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

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

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

Protein crystallography data

The structure of The Crystal Structure of Dg(Se-Sp)-Dna:Pol X Product Binary Complex, PDB code: 8ilh 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 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.471, 87.28, 87.056, 90, 91.15, 90
R / Rfree (%) 18.1 / 22.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Dg(Se-Sp)-Dna:Pol X Product Binary Complex (pdb code 8ilh). 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-Sp)-Dna:Pol X Product Binary Complex, PDB code: 8ilh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8ilh

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Magnesium binding site 1 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:4.8
occ:1.00
 O A:HOH303 2.1 25.9 1.0
SE1 E:8H2101 2.1 51.8 1.0
OD2 A:ASP51 2.2 12.4 1.0
OD1 A:ASP49 2.4 21.4 1.0
O A:HOH334 2.5 23.2 1.0
O3 A:SO4205 2.5 50.6 1.0
CG A:ASP51 3.2 10.9 1.0
MG A:MG202 3.3 11.8 1.0
S A:SO4205 3.3 49.0 1.0
O4 A:SO4205 3.3 45.0 1.0
CG A:ASP49 3.3 21.3 1.0
OD1 A:ASP51 3.4 12.3 1.0
O A:HOH343 3.5 33.0 1.0
O2 A:SO4205 3.6 50.2 1.0
OD2 A:ASP49 3.7 27.4 1.0
P E:8H2101 3.9 30.3 1.0
OG A:SER39 4.0 19.3 1.0
O A:HOH372 4.0 16.8 1.0
O A:ASP49 4.2 13.2 1.0
N A:SER39 4.3 13.4 1.0
O5' E:8H2101 4.3 20.7 1.0
C5' E:8H2101 4.4 20.1 1.0
CB A:ASP51 4.5 9.7 1.0
C A:ASP49 4.6 13.0 1.0
CB A:ASP49 4.6 17.4 1.0
N A:ASP49 4.6 15.7 1.0
CA A:GLY38 4.7 11.4 1.0
O1 A:SO4205 4.7 58.0 1.0
CB A:SER39 4.7 17.4 1.0
OP2 E:8H2101 4.8 14.4 1.0
CA A:ASP49 4.8 15.2 1.0
O3' E:DC7 4.9 21.1 1.0

Magnesium binding site 2 out of 8 in 8ilh

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Magnesium binding site 2 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:11.8
occ:1.00
 OD1 A:ASP51 2.0 12.3 1.0
SE1 E:8H2101 2.1 51.8 1.0
OD2 A:ASP100 2.2 13.8 1.0
OD1 A:ASP49 2.7 21.4 1.0
O3' E:DC7 2.9 21.1 1.0
CG A:ASP100 3.0 9.0 1.0
CG A:ASP51 3.1 10.9 1.0
P E:8H2101 3.1 30.3 1.0
CG A:ASP49 3.2 21.3 1.0
MG A:MG201 3.3 4.8 1.0
CB A:ASP100 3.4 11.3 1.0
OD2 A:ASP51 3.4 12.4 1.0
OD2 A:ASP49 3.5 27.4 1.0
O5' E:8H2101 4.1 20.7 1.0
C5' E:8H2101 4.1 20.1 1.0
OD1 A:ASP100 4.1 12.8 1.0
C3' E:DC7 4.2 21.2 1.0
OP2 E:8H2101 4.3 14.4 1.0
CB A:ASP49 4.3 17.4 1.0
O A:HOH334 4.3 23.2 1.0
CB A:ASP51 4.4 9.7 1.0
C4' E:DC7 4.7 23.1 1.0
C5' E:DC7 4.7 28.1 1.0
CZ A:PHE102 4.7 5.3 1.0
NE2 A:GLN98 4.7 16.4 1.0
CA A:ASP100 4.8 9.0 1.0
CE2 A:PHE102 4.8 5.3 1.0
O A:VAL50 4.8 10.7 1.0
O4 A:SO4205 4.9 45.0 1.0
CA A:ASP51 4.9 9.1 1.0
O A:HOH303 5.0 25.9 1.0

Magnesium binding site 3 out of 8 in 8ilh

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Magnesium binding site 3 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:15.2
occ:1.00
 O2B B:8EB201 1.9 42.0 1.0
O B:HOH303 2.0 21.6 1.0
SEA B:8EB201 2.2 88.9 1.0
OD2 B:ASP51 2.2 20.8 1.0
OD1 B:ASP49 2.2 21.2 1.0
O B:HOH359 2.6 34.4 1.0
CG B:ASP51 3.1 21.2 1.0
PB B:8EB201 3.2 47.3 1.0
CG B:ASP49 3.2 29.0 1.0
MG B:MG203 3.2 29.9 1.0
OD1 B:ASP51 3.3 22.0 1.0
PA B:8EB201 3.5 53.4 1.0
OD2 B:ASP49 3.6 26.5 1.0
O3A B:8EB201 3.6 49.5 1.0
O3B B:8EB201 3.8 51.6 1.0
OG B:SER39 4.0 27.2 1.0
O B:HOH345 4.1 32.2 1.0
O B:ASP49 4.2 24.8 1.0
C5' B:8EB201 4.2 33.8 1.0
N B:SER39 4.2 23.9 1.0
O5' B:8EB201 4.3 38.8 1.0
CB B:ASP51 4.5 20.8 1.0
O1B B:8EB201 4.5 37.6 1.0
CB B:ASP49 4.5 30.3 1.0
C B:ASP49 4.5 28.1 1.0
N B:ASP49 4.7 32.5 1.0
O1A B:8EB201 4.7 31.3 1.0
CA B:GLY38 4.7 18.9 1.0
CB B:SER39 4.7 28.9 1.0
CA B:ASP49 4.8 31.3 1.0

Magnesium binding site 4 out of 8 in 8ilh

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Magnesium binding site 4 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg203

b:29.9
occ:1.00
 OD1 B:ASP51 2.0 22.0 1.0
OD2 B:ASP100 2.1 26.3 1.0
SEA B:8EB201 2.1 88.9 1.0
OD1 B:ASP49 2.7 21.2 1.0
CG B:ASP100 3.0 23.6 1.0
O3' F:DC7 3.0 26.8 1.0
CG B:ASP51 3.0 21.2 1.0
CG B:ASP49 3.1 29.0 1.0
MG B:MG202 3.2 15.2 1.0
CB B:ASP100 3.3 21.7 1.0
OD2 B:ASP49 3.3 26.5 1.0
OD2 B:ASP51 3.4 20.8 1.0
PA B:8EB201 3.7 53.4 1.0
O5' B:8EB201 3.9 38.8 1.0
C5' B:8EB201 4.0 33.8 1.0
OD1 B:ASP100 4.1 22.5 1.0
CB B:ASP49 4.2 30.3 1.0
CB B:ASP51 4.3 20.8 1.0
C3' F:DC7 4.3 29.1 1.0
O1A B:8EB201 4.4 31.3 1.0
O B:HOH359 4.7 34.4 1.0
CZ B:PHE102 4.7 22.6 1.0
CA B:ASP100 4.7 20.9 1.0
O2B B:8EB201 4.7 42.0 1.0
NE2 B:GLN98 4.8 25.2 1.0
O B:VAL50 4.8 20.7 1.0
CA B:ASP51 4.8 20.5 1.0
CE2 B:PHE102 4.8 22.1 1.0
O B:HOH303 4.8 21.6 1.0
O3A B:8EB201 4.9 49.5 1.0
N B:ASP100 5.0 20.6 1.0
C B:VAL50 5.0 22.7 1.0

Magnesium binding site 5 out of 8 in 8ilh

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Magnesium binding site 5 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg201

b:23.2
occ:1.00
 OD2 C:ASP100 2.0 16.8 1.0
OD1 C:ASP51 2.1 18.8 1.0
SE1 G:8H2101 2.2 56.1 1.0
OD1 C:ASP49 2.5 22.4 1.0
O3' G:DC7 2.9 21.7 1.0
CG C:ASP100 2.9 15.2 1.0
CG C:ASP49 3.1 24.1 1.0
CG C:ASP51 3.1 18.4 1.0
P G:8H2101 3.3 31.1 1.0
CB C:ASP100 3.3 13.7 1.0
MG C:MG202 3.4 11.3 1.0
OD2 C:ASP51 3.5 20.2 1.0
OD2 C:ASP49 3.5 28.0 1.0
CB C:ASP49 4.0 21.6 1.0
OD1 C:ASP100 4.0 16.6 1.0
C3' G:DC7 4.2 20.8 1.0
O5' G:8H2101 4.3 23.0 1.0
OP2 G:8H2101 4.3 17.6 1.0
C5' G:8H2101 4.4 20.3 1.0
CB C:ASP51 4.4 16.2 1.0
NE2 C:GLN98 4.6 28.4 1.0
CA C:ASP100 4.6 12.9 1.0
O C:VAL50 4.7 16.3 1.0
C4' G:DC7 4.7 20.4 1.0
C5' G:DC7 4.8 22.4 1.0
CZ C:PHE102 4.8 11.5 1.0
CA C:ASP51 4.8 15.7 1.0
N C:ASP100 4.8 13.2 1.0
C C:VAL50 4.9 18.1 1.0
CE2 C:PHE102 4.9 12.3 1.0
N C:ASP51 5.0 18.5 1.0

Magnesium binding site 6 out of 8 in 8ilh

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Magnesium binding site 6 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:11.3
occ:1.00
 OD2 C:ASP51 2.1 20.2 1.0
O C:HOH301 2.1 28.6 1.0
SE1 G:8H2101 2.3 56.1 1.0
OD1 C:ASP49 2.4 22.4 1.0
O3 C:SO4204 2.6 55.2 1.0
CG C:ASP51 3.1 18.4 1.0
OD1 C:ASP51 3.4 18.8 1.0
MG C:MG201 3.4 23.2 1.0
CG C:ASP49 3.5 24.1 1.0
O4 C:SO4204 3.5 66.9 1.0
S C:SO4204 3.6 56.8 1.0
O C:HOH365 3.8 35.9 1.0
OG C:SER39 3.9 25.8 1.0
P G:8H2101 3.9 31.1 1.0
OD2 C:ASP49 3.9 28.0 1.0
O C:HOH354 4.0 23.7 1.0
N C:SER39 4.1 19.8 1.0
O2 C:SO4204 4.1 63.4 1.0
O C:ASP49 4.2 21.4 1.0
C5' G:8H2101 4.2 20.3 1.0
CB C:ASP51 4.4 16.2 1.0
CA C:GLY38 4.5 17.6 1.0
O5' G:8H2101 4.5 23.0 1.0
C C:ASP49 4.6 20.6 1.0
CB C:SER39 4.6 24.0 1.0
CB C:ASP49 4.7 21.6 1.0
OP2 G:8H2101 4.7 17.6 1.0
N C:ASP49 4.8 21.0 1.0
C C:GLY38 4.8 18.6 1.0
O1 C:SO4204 4.8 63.3 1.0
O3' G:DC7 4.9 21.7 1.0
CA C:ASP49 5.0 21.4 1.0
CA C:SER39 5.0 22.1 1.0
N C:ASP51 5.0 18.5 1.0

Magnesium binding site 7 out of 8 in 8ilh

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Magnesium binding site 7 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg201

b:13.7
occ:1.00
 SE1 H:8H2101 2.0 75.1 1.0
OD1 D:ASP51 2.1 19.6 1.0
OD2 D:ASP49 2.2 40.6 1.0
OD2 D:ASP100 2.4 30.2 1.0
CG D:ASP49 2.8 31.7 1.0
OD1 D:ASP49 2.9 33.0 1.0
CG D:ASP100 3.0 26.7 1.0
CG D:ASP51 3.2 19.5 1.0
P H:8H2101 3.3 51.9 1.0
CB D:ASP100 3.3 24.1 1.0
OD2 D:ASP51 3.5 20.1 1.0
MG D:MG202 3.6 20.2 1.0
O3' H:DC7 3.7 39.9 1.0
OD1 D:ASP100 4.0 29.6 1.0
CB D:ASP49 4.1 30.2 1.0
OD1 D:ASN48 4.2 45.5 1.0
O5' H:8H2101 4.3 37.1 1.0
OP2 H:8H2101 4.3 29.7 1.0
C5' H:8H2101 4.3 29.8 1.0
CB D:ASP51 4.5 18.7 1.0
NE2 D:GLN98 4.6 34.5 1.0
CA D:ASP100 4.7 21.9 1.0
CZ D:PHE102 4.8 15.3 1.0
O D:VAL50 4.8 19.0 1.0
O H:HOH225 4.9 32.0 1.0
CE2 D:PHE102 4.9 15.9 1.0
CA D:ASP51 4.9 18.3 1.0
N D:ASP100 5.0 22.8 1.0

Magnesium binding site 8 out of 8 in 8ilh

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Magnesium binding site 8 out of 8 in the The Crystal Structure of Dg(Se-Sp)-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-Sp)-Dna:Pol X Product Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:20.2
occ:1.00
 OD2 D:ASP51 2.2 20.1 1.0
OD1 D:ASP49 2.4 33.0 1.0
SE1 H:8H2101 2.8 75.1 1.0
O H:HOH225 2.9 32.0 1.0
CG D:ASP51 3.2 19.5 1.0
ND2 D:ASN48 3.3 47.4 1.0
OD1 D:ASN48 3.5 45.5 1.0
OD1 D:ASP51 3.5 19.6 1.0
CG D:ASP49 3.5 31.7 1.0
MG D:MG201 3.6 13.7 1.0
OG D:SER39 3.7 24.8 1.0
CG D:ASN48 3.8 44.5 1.0
O D:HOH352 3.8 32.8 1.0
N D:SER39 4.0 23.1 1.0
OD2 D:ASP49 4.0 40.6 1.0
O D:ASP49 4.2 26.9 1.0
CB D:SER39 4.4 26.2 1.0
P H:8H2101 4.4 51.9 1.0
CB D:ASP51 4.5 18.7 1.0
CA D:GLY38 4.5 18.3 1.0
C5' H:8H2101 4.6 29.8 1.0
O5' H:8H2101 4.6 37.1 1.0
C D:ASP49 4.6 27.0 1.0
N D:ASP49 4.7 32.3 1.0
CB D:ASP49 4.8 30.2 1.0
C D:GLY38 4.8 20.8 1.0
CA D:SER39 4.8 25.7 1.0
CA D:ASP49 5.0 29.4 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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