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Magnesium in PDB 6vnp: Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt

Enzymatic activity of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt

All present enzymatic activity of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt, PDB code: 6vnp was solved by H.Jung, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 2.42
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.255, 98.984, 102.875, 90.03, 89.99, 89.92
R / Rfree (%) 19.9 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt (pdb code 6vnp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt, PDB code: 6vnp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6vnp

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Magnesium binding site 1 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:26.3
occ:1.00
 OE1 A:GLU106 2.1 36.6 1.0
OD2 A:ASP7 2.1 58.1 1.0
O3' P:DT13 2.1 30.6 1.0
OD1 A:ASP105 2.2 35.1 1.0
O1A A:DZ4401 2.2 30.1 1.0
O P:HOH108 2.6 31.0 1.0
CD A:GLU106 2.8 37.5 1.0
CG A:ASP105 2.9 31.6 1.0
OD2 A:ASP105 3.0 29.4 1.0
CG A:ASP7 3.0 39.3 1.0
CG A:GLU106 3.1 40.4 1.0
PA A:DZ4401 3.3 28.4 1.0
OD1 A:ASP7 3.3 39.6 1.0
C3' P:DT13 3.3 28.2 1.0
MG A:MG403 3.5 24.1 1.0
O2A A:DZ4401 3.6 30.4 1.0
O5' A:DZ4401 3.9 27.0 1.0
OE2 A:GLU106 3.9 38.2 1.0
OG A:SER103 3.9 29.7 1.0
C4' P:DT13 4.0 32.9 1.0
C5' A:DZ4401 4.1 25.6 1.0
C5' P:DT13 4.2 28.1 1.0
O A:HOH529 4.2 29.3 1.0
CB A:ASP7 4.3 34.8 1.0
CB A:ASP105 4.4 24.6 1.0
CB A:GLU106 4.4 35.4 1.0
C A:ASP105 4.4 33.3 1.0
O A:ASP105 4.4 34.9 1.0
C2' P:DT13 4.5 29.2 1.0
O3G A:DZ4401 4.6 29.7 1.0
N A:GLU106 4.7 30.7 1.0
O2B A:DZ4401 4.7 29.1 1.0
O5' P:DT13 4.7 32.1 1.0
N3A A:DZ4401 4.7 28.9 1.0
CA A:ASP105 4.8 29.5 1.0
NZ A:LYS152 4.9 33.5 1.0
CA A:GLU106 5.0 34.8 1.0

Magnesium binding site 2 out of 8 in 6vnp

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Magnesium binding site 2 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:24.1
occ:1.00
 OD1 A:ASP7 1.9 39.6 1.0
O3G A:DZ4401 2.0 29.7 1.0
O2B A:DZ4401 2.0 29.1 1.0
O A:PHE8 2.1 36.4 1.0
O1A A:DZ4401 2.2 30.1 1.0
OD2 A:ASP105 2.4 29.4 1.0
CG A:ASP7 3.0 39.3 1.0
PB A:DZ4401 3.1 23.2 1.0
PG A:DZ4401 3.2 40.6 1.0
PA A:DZ4401 3.3 28.4 1.0
C A:PHE8 3.3 34.2 1.0
OD2 A:ASP7 3.5 58.1 1.0
N3A A:DZ4401 3.5 28.9 1.0
O3B A:DZ4401 3.5 29.9 1.0
CG A:ASP105 3.5 31.6 1.0
MG A:MG402 3.5 26.3 1.0
O2G A:DZ4401 3.6 35.4 1.0
NZ A:LYS159 3.7 79.5 1.0
O A:HOH529 3.9 29.3 1.0
N A:PHE8 3.9 33.6 1.0
OD1 A:ASP105 4.0 35.1 1.0
C5' A:DZ4401 4.2 25.6 1.0
CA A:PHE8 4.2 32.8 1.0
O5' A:DZ4401 4.2 27.0 1.0
CE A:LYS159 4.3 53.3 1.0
C A:ASP7 4.3 34.8 1.0
N A:ASP9 4.3 32.9 1.0
CB A:ASP7 4.3 34.8 1.0
O1B A:DZ4401 4.4 23.3 1.0
CA A:ASP9 4.4 31.9 1.0
O1G A:DZ4401 4.5 35.8 1.0
O2A A:DZ4401 4.5 30.4 1.0
N A:TYR10 4.5 27.1 1.0
C A:ASP9 4.7 32.8 1.0
CB A:ASP105 4.7 24.6 1.0
O A:ASP7 4.8 33.5 1.0
CA A:ASP7 4.8 34.3 1.0
O P:HOH108 4.8 31.0 1.0
N A:PHE11 4.9 23.9 1.0
CB A:PHE8 4.9 34.4 1.0
O3' P:DT13 5.0 30.6 1.0

Magnesium binding site 3 out of 8 in 6vnp

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Magnesium binding site 3 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:24.4
occ:1.00
 OD1 D:ASP7 2.0 34.9 1.0
O2G D:DZ4401 2.1 31.3 1.0
OD2 D:ASP105 2.1 40.0 1.0
O2B D:DZ4401 2.1 27.7 1.0
O D:PHE8 2.2 38.2 1.0
O1A D:DZ4401 2.3 25.6 1.0
CG D:ASP7 3.0 32.9 1.0
PB D:DZ4401 3.1 20.3 1.0
CG D:ASP105 3.1 33.4 1.0
PG D:DZ4401 3.3 34.4 1.0
PA D:DZ4401 3.3 26.4 1.0
OD2 D:ASP7 3.4 37.5 1.0
C D:PHE8 3.4 32.3 1.0
N3A D:DZ4401 3.5 23.8 1.0
NZ D:LYS159 3.5 82.9 1.0
O3B D:DZ4401 3.6 25.6 1.0
OD1 D:ASP105 3.6 45.2 1.0
MG D:MG403 3.7 30.6 1.0
O1G D:DZ4401 3.7 32.7 1.0
O D:HOH535 3.8 29.3 1.0
N D:PHE8 4.0 34.6 1.0
C5' D:DZ4401 4.0 22.9 1.0
O5' D:DZ4401 4.1 23.5 1.0
CA D:PHE8 4.3 34.6 1.0
C D:ASP7 4.3 36.7 1.0
O D:HOH524 4.3 31.9 1.0
CB D:ASP7 4.3 35.7 1.0
CB D:ASP105 4.4 35.4 1.0
N D:ASP9 4.4 34.7 1.0
CA D:ASP9 4.4 36.7 1.0
O1B D:DZ4401 4.5 23.8 1.0
N D:TYR10 4.5 30.0 1.0
O3G D:DZ4401 4.5 29.9 1.0
O2A D:DZ4401 4.6 31.3 1.0
C D:ASP9 4.6 29.8 1.0
CE D:LYS159 4.6 48.8 1.0
O D:ASP7 4.7 32.6 1.0
N D:PHE11 4.7 24.5 1.0
CA D:ASP7 4.8 36.0 1.0
CB D:PHE11 4.9 24.8 1.0
CB D:PHE8 4.9 30.9 1.0
O3' B:DT13 5.0 30.2 1.0

Magnesium binding site 4 out of 8 in 6vnp

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Magnesium binding site 4 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:30.6
occ:1.00
 OD2 D:ASP7 2.0 37.5 1.0
O3' B:DT13 2.1 30.2 1.0
O D:HOH524 2.2 31.9 1.0
O1A D:DZ4401 2.4 25.6 1.0
OD2 D:ASP105 2.6 40.0 1.0
CG D:GLU106 2.6 41.9 1.0
CD D:GLU106 2.9 36.7 1.0
CG D:ASP7 3.1 32.9 1.0
CB D:ASP105 3.2 35.4 1.0
CG D:ASP105 3.2 33.4 1.0
OE1 D:GLU106 3.3 47.8 1.0
C3' B:DT13 3.3 27.1 1.0
OE2 D:GLU106 3.5 50.7 1.0
OD1 D:ASP7 3.5 34.9 1.0
PA D:DZ4401 3.5 26.4 1.0
OG D:SER103 3.6 33.7 1.0
MG D:MG402 3.7 24.4 1.0
C4' B:DT13 4.0 32.3 1.0
O5' D:DZ4401 4.0 23.5 1.0
O2A D:DZ4401 4.0 31.3 1.0
CB D:GLU106 4.1 36.9 1.0
C D:ASP105 4.1 37.7 1.0
C5' D:DZ4401 4.2 22.9 1.0
CA D:ASP105 4.2 34.8 1.0
O D:ASP105 4.2 35.8 1.0
C5' B:DT13 4.3 28.4 1.0
CB D:ASP7 4.3 35.7 1.0
O D:HOH535 4.3 29.3 1.0
N D:GLU106 4.4 32.5 1.0
OD1 D:ASP105 4.5 45.2 1.0
C2' B:DT13 4.5 27.9 1.0
CA D:GLU106 4.7 31.8 1.0
CB D:SER103 4.8 38.8 1.0
O2G D:DZ4401 4.8 31.3 1.0
O5' B:DT13 4.9 33.4 1.0
N D:ASP105 4.9 30.7 1.0
CA D:ASP7 4.9 36.0 1.0
NZ D:LYS152 4.9 29.3 1.0
O2B D:DZ4401 5.0 27.7 1.0

Magnesium binding site 5 out of 8 in 6vnp

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Magnesium binding site 5 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg402

b:28.6
occ:1.00
 OD1 G:ASP7 2.0 33.6 1.0
O1G G:DZ4401 2.0 32.9 1.0
O G:PHE8 2.1 40.0 1.0
OD2 G:ASP105 2.2 34.5 1.0
O1A G:DZ4401 2.2 26.2 1.0
O2B G:DZ4401 2.3 27.6 1.0
CG G:ASP7 3.1 34.6 1.0
PB G:DZ4401 3.2 28.9 1.0
PG G:DZ4401 3.2 49.7 1.0
CG G:ASP105 3.3 32.3 1.0
C G:PHE8 3.3 32.7 1.0
PA G:DZ4401 3.4 27.0 1.0
O3B G:DZ4401 3.6 28.3 1.0
MG G:MG403 3.6 27.9 1.0
OD2 G:ASP7 3.6 42.6 1.0
N3A G:DZ4401 3.6 28.5 1.0
O3G G:DZ4401 3.6 33.5 1.0
NZ G:LYS159 3.7 69.5 1.0
OD1 G:ASP105 3.7 41.6 1.0
N G:PHE8 3.8 32.7 1.0
O G:HOH536 4.0 29.3 1.0
CA G:PHE8 4.1 32.3 1.0
C5' G:DZ4401 4.1 25.6 1.0
C G:ASP7 4.2 32.8 1.0
O5' G:DZ4401 4.2 26.7 1.0
N G:ASP9 4.3 35.6 1.0
CB G:ASP7 4.3 35.0 1.0
CA G:ASP9 4.4 36.6 1.0
CE G:LYS159 4.5 53.8 1.0
CB G:ASP105 4.5 27.1 1.0
O2G G:DZ4401 4.5 33.1 1.0
N G:TYR10 4.5 25.5 1.0
O1B G:DZ4401 4.6 28.6 1.0
O2A G:DZ4401 4.6 31.0 1.0
C G:ASP9 4.7 31.8 1.0
O G:HOH535 4.7 29.3 1.0
O G:ASP7 4.7 33.7 1.0
CA G:ASP7 4.7 33.7 1.0
CB G:PHE8 4.7 31.1 1.0
O G:ASP105 4.8 33.4 1.0
N G:PHE11 4.8 25.0 1.0
CB G:PHE11 5.0 27.2 1.0

Magnesium binding site 6 out of 8 in 6vnp

Go back to Magnesium Binding Sites List in 6vnp
Magnesium binding site 6 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


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 DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg403

b:27.9
occ:1.00
 O3' E:DT13 2.0 37.3 1.0
OD1 G:ASP105 2.0 41.6 1.0
OE1 G:GLU106 2.1 35.5 1.0
OD2 G:ASP7 2.2 42.6 1.0
O1A G:DZ4401 2.2 26.2 1.0
O G:HOH535 2.3 29.3 1.0
CG G:ASP105 2.9 32.3 1.0
CG G:ASP7 3.1 34.6 1.0
OD2 G:ASP105 3.2 34.5 1.0
C3' E:DT13 3.2 31.3 1.0
CD G:GLU106 3.3 37.3 1.0
PA G:DZ4401 3.3 27.0 1.0
OD1 G:ASP7 3.4 33.6 1.0
MG G:MG402 3.6 28.6 1.0
O2A G:DZ4401 3.7 31.0 1.0
OG G:SER103 3.8 33.0 1.0
O5' G:DZ4401 3.8 26.7 1.0
CG G:GLU106 4.0 36.8 1.0
C4' E:DT13 4.0 31.5 1.0
CB G:GLU106 4.1 34.1 1.0
O G:HOH536 4.1 29.3 1.0
C5' G:DZ4401 4.1 25.6 1.0
C5' E:DT13 4.2 28.2 1.0
OE2 G:GLU106 4.2 39.8 1.0
CB G:ASP105 4.4 27.1 1.0
C2' E:DT13 4.4 28.9 1.0
CB G:ASP7 4.4 35.0 1.0
O G:ASP105 4.4 33.4 1.0
C G:ASP105 4.5 33.6 1.0
O1G G:DZ4401 4.5 32.9 1.0
O5' E:DT13 4.6 36.7 1.0
N3A G:DZ4401 4.8 28.5 1.0
N G:GLU106 4.8 31.6 1.0
O2B G:DZ4401 4.8 27.6 1.0
CA G:ASP105 4.9 29.5 1.0

Magnesium binding site 7 out of 8 in 6vnp

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Magnesium binding site 7 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg402

b:28.8
occ:1.00
 OD1 J:ASP7 2.0 37.8 1.0
O1G J:DZ4401 2.1 38.2 1.0
O2B J:DZ4401 2.1 33.3 1.0
O J:PHE8 2.2 43.1 1.0
O1A J:DZ4401 2.3 25.4 1.0
OD2 J:ASP105 2.3 40.1 1.0
PB J:DZ4401 3.0 54.4 1.0
CG J:ASP7 3.1 36.7 1.0
PG J:DZ4401 3.2 38.0 1.0
PA J:DZ4401 3.3 28.3 1.0
C J:PHE8 3.4 33.9 1.0
O3B J:DZ4401 3.4 33.2 1.0
N3A J:DZ4401 3.4 28.4 1.0
CG J:ASP105 3.5 38.0 1.0
OD2 J:ASP7 3.6 58.6 1.0
NZ J:LYS159 3.6 86.5 1.0
O3G J:DZ4401 3.7 34.1 1.0
MG J:MG403 3.8 31.9 1.0
O J:HOH526 3.8 32.1 1.0
N J:PHE8 4.0 36.5 1.0
OD1 J:ASP105 4.1 46.1 1.0
C5' J:DZ4401 4.2 21.9 1.0
O5' J:DZ4401 4.2 27.7 1.0
CA J:PHE8 4.3 37.0 1.0
C J:ASP7 4.3 40.4 1.0
O1B J:DZ4401 4.3 24.4 1.0
N J:ASP9 4.4 34.7 1.0
CB J:ASP7 4.4 39.8 1.0
CA J:ASP9 4.4 37.4 1.0
CE J:LYS159 4.4 54.8 1.0
O2A J:DZ4401 4.5 30.6 1.0
N J:TYR10 4.5 31.3 1.0
O2G J:DZ4401 4.5 36.8 1.0
O J:HOH546 4.6 30.2 1.0
CB J:ASP105 4.6 29.6 1.0
C J:ASP9 4.6 35.4 1.0
O J:ASP7 4.7 37.0 1.0
CA J:ASP7 4.8 36.9 1.0
N J:PHE11 4.8 28.1 1.0
CB J:PHE8 4.9 34.8 1.0
O J:ASP105 5.0 39.0 1.0
O3' H:DT13 5.0 34.1 1.0

Magnesium binding site 8 out of 8 in 6vnp

Go back to Magnesium Binding Sites List in 6vnp
Magnesium binding site 8 out of 8 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg403

b:31.9
occ:1.00
 O3' H:DT13 2.0 34.1 1.0
O J:HOH546 2.2 30.2 1.0
OD1 J:ASP105 2.3 46.1 1.0
O1A J:DZ4401 2.3 25.4 1.0
OD2 J:ASP7 2.3 58.6 1.0
CG J:GLU106 2.8 42.3 1.0
CD J:GLU106 2.8 38.2 1.0
CG J:ASP105 3.0 38.0 1.0
OE1 J:GLU106 3.1 44.9 1.0
OD2 J:ASP105 3.1 40.1 1.0
CG J:ASP7 3.2 36.7 1.0
C3' H:DT13 3.2 30.9 1.0
OE2 J:GLU106 3.3 47.2 1.0
PA J:DZ4401 3.4 28.3 1.0
OD1 J:ASP7 3.5 37.8 1.0
OG J:SER103 3.7 31.6 1.0
MG J:MG402 3.8 28.8 1.0
O2A J:DZ4401 3.8 30.6 1.0
C4' H:DT13 3.9 35.9 1.0
O5' J:DZ4401 4.1 27.7 1.0
C5' H:DT13 4.1 30.9 1.0
CB J:GLU106 4.2 38.7 1.0
O J:HOH526 4.2 32.1 1.0
C5' J:DZ4401 4.4 21.9 1.0
C J:ASP105 4.4 37.9 1.0
C2' H:DT13 4.4 31.0 1.0
O J:ASP105 4.4 39.0 1.0
CB J:ASP105 4.5 29.6 1.0
CB J:ASP7 4.5 39.8 1.0
O5' H:DT13 4.6 39.0 1.0
N J:GLU106 4.6 33.7 1.0
O1G J:DZ4401 4.8 38.2 1.0
NZ J:LYS152 4.8 34.8 1.0
CA J:GLU106 4.9 36.3 1.0
CA J:ASP105 4.9 31.2 1.0
CB J:SER103 4.9 38.3 1.0
N3A J:DZ4401 4.9 28.4 1.0
O J:HOH544 4.9 37.8 1.0

Reference:

H.Jung, S.Lee. Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dt To Be Published.
Page generated: Tue Oct 1 22:11:26 2024

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