Atomistry » Magnesium » PDB 6vcl-6vno » 6vkp
Atomistry »
  Magnesium »
    PDB 6vcl-6vno »
      6vkp »

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

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

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

Protein crystallography data

The structure of Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg, PDB code: 6vkp 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) 49.55 / 2.54
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.098, 103.69, 99.105, 90, 89.94, 90
R / Rfree (%) 21 / 26

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 4 in 6vkp

Go back to Magnesium Binding Sites List in 6vkp
Magnesium binding site 1 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:37.3
occ:1.00
OD1 A:ASP105 2.0 44.3 1.0
O P:HOH103 2.1 42.9 1.0
O A:HOH507 2.2 42.9 1.0
OD2 A:ASP7 2.2 46.8 1.0
OE2 A:GLU106 2.5 63.8 1.0
O1A A:DZ4403 2.5 36.0 1.0
CG A:GLU106 2.7 50.7 1.0
CD A:GLU106 3.0 50.9 1.0
CG A:ASP105 3.0 38.3 1.0
CG A:ASP7 3.3 49.1 1.0
OG A:SER103 3.4 39.4 1.0
PA A:DZ4403 3.4 30.7 1.0
OD2 A:ASP105 3.4 41.2 1.0
O2A A:DZ4403 3.7 35.3 1.0
OP2 P:DG13 3.7 62.8 1.0
O5' A:DZ4403 3.8 34.0 1.0
OD1 A:ASP7 3.9 46.8 1.0
MG A:MG402 3.9 36.1 1.0
OE1 A:GLU106 4.2 58.9 1.0
C5' A:DZ4403 4.2 23.4 1.0
CB A:GLU106 4.2 48.0 1.0
O A:HOH510 4.4 42.9 1.0
CB A:ASP105 4.4 36.5 1.0
CB A:SER103 4.4 39.4 1.0
C A:ASP105 4.5 42.0 1.0
CB A:ASP7 4.5 46.6 1.0
O A:ASP105 4.6 37.8 1.0
N A:GLU106 4.6 41.5 1.0
CA A:ASP105 4.8 42.3 1.0
O2G A:DZ4403 4.8 44.6 1.0
CA A:GLU106 4.9 39.2 1.0
O P:HOH101 4.9 42.9 1.0
N A:ASP105 4.9 41.2 1.0

Magnesium binding site 2 out of 4 in 6vkp

Go back to Magnesium Binding Sites List in 6vkp
Magnesium binding site 2 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:36.1
occ:1.00
O2G A:DZ4403 2.0 44.6 1.0
OD1 A:ASP7 2.1 46.8 1.0
O1A A:DZ4403 2.1 36.0 1.0
O A:PHE8 2.1 43.1 1.0
OD2 A:ASP105 2.2 41.2 1.0
O2B A:DZ4403 2.2 36.1 1.0
CG A:ASP7 3.0 49.1 1.0
PG A:DZ4403 3.2 42.5 1.0
PB A:DZ4403 3.2 37.2 1.0
CG A:ASP105 3.3 38.3 1.0
PA A:DZ4403 3.3 30.7 1.0
C A:PHE8 3.4 41.0 1.0
OD2 A:ASP7 3.4 46.8 1.0
O3B A:DZ4403 3.5 38.8 1.0
N3A A:DZ4403 3.6 31.7 1.0
O1G A:DZ4403 3.6 42.3 1.0
OD1 A:ASP105 3.7 44.3 1.0
O A:HOH510 3.7 42.9 1.0
NZ A:LYS159 3.9 66.8 1.0
MG A:MG401 3.9 37.3 1.0
N A:PHE8 3.9 45.5 1.0
C5' A:DZ4403 4.0 23.4 1.0
O5' A:DZ4403 4.1 34.0 1.0
CA A:PHE8 4.2 40.0 1.0
C A:ASP7 4.2 43.9 1.0
CE A:LYS159 4.3 50.7 1.0
N A:ASP9 4.3 44.1 1.0
O A:HOH507 4.4 42.9 1.0
CB A:ASP7 4.4 46.6 1.0
N A:TYR10 4.4 34.8 1.0
CA A:ASP9 4.4 44.7 1.0
O2A A:DZ4403 4.5 35.3 1.0
O3G A:DZ4403 4.5 43.4 1.0
O A:ASP7 4.5 42.0 1.0
O1B A:DZ4403 4.5 34.3 1.0
CB A:ASP105 4.6 36.5 1.0
C A:ASP9 4.6 38.3 1.0
N A:PHE11 4.8 33.0 1.0
CA A:ASP7 4.8 42.5 1.0
CB A:PHE8 4.8 40.5 1.0
CB A:PHE11 4.9 33.0 1.0

Magnesium binding site 3 out of 4 in 6vkp

Go back to Magnesium Binding Sites List in 6vkp
Magnesium binding site 3 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg401

b:39.8
occ:1.00
OD1 D:ASP105 2.1 56.4 1.0
O B:HOH105 2.2 46.7 1.0
OE2 D:GLU106 2.2 62.5 1.0
OD2 D:ASP7 2.2 46.0 1.0
O1A D:DZ4403 2.4 35.7 1.0
O D:HOH505 2.7 42.9 1.0
CG D:ASP105 2.9 42.8 1.0
CD D:GLU106 3.0 51.4 1.0
OD2 D:ASP105 3.1 42.1 1.0
CG D:GLU106 3.1 50.9 1.0
PA D:DZ4403 3.2 39.0 1.0
CG D:ASP7 3.3 49.0 1.0
O2A D:DZ4403 3.4 38.9 1.0
O5' D:DZ4403 3.6 34.0 1.0
OP2 B:DG13 3.7 65.3 1.0
OG D:SER103 3.7 43.5 1.0
OD1 D:ASP7 3.7 46.7 1.0
MG D:MG402 3.8 37.0 1.0
O D:HOH504 3.8 42.9 1.0
C5' D:DZ4403 3.9 24.0 1.0
OE1 D:GLU106 4.2 58.8 1.0
CB D:ASP105 4.4 37.5 1.0
CB D:GLU106 4.5 49.5 1.0
O B:HOH102 4.6 45.4 1.0
CB D:ASP7 4.6 47.7 1.0
CB D:SER103 4.6 45.3 1.0
C D:ASP105 4.6 41.5 1.0
O1G D:DZ4403 4.6 42.0 1.0
O D:ASP105 4.8 41.5 1.0
N D:GLU106 4.8 45.9 1.0
N3A D:DZ4403 4.8 31.4 1.0
O2B D:DZ4403 4.9 36.2 1.0
CA D:ASP105 4.9 42.5 1.0

Magnesium binding site 4 out of 4 in 6vkp

Go back to Magnesium Binding Sites List in 6vkp
Magnesium binding site 4 out of 4 in the Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg


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 Dg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:37.0
occ:1.00
O D:PHE8 2.1 48.3 1.0
O1G D:DZ4403 2.1 42.0 1.0
OD1 D:ASP7 2.1 46.7 1.0
O1A D:DZ4403 2.1 35.7 1.0
O2B D:DZ4403 2.2 36.2 1.0
OD2 D:ASP105 2.3 42.1 1.0
CG D:ASP7 3.1 49.0 1.0
PG D:DZ4403 3.2 85.5 1.0
PB D:DZ4403 3.2 30.3 1.0
C D:PHE8 3.3 44.8 1.0
O D:HOH504 3.3 42.9 1.0
PA D:DZ4403 3.3 39.0 1.0
OD2 D:ASP7 3.4 46.0 1.0
O3G D:DZ4403 3.4 42.5 1.0
CG D:ASP105 3.5 42.8 1.0
O3B D:DZ4403 3.6 49.9 1.0
N3A D:DZ4403 3.7 31.4 1.0
MG D:MG401 3.8 39.8 1.0
N D:PHE8 3.9 42.9 1.0
C5' D:DZ4403 4.0 24.0 1.0
OD1 D:ASP105 4.1 56.4 1.0
CA D:PHE8 4.1 43.9 1.0
O5' D:DZ4403 4.2 34.0 1.0
NZ D:LYS159 4.2 70.4 1.0
CE D:LYS159 4.2 51.1 1.0
C D:ASP7 4.2 45.5 1.0
N D:ASP9 4.2 45.2 1.0
CA D:ASP9 4.3 48.7 1.0
CB D:ASP7 4.4 47.7 1.0
N D:TYR10 4.4 40.9 1.0
O2G D:DZ4403 4.5 41.5 1.0
O2A D:DZ4403 4.5 38.9 1.0
O D:HOH505 4.5 42.9 1.0
O D:ASP7 4.5 44.4 1.0
O1B D:DZ4403 4.6 39.5 1.0
CB D:ASP105 4.6 37.5 1.0
C D:ASP9 4.6 44.6 1.0
CB D:PHE8 4.8 40.7 1.0
CA D:ASP7 4.8 44.3 1.0
N D:PHE11 4.8 40.9 1.0
CB D:PHE11 4.9 35.8 1.0

Reference:

H.Jung, S.Lee. Crystal Structure of DPO4 Extension Past 8-Oxoadenine (Oxoa) and Dg To Be Published.
Page generated: Tue Oct 1 22:06:42 2024

Last articles

W in 1H9R
W in 1GUG
W in 1H9K
W in 1H0H
W in 1FKA
W in 1FEZ
W in 1CKJ
W in 1E3P
W in 1E18
W in 1B4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy