Atomistry » Magnesium » PDB 7oug-7p84 » 7oyf
Atomistry »
  Magnesium »
    PDB 7oug-7p84 »
      7oyf »

Magnesium in PDB 7oyf: Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate

Protein crystallography data

The structure of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate, PDB code: 7oyf was solved by H.Cui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.65 / 1.88
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.334, 106.334, 107.384, 90, 90, 120
R / Rfree (%) 15.9 / 18.8

Other elements in 7oyf:

The structure of Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate (pdb code 7oyf). 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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate, PDB code: 7oyf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 7oyf

Go back to Magnesium Binding Sites List in 7oyf
Magnesium binding site 1 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:25.6
occ:1.00
F1 A:KQB617 1.9 27.2 1.0
OE2 A:GLU99 2.0 22.4 1.0
O3B A:ADP604 2.1 28.1 1.0
O2A A:ADP604 2.1 26.2 1.0
OE1 A:GLU8 2.1 23.6 1.0
OH A:TYR92 2.2 27.9 1.0
CD A:GLU99 3.0 26.3 1.0
CD A:GLU8 3.1 33.4 1.0
MG1 A:KQB617 3.1 29.2 1.0
PA A:ADP604 3.2 28.2 1.0
PB A:ADP604 3.2 34.5 1.0
CZ A:TYR92 3.3 27.0 1.0
OE1 A:GLU99 3.4 20.8 1.0
O3A A:ADP604 3.4 27.3 1.0
MG A:MG602 3.4 26.0 1.0
CE1 A:TYR92 3.7 25.1 1.0
F2 A:KQB617 3.7 29.8 1.0
O A:HOH905 3.8 28.9 1.0
CG A:GLU8 3.8 23.3 1.0
O1 A:KQB617 3.9 31.5 1.0
MG A:MG603 3.9 23.6 0.5
O2B A:ADP604 4.0 35.8 1.0
OE2 A:GLU8 4.0 27.6 1.0
OG A:SER101 4.0 27.9 1.0
CB A:GLU8 4.1 23.3 1.0
O A:HOH716 4.1 32.5 1.0
O5' A:ADP604 4.2 27.0 1.0
CG A:GLU99 4.3 24.1 1.0
O A:HOH702 4.3 45.2 1.0
O1A A:ADP604 4.4 30.8 1.0
OD2 A:ASP94 4.4 27.9 1.0
OE1 B:GLU71 4.4 28.5 1.0
O1B A:ADP604 4.4 36.2 1.0
CE2 A:TYR92 4.5 31.3 1.0
F3 A:KQB617 4.7 36.8 1.0
NH1 A:ARG90 4.9 28.2 1.0
CG A:ASP94 5.0 36.5 1.0

Magnesium binding site 2 out of 4 in 7oyf

Go back to Magnesium Binding Sites List in 7oyf
Magnesium binding site 2 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg602

b:26.0
occ:1.00
F1 A:KQB617 1.9 27.2 1.0
OE1 A:GLU99 2.0 20.8 1.0
OD2 A:ASP94 2.0 27.9 1.0
OE2 A:GLU10 2.1 28.1 1.0
O A:HOH905 2.1 28.9 1.0
OE1 B:GLU71 2.3 28.5 1.0
CD A:GLU99 2.9 26.3 1.0
CD A:GLU10 3.1 27.0 1.0
CG A:ASP94 3.1 36.5 1.0
OE2 A:GLU99 3.2 22.4 1.0
MG1 A:KQB617 3.3 29.2 1.0
CD B:GLU71 3.4 29.9 1.0
MG A:MG601 3.4 25.6 1.0
CG A:GLU10 3.5 23.7 1.0
O1 A:KQB617 3.7 31.5 1.0
CB A:ASP94 3.8 27.7 1.0
CG B:GLU71 3.9 25.8 1.0
OH A:TYR92 3.9 27.9 1.0
F2 A:KQB617 4.0 29.8 1.0
OD1 A:ASP94 4.2 41.8 1.0
OE1 A:GLU8 4.2 23.6 1.0
OE1 A:GLU10 4.2 26.2 1.0
CB B:GLU71 4.2 25.5 1.0
CG A:GLU99 4.3 24.1 1.0
O3B A:ADP604 4.4 28.1 1.0
CE1 A:HIS155 4.5 27.2 1.0
OE2 B:GLU71 4.5 31.9 1.0
ND1 A:HIS95 4.7 45.5 1.0
CZ A:TYR92 4.8 27.0 1.0
CB A:GLU99 4.8 22.9 1.0
ND1 A:HIS155 4.9 24.9 1.0
MG A:MG603 5.0 23.6 0.5

Magnesium binding site 3 out of 4 in 7oyf

Go back to Magnesium Binding Sites List in 7oyf
Magnesium binding site 3 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg603

b:23.6
occ:0.53
F2 A:KQB617 1.7 29.8 1.0
NE2 A:HIS241 2.1 30.5 1.0
ND1 A:HIS155 2.2 24.9 1.0
OE2 A:GLU8 2.3 27.6 1.0
OE1 A:GLU8 2.4 23.6 1.0
O2B A:ADP604 2.5 35.8 1.0
CD A:GLU8 2.7 33.4 1.0
CE1 A:HIS241 2.9 25.0 1.0
CE1 A:HIS155 3.1 27.2 1.0
CD2 A:HIS241 3.2 23.4 1.0
CG A:HIS155 3.3 25.4 1.0
MG1 A:KQB617 3.4 29.2 1.0
O3B A:ADP604 3.5 28.1 1.0
PB A:ADP604 3.5 34.5 1.0
CB A:HIS155 3.6 23.8 1.0
F1 A:KQB617 3.8 27.2 1.0
O A:HOH786 3.8 37.2 1.0
MG A:MG601 3.9 25.6 1.0
O A:HOH905 3.9 28.9 1.0
ND1 A:HIS241 4.1 28.2 1.0
F3 A:KQB617 4.1 36.8 1.0
CG A:GLU8 4.2 23.3 1.0
O3A A:ADP604 4.2 27.3 1.0
NH2 A:ARG239 4.2 29.7 1.0
NE2 A:HIS155 4.2 26.9 1.0
CG A:HIS241 4.3 23.7 1.0
CD2 A:HIS155 4.4 22.6 1.0
OE1 B:GLU71 4.4 28.5 1.0
CB A:GLU8 4.7 23.3 1.0
O1B A:ADP604 4.8 36.2 1.0
OD1 A:ASN157 4.9 23.5 1.0
MG A:MG602 5.0 26.0 1.0

Magnesium binding site 4 out of 4 in 7oyf

Go back to Magnesium Binding Sites List in 7oyf
Magnesium binding site 4 out of 4 in the Crystal Structure of Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate


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 Depupylase Dop in Complex with Pup and Adp/Trifluoromagnesate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg617

b:29.2
occ:1.00
MG1 A:KQB617 0.0 29.2 1.0
F1 A:KQB617 1.9 27.2 1.0
F3 A:KQB617 1.9 36.8 1.0
F2 A:KQB617 1.9 29.8 1.0
O1 A:KQB617 2.0 31.5 1.0
OE1 B:GLU71 2.2 28.5 1.0
O3B A:ADP604 2.3 28.1 1.0
CD B:GLU71 3.1 29.9 1.0
MG A:MG601 3.1 25.6 1.0
OE2 B:GLU71 3.2 31.9 1.0
MG A:MG602 3.3 26.0 1.0
PB A:ADP604 3.3 34.5 1.0
MG A:MG603 3.4 23.6 0.5
O2B A:ADP604 3.6 35.8 1.0
OD2 A:ASP94 3.6 27.9 1.0
OE1 A:GLU8 3.6 23.6 1.0
O A:HOH716 3.8 32.5 1.0
OH A:TYR92 3.8 27.9 1.0
O A:HOH905 4.0 28.9 1.0
O1B A:ADP604 4.0 36.2 1.0
O A:HOH786 4.0 37.2 1.0
CE1 A:HIS155 4.4 27.2 1.0
O A:HOH702 4.5 45.2 1.0
ND1 A:HIS155 4.5 24.9 1.0
CG B:GLU71 4.5 25.8 1.0
CG A:ASP94 4.5 36.5 1.0
OE2 A:GLU99 4.6 22.4 1.0
OE1 A:GLU99 4.7 20.8 1.0
O3A A:ADP604 4.7 27.3 1.0
OD1 A:ASP94 4.7 41.8 1.0
CD A:GLU8 4.8 33.4 1.0
O2A A:ADP604 4.9 26.2 1.0
OE2 A:GLU10 5.0 28.1 1.0
NE2 A:HIS241 5.0 30.5 1.0

Reference:

H.Cui, A.U.Muller, M.Leibundgut, J.Tian, N.Ban, E.Weber-Ban. Structures of Prokaryotic Ubiquitin-Like Protein Pup in Complex with Depupylase Dop Reveal the Mechanism of Catalytic Phosphate Formation. Nat Commun V. 12 6635 2021.
ISSN: ESSN 2041-1723
PubMed: 34789727
DOI: 10.1038/S41467-021-26848-X
Page generated: Thu Oct 3 03:56:48 2024

Last articles

Cl in 2Y2M
Cl in 2Y2G
Cl in 2Y2K
Cl in 2Y2H
Cl in 2Y2J
Cl in 2Y2I
Cl in 2Y1X
Cl in 2Y1G
Cl in 2Y1F
Cl in 2Y05
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy