ASP51 2.2 16.4 1.0
OP1 F:7S88 2.2 22.1 1.0
OD1 B:ASP49 2.2 22.0 1.0
O B:HOH351 2.3 22.9 1.0
O B:HOH301 2.4 30.0 1.0
MG F:MG101 2.6 27.9 1.0
CG B:ASP51 3.0 16.4 1.0
OD1 B:ASP51 3.2 16.3 1.0
CG B:ASP49 3.2 22.3 1.0
P F:7S88 3.5 20.9 1.0
OD2 B:ASP49 3.6 22.8 1.0
O B:HOH312 4.0 38.0 1.0
O5' F:7S88 4.1 19.7 1.0
C5' F:7S88 4.1 18.2 1.0
O B:HOH373 4.3 20.1 1.0
SE1 F:7S88 4.4 27.6 1.0
OG B:SER39 4.4 21.7 1.0
CB B:ASP51 4.4 16.2 1.0
O B:ASP49 4.4 21.4 1.0
N B:SER39 4.4 20.1 1.0
OD2 B:ASP100 4.5 16.8 1.0
CB B:ASP49 4.6 22.0 1.0
O3' F:DC7 4.7 20.4 1.0
CA B:GLY38 4.7 17.7 1.0
C B:ASP49 4.7 20.9 1.0
N B:ASP49 5.0 22.9 1.0

Magnesium binding site 5 out of 8 in 8ili

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Magnesium binding site 5 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:12.2
occ:1.00
 OP1 G:7S88 2.0 19.6 1.0
OD1 C:ASP51 2.0 13.4 1.0
OD2 C:ASP100 2.0 12.8 1.0
OD1 C:ASP49 2.2 18.5 1.0
MG C:MG203 2.7 8.2 1.0
CG C:ASP51 2.8 13.4 1.0
CG C:ASP49 2.8 18.7 1.0
OD2 C:ASP51 3.0 13.3 1.0
CG C:ASP100 3.0 12.7 1.0
P G:7S88 3.2 19.6 1.0
OD2 C:ASP49 3.2 19.3 1.0
O3' G:DC7 3.3 19.0 1.0
CB C:ASP100 3.4 12.1 1.0
CB C:ASP49 3.9 18.3 1.0
O C:HOH368 4.1 30.1 1.0
O5' G:7S88 4.1 18.4 1.0
OD1 C:ASP100 4.2 12.9 1.0
C5' G:7S88 4.2 16.6 1.0
CB C:ASP51 4.2 13.2 1.0
O C:HOH372 4.5 22.3 1.0
O C:HOH301 4.5 31.0 1.0
SE1 G:7S88 4.6 25.0 1.0
O C:VAL50 4.6 13.4 1.0
CA C:ASP51 4.7 13.0 1.0
C3' G:DC7 4.7 19.9 1.0
C C:VAL50 4.8 14.1 1.0
CA C:ASP100 4.8 11.8 1.0
CZ C:PHE102 4.8 9.5 1.0
NE2 C:GLN98 4.8 17.2 1.0
N C:ASP51 4.8 13.5 1.0
CE2 C:PHE102 4.9 9.4 1.0
N C:ASP100 5.0 12.0 1.0
C C:ASP49 5.0 17.2 1.0

Magnesium binding site 6 out of 8 in 8ili

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Magnesium binding site 6 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg203

b:8.2
occ:1.00
 OD2 C:ASP51 2.0 13.3 1.0
O C:HOH372 2.1 22.3 1.0
OD1 C:ASP49 2.2 18.5 1.0
OP1 G:7S88 2.2 19.6 1.0
O C:HOH301 2.3 31.0 1.0
O C:HOH368 2.6 30.1 1.0
MG C:MG202 2.7 12.2 1.0
CG C:ASP51 3.0 13.4 1.0
CG C:ASP49 3.2 18.7 1.0
OD1 C:ASP51 3.2 13.4 1.0
OD2 C:ASP49 3.5 19.3 1.0
P G:7S88 3.6 19.6 1.0
O C:HOH342 4.0 25.2 1.0
O5' G:7S88 4.0 18.4 1.0
C5' G:7S88 4.1 16.6 1.0
O C:HOH393 4.2 19.3 1.0
OG C:SER39 4.3 20.1 1.0
N C:SER39 4.3 17.9 1.0
O C:ASP49 4.4 17.2 1.0
CB C:ASP51 4.4 13.2 1.0
O C:HOH398 4.4 37.3 1.0
SE1 G:7S88 4.5 25.0 1.0
CB C:ASP49 4.5 18.3 1.0
CA C:GLY38 4.6 15.4 1.0
OD2 C:ASP100 4.6 12.8 1.0
C C:ASP49 4.7 17.2 1.0
O3' G:DC7 4.7 19.0 1.0
N C:ASP49 4.9 18.8 1.0
CB C:SER39 4.9 19.3 1.0
CA C:ASP49 5.0 18.1 1.0

Magnesium binding site 7 out of 8 in 8ili

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Magnesium binding site 7 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg203

b:9.1
occ:1.00
 OP1 H:7S88 2.0 20.4 1.0
OD2 D:ASP49 2.0 29.2 1.0
OD2 D:ASP100 2.2 25.4 1.0
OD1 D:ASP51 2.2 22.0 1.0
MG D:MG204 2.3 22.4 1.0
O H:HOH120 2.7 47.1 1.0
CG D:ASP51 3.1 21.9 1.0
CG D:ASP49 3.1 30.1 1.0
OD2 D:ASP51 3.2 22.6 1.0
CG D:ASP100 3.2 26.0 1.0
P H:7S88 3.4 20.8 1.0
OD1 D:ASP49 3.6 32.4 1.0
CB D:ASP100 3.7 25.2 1.0
O3' H:DC7 4.1 20.6 1.0
OD1 D:ASP100 4.3 26.0 1.0
CB D:ASP49 4.3 29.8 1.0
O5' H:7S88 4.3 19.1 1.0
C5' H:7S88 4.4 17.7 1.0
CB D:ASP51 4.5 21.5 1.0
SE1 H:7S88 4.5 27.3 1.0
O H:HOH126 4.6 32.2 1.0
NE2 D:GLN98 4.8 39.8 1.0
CA D:ASP51 5.0 21.2 1.0

Magnesium binding site 8 out of 8 in 8ili

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Magnesium binding site 8 out of 8 in the The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of The Crystal Structure of Dg(Se-Rp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg204

b:22.4
occ:1.00
 MG D:MG203 2.3 9.1 1.0
OD2 D:ASP51 2.3 22.6 1.0
O H:HOH126 2.4 32.2 1.0
OP1 H:7S88 2.5 20.4 1.0
OD2 D:ASP49 3.0 29.2 1.0
CG D:ASP51 3.1 21.9 1.0
OD1 D:ASP51 3.1 22.0 1.0
P H:7S88 3.6 20.8 1.0
O H:HOH120 3.8 47.1 1.0
O5' H:7S88 3.8 19.1 1.0
CG D:ASP49 3.9 30.1 1.0
C5' H:7S88 4.0 17.7 1.0
OD1 D:ASP49 4.1 32.4 1.0
SE1 H:7S88 4.3 27.3 1.0
OD2 D:ASP100 4.5 25.4 1.0
O D:HOH362 4.5 28.3 1.0
O D:HOH346 4.5 27.8 1.0
CB D:ASP51 4.5 21.5 1.0
OG D:SER39 4.6 23.5 1.0
N D:SER39 4.6 22.0 1.0
CA D:GLY38 4.8 20.3 1.0
O H:HOH128 4.8 28.4 1.0
O3' H:DC7 4.9 20.6 1.0

Reference:

T.Qin, B.Hu, Q.Zhao, Y.Wang, S.Wang, D.Luo, J.Lyu, Y.Chen, J.Gan, Z.Huang. Structural Insight Into Polymerase Mechanism Via A Chiral Center Generated with A Single Selenium Atom. Int J Mol Sci V. 24 2023.
ISSN: ESSN 1422-0067
PubMed: 37958741
DOI: 10.3390/IJMS242115758
Page generated: Fri Oct 4 09:29:07 2024

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