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Magnesium in PDB 4q43: Polymerase-Damaged Dna Complex

Enzymatic activity of Polymerase-Damaged Dna Complex

All present enzymatic activity of Polymerase-Damaged Dna Complex:
2.7.7.7;

Protein crystallography data

The structure of Polymerase-Damaged Dna Complex, PDB code: 4q43 was solved by J.Kottur, A.Sharma, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.52 / 2.45
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.830, 56.790, 112.020, 90.00, 91.96, 90.00
R / Rfree (%) 21.4 / 26.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Polymerase-Damaged Dna Complex (pdb code 4q43). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Polymerase-Damaged Dna Complex, PDB code: 4q43:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4q43

Go back to Magnesium Binding Sites List in 4q43
Magnesium binding site 1 out of 4 in the Polymerase-Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Polymerase-Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:38.5
occ:1.00
OD1 A:ASP8 2.0 44.5 1.0
O1G A:0KX401 2.1 61.5 1.0
O2B A:0KX401 2.2 49.9 1.0
O1A A:0KX401 2.3 56.3 1.0
O A:MET9 2.3 58.3 1.0
OD2 A:ASP103 2.5 51.0 1.0
CG A:ASP8 3.2 51.1 1.0
PG A:0KX401 3.3 57.8 1.0
PB A:0KX401 3.3 50.9 1.0
C A:MET9 3.4 57.8 1.0
PA A:0KX401 3.6 53.0 1.0
CG A:ASP103 3.7 53.6 1.0
NZ A:LYS157 3.7 58.5 1.0
O3B A:0KX401 3.7 51.0 1.0
MG A:MG403 3.7 65.2 1.0
O2G A:0KX401 3.7 59.3 1.0
OD2 A:ASP8 3.8 68.2 1.0
N3A A:0KX401 3.9 56.0 1.0
N A:MET9 4.0 49.4 1.0
C5' A:0KX401 4.1 44.2 1.0
CA A:MET9 4.2 46.9 1.0
OD1 A:ASP103 4.3 56.9 1.0
C A:ASP8 4.3 55.0 1.0
O5' A:0KX401 4.3 46.6 1.0
CE A:LYS157 4.3 58.8 1.0
N A:ASP10 4.4 60.7 1.0
N A:CYS11 4.4 49.1 1.0
CB A:ASP8 4.4 57.8 1.0
CA A:ASP10 4.5 51.8 1.0
O3G A:0KX401 4.6 64.4 1.0
CB A:MET9 4.6 49.2 1.0
O1B A:0KX401 4.6 46.6 1.0
O2A A:0KX401 4.7 50.7 1.0
C A:ASP10 4.7 56.7 1.0
CA A:ASP8 4.7 55.9 1.0
O A:ASP8 4.7 55.7 1.0
N A:PHE12 4.8 53.0 1.0
CB A:ASP103 4.8 58.2 1.0
CB A:PHE12 5.0 57.9 1.0

Magnesium binding site 2 out of 4 in 4q43

Go back to Magnesium Binding Sites List in 4q43
Magnesium binding site 2 out of 4 in the Polymerase-Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Polymerase-Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:65.2
occ:1.00
OE2 A:GLU104 1.9 62.5 1.0
O1A A:0KX401 2.2 56.3 1.0
OD2 A:ASP8 2.7 68.2 1.0
O2A A:0KX401 2.9 50.7 1.0
PA A:0KX401 3.0 53.0 1.0
CD A:GLU104 3.1 66.1 1.0
OD1 A:ASP8 3.4 44.5 1.0
CG A:ASP8 3.4 51.1 1.0
O3' C:DC873 3.5 47.3 1.0
O5' A:0KX401 3.6 46.6 1.0
C3' C:DC873 3.7 52.3 1.0
CG A:GLU104 3.7 59.1 1.0
MG A:MG402 3.7 38.5 1.0
NZ A:LYS150 4.0 66.8 1.0
OD1 A:ASP103 4.1 56.9 1.0
O1G A:0KX401 4.1 61.5 1.0
OE1 A:GLU104 4.1 65.1 1.0
O5' C:DC873 4.2 54.4 1.0
OD2 A:ASP103 4.2 51.0 1.0
N3A A:0KX401 4.4 56.0 1.0
C5' C:DC873 4.5 49.3 1.0
C5' A:0KX401 4.5 44.2 1.0
CG A:ASP103 4.6 53.6 1.0
C4' C:DC873 4.6 44.3 1.0
C2' C:DC873 4.8 52.6 1.0
OP1 C:DC873 4.8 63.9 1.0
CB A:ASP8 4.9 57.8 1.0
P C:DC873 4.9 76.0 1.0
O2B A:0KX401 5.0 49.9 1.0

Magnesium binding site 3 out of 4 in 4q43

Go back to Magnesium Binding Sites List in 4q43
Magnesium binding site 3 out of 4 in the Polymerase-Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Polymerase-Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:15.7
occ:1.00
OD1 F:ASP8 1.9 46.1 1.0
O F:MET9 2.2 25.4 1.0
O1B F:0KX401 2.2 31.0 1.0
O2A F:0KX401 2.3 28.0 1.0
OD2 F:ASP103 2.4 40.4 1.0
O1G F:0KX401 2.5 29.5 1.0
CG F:ASP8 3.1 28.8 1.0
C F:MET9 3.4 27.3 1.0
PB F:0KX401 3.4 23.6 1.0
NZ F:LYS157 3.5 33.4 1.0
CG F:ASP103 3.5 39.4 1.0
PG F:0KX401 3.5 32.2 1.0
PA F:0KX401 3.6 29.2 1.0
OD2 F:ASP8 3.6 35.5 1.0
O3G F:0KX401 3.8 34.1 1.0
N3A F:0KX401 3.9 33.4 1.0
O3B F:0KX401 3.9 37.0 1.0
OD1 F:ASP103 4.0 38.8 1.0
N F:MET9 4.0 29.4 1.0
C5' F:0KX401 4.2 29.6 1.0
CA F:MET9 4.2 34.7 1.0
C F:ASP8 4.2 32.3 1.0
O F:HOH516 4.2 39.7 1.0
CE F:LYS157 4.2 44.8 1.0
CB F:ASP8 4.3 29.4 1.0
O5' F:0KX401 4.3 32.0 1.0
N F:ASP10 4.4 26.6 1.0
MG F:MG403 4.4 50.6 1.0
CA F:ASP10 4.5 32.3 1.0
OE2 F:GLU104 4.5 46.6 1.0
O F:ASP8 4.6 28.3 1.0
CA F:ASP8 4.6 35.0 1.0
N F:CYS11 4.6 26.2 1.0
O2B F:0KX401 4.7 34.8 1.0
CB F:MET9 4.7 35.8 1.0
O1A F:0KX401 4.8 23.9 1.0
C F:ASP10 4.8 24.7 1.0
CB F:ASP103 4.8 29.4 1.0
O2G F:0KX401 4.9 29.1 1.0
CB F:PHE12 4.9 30.3 1.0
N F:PHE12 4.9 35.2 1.0
CG F:GLU104 4.9 38.9 1.0

Magnesium binding site 4 out of 4 in 4q43

Go back to Magnesium Binding Sites List in 4q43
Magnesium binding site 4 out of 4 in the Polymerase-Damaged Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Polymerase-Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:50.6
occ:1.00
OD1 F:ASP103 2.0 38.8 1.0
O3' H:DC873 2.1 43.3 1.0
C3' H:DC873 2.4 31.8 1.0
CG F:GLU104 2.5 38.9 1.0
OE2 F:GLU104 2.5 46.6 1.0
CD F:GLU104 2.6 38.3 1.0
CG F:ASP103 3.2 39.4 1.0
OG F:SER101 3.2 33.1 1.0
O2A F:0KX401 3.2 28.0 1.0
O5' F:0KX401 3.3 32.0 1.0
C4' H:DC873 3.4 41.0 1.0
OE1 F:GLU104 3.6 40.0 1.0
C2' H:DC873 3.6 33.1 1.0
C5' F:0KX401 3.7 29.6 1.0
PA F:0KX401 3.7 29.2 1.0
OD2 F:ASP103 3.7 40.4 1.0
CB F:GLU104 3.7 31.6 1.0
C5' H:DC873 4.0 34.4 1.0
O1A F:0KX401 4.1 23.9 1.0
N F:GLU104 4.3 31.3 1.0
CB F:SER101 4.3 29.4 1.0
C F:ASP103 4.4 36.9 1.0
CB F:ASP103 4.4 29.4 1.0
MG F:MG402 4.4 15.7 1.0
OD2 F:ASP8 4.5 35.5 1.0
OD1 F:ASP8 4.5 46.1 1.0
O5' H:DC873 4.5 43.6 1.0
CA F:GLU104 4.6 27.8 1.0
O4' H:DC873 4.6 27.9 1.0
C1' H:DC873 4.6 33.0 1.0
O F:ASP103 4.7 38.1 1.0
CA F:ASP103 4.7 34.5 1.0
CG F:ASP8 4.7 28.8 1.0
N F:ASP103 4.8 31.4 1.0
C4' F:0KX401 4.9 33.0 1.0
O4' F:0KX401 5.0 32.3 1.0

Reference:

J.Kottur, A.Sharma, K.R.Gore, N.Narayanan, B.Samanta, P.I.Pradeepkumar, D.T.Nair. Unique Structural Features in Dna Polymerase IV Enable Efficient Bypass of the N2 Adduct Induced By the Nitrofurazone Antibiotic Structure V. 23 56 2015.
ISSN: ISSN 0969-2126
PubMed: 25497730
DOI: 10.1016/J.STR.2014.10.019
Page generated: Mon Dec 14 19:21:35 2020

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