Atomistry » Magnesium » PDB 3n8u-3nky » 3n8u
Atomistry »
  Magnesium »
    PDB 3n8u-3nky »
      3n8u »

Magnesium in PDB 3n8u: Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution

Protein crystallography data

The structure of Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution, PDB code: 3n8u was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.74 / 1.44
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.470, 49.930, 128.320, 90.00, 117.58, 90.00
R / Rfree (%) 16.7 / 19

Other elements in 3n8u:

The structure of Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution (pdb code 3n8u). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution, PDB code: 3n8u:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3n8u

Go back to Magnesium Binding Sites List in 3n8u
Magnesium binding site 1 out of 3 in the Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution


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 An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1

b:17.2
occ:1.00
O A:HOH572 2.0 17.2 1.0
O A:HOH527 2.1 14.0 1.0
O A:HOH620 2.1 19.1 1.0
O A:HOH578 2.1 16.9 1.0
O A:HOH543 2.1 15.3 1.0
O A:HOH662 2.1 20.0 1.0
OE2 A:GLU111 3.7 30.5 0.5
OD2 A:ASP326 3.7 16.6 1.0
O A:HOH684 4.0 21.5 1.0
OE1 A:GLU309 4.0 14.9 1.0
OE1 A:GLU111 4.0 22.6 0.5
O A:HOH448 4.0 15.7 0.5
O A:HOH670 4.1 22.8 1.0
CD A:GLU111 4.2 34.3 0.5
O A:HOH604 4.2 19.0 1.0
O A:HOH1005 4.2 33.5 0.5
OD1 A:ASP322 4.3 21.6 1.0
O A:HOH853 4.3 27.1 1.0
O A:ASP326 4.3 17.2 1.0
CE A:LYS116 4.4 12.4 1.0
OE2 A:GLU111 4.4 15.8 0.5
NZ A:LYS116 4.4 16.4 1.0
OE1 A:GLU137 4.5 16.2 1.0
CG A:ASP326 4.6 17.0 1.0
CD A:GLU309 4.9 15.9 1.0
O A:HOH475 5.0 50.1 0.5

Magnesium binding site 2 out of 3 in 3n8u

Go back to Magnesium Binding Sites List in 3n8u
Magnesium binding site 2 out of 3 in the Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution


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 An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2

b:38.3
occ:1.00
O A:HOH1179 1.9 26.1 0.5
O B:HOH536 1.9 33.4 1.0
O A:HOH876 2.0 27.4 1.0
O A:HOH570 2.3 33.4 1.0
O B:HOH526 2.3 25.7 1.0
O B:HOH416 2.7 32.1 1.0
O A:HOH1179 3.7 23.0 0.5
OD2 A:ASP296 3.9 21.9 1.0
NZ B:LYS233 4.1 21.0 1.0
O A:HOH601 4.2 38.1 1.0
O B:HOH550 4.3 28.1 1.0
O B:HOH574 4.3 28.9 1.0
O B:HOH1151 4.4 62.4 1.0
OD1 A:ASP296 4.5 18.9 1.0
OD2 B:ASP103 4.6 24.3 1.0
CG A:ASP296 4.7 18.1 1.0
O A:HOH855 4.8 28.2 1.0
O B:HOH830 4.9 43.6 1.0
OE1 A:GLU292 5.0 28.0 1.0

Magnesium binding site 3 out of 3 in 3n8u

Go back to Magnesium Binding Sites List in 3n8u
Magnesium binding site 3 out of 3 in the Crystal Structure of An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution


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 An Imelysin Peptidase (BACOVA_03801) From Bacteroides Ovatus at 1.44 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3

b:21.2
occ:1.00
O B:HOH556 1.9 27.8 1.0
O B:HOH483 1.9 21.8 1.0
O B:HOH495 2.1 22.9 1.0
O B:HOH516 2.1 23.6 1.0
O B:HOH426 2.1 31.1 1.0
O B:HOH466 2.1 19.3 1.0
OD2 B:ASP326 3.7 27.4 1.0
OE2 B:GLU111 3.8 27.3 0.5
O B:HOH427 3.9 30.4 1.0
OE1 B:GLU309 4.0 21.8 1.0
O B:HOH583 4.0 30.2 1.0
O B:HOH898 4.1 23.5 0.5
OE1 B:GLU111 4.1 21.8 0.5
OD1 B:ASP322 4.2 31.5 1.0
O B:HOH689 4.3 36.8 1.0
O B:HOH547 4.3 26.7 1.0
O B:HOH388 4.3 57.8 1.0
CD B:GLU111 4.3 28.0 0.5
O B:ASP326 4.3 26.7 1.0
NZ B:LYS116 4.4 24.5 1.0
CE B:LYS116 4.5 22.8 1.0
OE1 B:GLU137 4.5 29.2 1.0
CG B:ASP326 4.6 26.7 1.0
OE2 B:GLU111 4.7 32.4 0.5
CD B:GLU309 4.8 22.4 1.0
OD2 B:ASP322 4.9 39.4 1.0

Reference:

Q.Xu, N.D.Rawlings, C.L.Farr, H.J.Chiu, J.C.Grant, L.Jaroszewski, H.E.Klock, M.W.Knuth, M.D.Miller, D.Weekes, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson. Structural and Sequence Analysis of Imelysin-Like Proteins Implicated in Bacterial Iron Uptake. Plos One V. 6 21875 2011.
ISSN: ESSN 1932-6203
PubMed: 21799754
DOI: 10.1371/JOURNAL.PONE.0021875
Page generated: Mon Aug 11 00:51:09 2025

Last articles

Mn in 9LJU
Mn in 9LJW
Mn in 9LJS
Mn in 9LJR
Mn in 9LJT
Mn in 9LJV
Mg in 9UA2
Mg in 9R96
Mg in 9VM1
Mg in 9P01
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy