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Magnesium in PDB 4q45: Dna Polymerase- Damaged Dna Complex

Enzymatic activity of Dna Polymerase- Damaged Dna Complex

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

Protein crystallography data

The structure of Dna Polymerase- Damaged Dna Complex, PDB code: 4q45 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) 51.34 / 2.18
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.500, 57.900, 111.040, 90.00, 90.44, 90.00
R / Rfree (%) 21.2 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase- Damaged Dna Complex (pdb code 4q45). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase- Damaged Dna Complex, PDB code: 4q45:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4q45

Go back to Magnesium Binding Sites List in 4q45
Magnesium binding site 1 out of 4 in the Dna 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 Dna Polymerase- Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg402

b:11.2
occ:1.00
OD1 F:ASP8 2.0 30.7 1.0
O2A F:1FZ401 2.1 26.6 1.0
O1B F:1FZ401 2.1 23.5 1.0
O F:MET9 2.3 27.7 1.0
O1G F:1FZ401 2.3 23.2 1.0
OD1 F:ASP103 2.3 29.5 1.0
CG F:ASP8 3.1 29.7 1.0
MG F:MG403 3.3 47.1 1.0
PB F:1FZ401 3.4 20.9 1.0
PA F:1FZ401 3.4 25.0 1.0
C F:MET9 3.5 24.2 1.0
CG F:ASP103 3.5 28.1 1.0
PG F:1FZ401 3.6 27.2 1.0
OD2 F:ASP8 3.6 32.8 1.0
O F:HOH673 3.8 35.9 1.0
O F:HOH635 3.8 30.8 1.0
N3A F:1FZ401 3.9 23.1 1.0
N F:MET9 3.9 20.9 1.0
O3B F:1FZ401 3.9 33.4 1.0
C5' F:1FZ401 4.1 24.8 1.0
OD2 F:ASP103 4.1 25.7 1.0
O5' F:1FZ401 4.2 31.1 1.0
C F:ASP8 4.2 28.2 1.0
CA F:MET9 4.2 23.7 1.0
O2G F:1FZ401 4.3 31.5 1.0
CB F:ASP8 4.4 28.3 1.0
O1A F:1FZ401 4.5 18.7 1.0
N F:ASP10 4.5 26.6 1.0
O2B F:1FZ401 4.6 24.2 1.0
CA F:ASP8 4.6 29.5 1.0
CB F:ASP103 4.7 29.3 1.0
O F:ASP8 4.7 26.1 1.0
CA F:ASP10 4.7 27.2 1.0
O3G F:1FZ401 4.7 28.3 1.0
OE1 F:GLU104 4.8 37.0 1.0
CB F:MET9 4.8 24.6 1.0
N F:CYS11 4.8 21.1 1.0
CB F:PHE12 4.8 24.7 1.0
N F:PHE12 4.9 23.5 1.0
C F:ASP10 5.0 22.5 1.0

Magnesium binding site 2 out of 4 in 4q45

Go back to Magnesium Binding Sites List in 4q45
Magnesium binding site 2 out of 4 in the Dna 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 Dna Polymerase- Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg403

b:47.1
occ:1.00
OD2 F:ASP103 2.1 25.7 1.0
OE1 F:GLU104 2.2 37.0 1.0
CG F:GLU104 2.5 34.9 1.0
O2A F:1FZ401 2.6 26.6 1.0
CD F:GLU104 2.7 36.9 1.0
OD1 F:ASP103 2.8 29.5 1.0
CG F:ASP103 2.8 28.1 1.0
O3' H:DC873 2.8 29.5 1.0
O F:HOH673 3.0 35.9 1.0
MG F:MG402 3.3 11.2 1.0
OD1 F:ASP8 3.4 30.7 1.0
C3' H:DC873 3.4 26.5 1.0
OD2 F:ASP8 3.5 32.8 1.0
O5' F:1FZ401 3.5 31.1 1.0
PA F:1FZ401 3.5 25.0 1.0
CG F:ASP8 3.7 29.7 1.0
C5' F:1FZ401 3.7 24.8 1.0
OE2 F:GLU104 3.8 36.9 1.0
CB F:GLU104 3.9 26.1 1.0
O1A F:1FZ401 3.9 18.7 1.0
OG F:SER101 4.0 32.6 1.0
CB F:ASP103 4.3 29.3 1.0
C F:ASP103 4.4 27.6 1.0
C4' H:DC873 4.5 29.3 1.0
N F:GLU104 4.5 34.0 1.0
O1B F:1FZ401 4.5 23.5 1.0
C2' H:DC873 4.5 23.3 1.0
O F:ASP103 4.5 31.1 1.0
CA F:GLU104 4.7 30.1 1.0
O H:HOH902 4.7 27.6 1.0
O5' H:DC873 4.7 29.7 1.0
C5' H:DC873 4.7 21.0 1.0
CA F:ASP103 4.9 31.7 1.0
CB F:ASP8 4.9 28.3 1.0

Magnesium binding site 3 out of 4 in 4q45

Go back to Magnesium Binding Sites List in 4q45
Magnesium binding site 3 out of 4 in the Dna 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 Dna Polymerase- Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:21.7
occ:1.00
O1A A:1FZ401 2.0 38.4 1.0
OD1 A:ASP8 2.1 38.3 1.0
O1G A:1FZ401 2.1 20.8 1.0
O2B A:1FZ401 2.1 30.2 1.0
O A:MET9 2.3 39.0 1.0
OD2 A:ASP103 2.4 34.0 1.0
CG A:ASP8 3.2 40.7 1.0
PB A:1FZ401 3.3 29.2 1.0
PA A:1FZ401 3.4 33.3 1.0
C A:MET9 3.4 39.0 1.0
PG A:1FZ401 3.5 28.1 1.0
CG A:ASP103 3.5 37.9 1.0
NZ A:LYS157 3.5 39.9 1.0
OD2 A:ASP8 3.8 47.4 1.0
O3B A:1FZ401 3.8 40.0 1.0
N3A A:1FZ401 3.8 28.6 1.0
MG A:MG403 3.9 45.4 1.0
N A:MET9 3.9 35.0 1.0
C5' A:1FZ401 4.0 32.9 1.0
OD1 A:ASP103 4.1 36.2 1.0
O5' A:1FZ401 4.1 35.0 1.0
O3G A:1FZ401 4.2 37.5 1.0
CA A:MET9 4.2 36.7 1.0
C A:ASP8 4.2 41.3 1.0
O A:HOH586 4.3 49.7 1.0
CB A:ASP8 4.4 36.2 1.0
N A:ASP10 4.5 33.8 1.0
O2A A:1FZ401 4.5 28.9 1.0
O2G A:1FZ401 4.6 27.4 1.0
O1B A:1FZ401 4.6 37.6 1.0
CE A:LYS157 4.6 40.8 1.0
O A:ASP8 4.6 39.6 1.0
CA A:ASP10 4.7 37.3 1.0
CA A:ASP8 4.7 41.1 1.0
N A:CYS11 4.7 36.8 1.0
CB A:ASP103 4.7 36.7 1.0
CB A:MET9 4.7 34.8 1.0
CB A:PHE12 4.8 33.7 1.0
N A:PHE12 4.8 31.9 1.0
C A:ASP10 4.9 33.1 1.0
OE2 A:GLU104 4.9 39.6 1.0

Magnesium binding site 4 out of 4 in 4q45

Go back to Magnesium Binding Sites List in 4q45
Magnesium binding site 4 out of 4 in the Dna 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 Dna Polymerase- Damaged Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:45.4
occ:1.00
OE2 A:GLU104 2.2 39.6 1.0
O1A A:1FZ401 2.5 38.4 1.0
OD2 A:ASP8 2.7 47.4 1.0
O2A A:1FZ401 2.7 28.9 1.0
O A:HOH586 2.8 49.7 1.0
PA A:1FZ401 3.2 33.3 1.0
CD A:GLU104 3.4 43.2 1.0
CG A:ASP8 3.5 40.7 1.0
O A:HOH592 3.6 40.0 1.0
OD1 A:ASP8 3.6 38.3 1.0
MG A:MG402 3.9 21.7 1.0
OP2 C:DC873 4.1 39.9 1.0
CG A:GLU104 4.1 50.7 1.0
O1G A:1FZ401 4.2 20.8 1.0
O5' C:DC873 4.2 39.2 1.0
O5' A:1FZ401 4.2 35.0 1.0
C3' C:DC873 4.3 35.8 1.0
OE1 A:GLU104 4.3 36.5 1.0
N3A A:1FZ401 4.5 28.6 1.0
P C:DC873 4.5 41.1 1.0
O3' C:DC873 4.5 31.1 1.0
O A:HOH510 4.6 42.6 1.0
OP1 C:DC873 4.7 42.1 1.0
CE A:LYS150 4.8 47.6 1.0
C5' C:DC873 4.9 32.3 1.0
CB A:ASP8 5.0 36.2 1.0
OD2 A:ASP103 5.0 34.0 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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