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Magnesium in PDB 4c30: Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2

Enzymatic activity of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2

All present enzymatic activity of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2, PDB code: 4c30 was solved by M.Stelter, S.Acajjaoui, S.Mcsweeney, J.Timmins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 66.18 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.489, 89.785, 293.798, 90.00, 89.97, 90.00
R / Rfree (%) 22.82 / 28.783

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 (pdb code 4c30). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2, PDB code: 4c30:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4c30

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Magnesium binding site 1 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1663

b:0.4
occ:1.00
 O A:HOH2002 2.1 37.1 1.0
OG1 A:THR39 2.1 71.7 1.0
O A:HOH2001 2.1 47.0 1.0
O A:HOH2003 2.1 41.1 1.0
O1G A:ANP1662 2.1 79.3 1.0
O1B A:ANP1662 2.1 89.6 1.0
CB A:THR39 2.7 72.2 1.0
PG A:ANP1662 3.4 77.5 1.0
PB A:ANP1662 3.4 92.2 1.0
N A:THR39 3.7 73.5 1.0
N3B A:ANP1662 3.8 86.6 1.0
CG2 A:THR39 3.8 71.4 1.0
CA A:THR39 3.8 72.8 1.0
O1A A:ANP1662 4.0 91.3 1.0
OD1 A:ASP227 4.1 85.3 1.0
O3G A:ANP1662 4.2 82.8 1.0
O3A A:ANP1662 4.3 90.7 1.0
OD2 A:ASP227 4.3 83.6 1.0
PA A:ANP1662 4.3 93.5 1.0
O2A A:ANP1662 4.3 92.2 1.0
O2G A:ANP1662 4.4 83.0 1.0
O2B A:ANP1662 4.6 90.3 1.0
CG A:ASP227 4.7 84.8 1.0
CA A:GLY575 4.7 73.5 1.0
OE2 A:GLU228 4.8 82.7 1.0
C A:LYS38 4.9 73.5 1.0
CB A:LYS38 4.9 74.2 1.0
NH2 A:ARG291 4.9 64.4 1.0
CD A:LYS38 5.0 81.9 1.0

Magnesium binding site 2 out of 6 in 4c30

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Magnesium binding site 2 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1664

b:0.8
occ:1.00
 OD1 A:ASP118 2.9 0.3 1.0
OD2 A:ASP118 3.4 0.8 1.0
CG A:ASP118 3.5 0.3 1.0
OD1 A:ASP391 3.7 0.4 1.0
OD2 A:ASP391 3.7 0.9 1.0
OD2 A:ASP119 3.9 0.4 1.0
CG A:ASP391 4.0 0.4 1.0
OD1 A:ASP119 4.2 0.6 1.0
CG A:ASP119 4.2 0.4 1.0
OD2 A:ASP117 4.8 0.9 1.0
CB A:ASP118 5.0 0.8 1.0

Magnesium binding site 3 out of 6 in 4c30

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Magnesium binding site 3 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1663

b:54.0
occ:1.00
 O D:HOH2010 2.2 25.1 1.0
O D:HOH2022 2.2 33.7 1.0
O D:HOH2019 2.2 36.6 1.0
O D:HOH2023 2.3 49.2 1.0
OD1 D:ASP397 2.3 76.9 1.0
O D:HOH2020 2.3 46.6 1.0
CG D:ASP397 3.5 78.4 1.0
N D:ASP397 3.8 79.2 1.0
CB D:ARG396 4.0 80.2 1.0
CA D:ASP397 4.0 76.9 1.0
C D:ARG396 4.0 81.0 1.0
O D:ARG393 4.1 0.2 1.0
OD2 D:ASP397 4.2 79.6 1.0
O D:ARG396 4.3 81.2 1.0
CB D:ASP397 4.3 77.9 1.0
CB D:ARG416 4.6 97.0 1.0
OD2 D:ASP119 4.6 74.2 1.0
CA D:ARG396 4.7 81.2 1.0
NH1 D:ARG420 4.9 97.4 1.0

Magnesium binding site 4 out of 6 in 4c30

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Magnesium binding site 4 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1664

b:98.2
occ:1.00
 OD1 F:ASP119 3.1 0.1 1.0
OD2 F:ASP118 3.1 0.5 1.0
CG F:ASP118 3.8 0.1 1.0
CB F:ASP118 3.8 0.1 1.0
OD2 F:ASP391 4.1 0.8 1.0
CG F:ASP119 4.1 0.9 1.0
OD1 F:ASP391 4.5 0.1 1.0
OD2 F:ASP119 4.6 0.7 1.0
CG F:ASP391 4.6 0.5 1.0
OD2 F:ASP117 4.9 0.5 1.0
N F:ASP119 4.9 0.1 1.0
OD1 F:ASP118 4.9 1.0 1.0
CA F:ASP118 5.0 0.4 1.0

Magnesium binding site 5 out of 6 in 4c30

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Magnesium binding site 5 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1665

b:0.3
occ:1.00
 O1G F:ANP1663 2.1 82.2 1.0
O1B F:ANP1663 2.2 96.0 1.0
OG1 F:THR39 2.2 73.4 1.0
O F:HOH2001 2.3 36.6 1.0
O F:HOH2002 2.3 39.4 1.0
O F:HOH2003 2.3 41.4 1.0
O1A F:ANP1663 2.8 95.7 1.0
N3B F:ANP1663 3.0 87.8 1.0
PG F:ANP1663 3.1 80.6 1.0
CB F:THR39 3.1 73.8 1.0
PB F:ANP1663 3.1 90.0 1.0
O2G F:ANP1663 3.7 83.5 1.0
N F:THR39 3.8 74.7 1.0
PA F:ANP1663 3.8 91.4 1.0
O3A F:ANP1663 4.0 91.2 1.0
CA F:THR39 4.0 74.1 1.0
CG2 F:THR39 4.2 73.5 1.0
NH2 F:ARG291 4.2 61.2 1.0
O2B F:ANP1663 4.3 91.1 1.0
O3G F:ANP1663 4.4 81.6 1.0
O2A F:ANP1663 4.4 89.9 1.0
CB F:LYS38 4.5 75.5 1.0
CA F:GLY575 4.9 73.2 1.0
C F:LYS38 4.9 75.0 1.0
OE2 F:GLU228 4.9 79.8 1.0
OD1 F:ASP227 4.9 89.6 1.0

Magnesium binding site 6 out of 6 in 4c30

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Magnesium binding site 6 out of 6 in the Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Deinococcus Radiodurans Uvrd in Complex with Dna, Form 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1663

b:45.8
occ:1.00
 OD1 I:ASP397 2.7 79.4 1.0
CB I:ARG396 3.6 80.2 1.0
N I:ASP397 3.7 78.5 1.0
C I:ARG396 3.7 79.7 1.0
CG I:ASP397 3.9 79.1 1.0
O I:ARG393 4.0 0.2 1.0
O I:ARG396 4.0 79.7 1.0
CA I:ASP397 4.2 77.0 1.0
CA I:ARG396 4.3 80.5 1.0
OD2 I:ASP119 4.5 78.5 1.0
CD I:ARG396 4.6 79.5 1.0
CB I:ASP397 4.7 78.1 1.0
CG I:ARG396 4.7 79.7 1.0
CB I:ARG416 4.8 97.5 1.0
OD2 I:ASP397 4.8 80.0 1.0
C I:ARG393 4.9 0.7 1.0
NH2 I:ARG420 5.0 0.3 1.0

Reference:

M.Stelter, S.Acajjaoui, S.Mcsweeney, J.Timmins. Structural and Mechanistic Insight Into Dna Unwinding By Deinococcus Radiodurans Uvrd. Plos One V. 8 77364 2013.
ISSN: ISSN 1932-6203
PubMed: 24143224
DOI: 10.1371/JOURNAL.PONE.0077364
Page generated: Thu Aug 15 16:41:40 2024

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