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Magnesium in PDB 4r8u: S-Sad Structure of Dinb-Dna Complex

Enzymatic activity of S-Sad Structure of Dinb-Dna Complex

All present enzymatic activity of S-Sad Structure of Dinb-Dna Complex:
2.7.7.7;

Protein crystallography data

The structure of S-Sad Structure of Dinb-Dna Complex, PDB code: 4r8u was solved by J.Kottur, D.T.Nair, T.Weinert, V.Oligeric, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.23 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.950, 57.210, 110.600, 90.00, 94.69, 90.00
R / Rfree (%) 18.1 / 22

Magnesium Binding Sites:

The binding sites of Magnesium atom in the S-Sad Structure of Dinb-Dna Complex (pdb code 4r8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the S-Sad Structure of Dinb-Dna Complex, PDB code: 4r8u:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4r8u

Go back to Magnesium Binding Sites List in 4r8u
Magnesium binding site 1 out of 2 in the S-Sad Structure of Dinb-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S-Sad Structure of Dinb-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:37.0
occ:1.00
O2B A:1FZ402 2.2 40.8 1.0
O A:MET10 2.2 54.3 1.0
O1A A:1FZ402 2.3 40.9 1.0
OD1 A:ASP9 2.3 51.0 1.0
OD2 A:ASP104 2.4 71.6 1.0
O1G A:1FZ402 2.4 40.4 1.0
OD1 A:ASP104 3.0 98.7 1.0
CG A:ASP104 3.0 72.8 1.0
PB A:1FZ402 3.4 40.6 1.0
CG A:ASP9 3.4 60.0 1.0
C A:MET10 3.4 49.3 1.0
PA A:1FZ402 3.5 40.8 1.0
PG A:1FZ402 3.6 40.3 1.0
N3A A:1FZ402 3.8 40.7 1.0
O3B A:1FZ402 3.9 40.4 1.0
NZ A:LYS158 3.9 49.8 1.0
OD2 A:ASP9 4.0 68.5 1.0
N A:MET10 4.0 40.4 1.0
C5' A:1FZ402 4.0 41.3 1.0
O3G A:1FZ402 4.2 40.2 1.0
O5' A:1FZ402 4.2 41.1 1.0
CA A:MET10 4.2 49.4 1.0
C A:ASP9 4.3 41.2 1.0
CB A:ASP104 4.4 43.2 1.0
N A:ASP11 4.4 54.4 1.0
CB A:ASP9 4.6 50.5 1.0
CA A:ASP11 4.6 48.9 1.0
OE1 A:GLU105 4.6 66.0 1.0
CE A:LYS158 4.6 59.7 1.0
N A:CYS12 4.6 45.2 1.0
O1B A:1FZ402 4.7 40.8 1.0
CB A:MET10 4.7 39.4 1.0
CB A:PHE13 4.7 39.6 1.0
CA A:ASP9 4.7 46.9 1.0
N A:PHE13 4.8 49.5 1.0
C A:ASP11 4.8 48.3 1.0
O2A A:1FZ402 4.8 40.9 1.0
O A:ASP9 4.8 51.0 1.0
O2G A:1FZ402 4.9 40.3 1.0

Magnesium binding site 2 out of 2 in 4r8u

Go back to Magnesium Binding Sites List in 4r8u
Magnesium binding site 2 out of 2 in the S-Sad Structure of Dinb-Dna Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S-Sad Structure of Dinb-Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:30.5
occ:1.00
O1A B:1FZ401 2.0 52.9 1.0
O1G B:1FZ401 2.3 51.9 1.0
OD1 B:ASP9 2.3 68.1 1.0
O2B B:1FZ401 2.3 51.5 1.0
O B:MET10 2.3 57.5 1.0
OD2 B:ASP104 2.4 72.7 1.0
PB B:1FZ401 3.3 50.7 1.0
PA B:1FZ401 3.3 51.7 1.0
CG B:ASP9 3.4 74.0 1.0
PG B:1FZ401 3.4 51.8 1.0
C B:MET10 3.5 62.2 1.0
CG B:ASP104 3.6 76.8 1.0
N3A B:1FZ401 3.6 50.7 1.0
O3B B:1FZ401 3.8 51.3 1.0
O3G B:1FZ401 3.9 52.3 1.0
N B:MET10 4.0 65.5 1.0
C5' B:1FZ401 4.0 51.0 1.0
OD2 B:ASP9 4.1 81.1 1.0
NZ B:LYS158 4.1 66.0 1.0
O5' B:1FZ401 4.2 51.1 1.0
CA B:MET10 4.3 62.7 1.0
OD1 B:ASP104 4.3 88.5 1.0
C B:ASP9 4.4 65.4 1.0
OE1 B:GLU105 4.4 85.7 1.0
O2A B:1FZ401 4.5 51.5 1.0
N B:ASP11 4.5 71.0 1.0
CB B:ASP9 4.6 71.2 1.0
CB B:ASP104 4.6 76.3 1.0
O1B B:1FZ401 4.7 50.3 1.0
CB B:MET10 4.7 65.5 1.0
N B:CYS12 4.7 61.4 1.0
N B:PHE13 4.7 62.9 1.0
CB B:PHE13 4.7 62.3 1.0
CA B:ASP11 4.7 66.3 1.0
CA B:ASP9 4.8 67.7 1.0
O2G B:1FZ401 4.8 52.1 1.0
O B:ASP9 4.8 65.2 1.0
C B:ASP11 4.9 67.5 1.0

Reference:

T.Weinert, V.Olieric, S.Waltersperger, E.Panepucci, L.Chen, H.Zhang, D.Zhou, J.Rose, A.Ebihara, S.Kuramitsu, D.Li, N.Howe, G.Schnapp, A.Pautsch, K.Bargsten, A.E.Prota, P.Surana, J.Kottur, D.T.Nair, F.Basilico, V.Cecatiello, S.Pasqualato, A.Boland, O.Weichenrieder, B.Wang, M.O.Steinmetz, M.Caffrey, M.Wang. Fast Native-Sad Phasing For Routine Macromolecular Structure Determination Nat.Methods 2014.
ISSN: ESSN 1548-7105
PubMed: 25506719
DOI: 10.1038/NMETH.3211
Page generated: Mon Dec 14 19:29:58 2020

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