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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 Dec 14 08:27:58 2020

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