Atomistry » Magnesium » PDB 5chg-5cqz » 5ckw
Atomistry »
  Magnesium »
    PDB 5chg-5cqz »
      5ckw »

Magnesium in PDB 5ckw: Crystal Structure of LEGK4_AMPPNP Kinase

Protein crystallography data

The structure of Crystal Structure of LEGK4_AMPPNP Kinase, PDB code: 5ckw was solved by A.Flayhan, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.35 / 2.49
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.684, 76.871, 86.441, 90.00, 98.19, 90.00
R / Rfree (%) 20.4 / 25.8

Other elements in 5ckw:

The structure of Crystal Structure of LEGK4_AMPPNP Kinase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of LEGK4_AMPPNP Kinase (pdb code 5ckw). 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 LEGK4_AMPPNP Kinase, PDB code: 5ckw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ckw

Go back to Magnesium Binding Sites List in 5ckw
Magnesium binding site 1 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg502

b:40.5
occ:1.00
OD1 B:ASN200 2.2 46.2 1.0
O B:HOH675 2.2 48.0 1.0
O2A B:ANP501 2.2 38.1 1.0
N3B B:ANP501 2.4 72.1 1.0
OD2 B:ASP213 2.6 49.2 1.0
CG B:ASN200 3.2 40.9 1.0
CG B:ASP213 3.4 49.1 1.0
PB B:ANP501 3.5 65.5 1.0
PA B:ANP501 3.5 42.8 1.0
O3G B:ANP501 3.6 0.9 1.0
PG B:ANP501 3.6 0.7 1.0
ND2 B:ASN200 3.6 33.5 1.0
O2B B:ANP501 3.7 67.8 1.0
O3A B:ANP501 3.8 46.7 1.0
CB B:ASP213 3.8 52.1 1.0
O B:HOH642 4.1 19.4 0.7
MG B:MG503 4.2 33.5 1.0
OD1 B:ASP213 4.3 42.9 1.0
O2G B:ANP501 4.4 1.0 1.0
O B:GLY199 4.4 49.4 1.0
O1A B:ANP501 4.5 29.9 1.0
CB B:ASN200 4.6 37.7 1.0
O5' B:ANP501 4.6 57.9 1.0
C5' B:ANP501 4.7 50.2 1.0
O3' B:ANP501 4.7 46.8 1.0
O1G B:ANP501 4.8 0.1 1.0
O1B B:ANP501 4.8 57.7 1.0
CA B:ASN200 4.8 41.5 1.0
C3' B:ANP501 4.9 42.8 1.0
OD2 B:ASP195 5.0 39.5 1.0
C B:GLY199 5.0 44.2 1.0

Magnesium binding site 2 out of 4 in 5ckw

Go back to Magnesium Binding Sites List in 5ckw
Magnesium binding site 2 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg503

b:33.5
occ:1.00
O B:HOH642 1.9 19.4 0.7
O B:HOH649 2.0 72.9 1.0
O2B B:ANP501 2.4 67.8 1.0
OD2 B:ASP213 2.5 49.2 1.0
OD1 B:ASP213 2.6 42.9 1.0
CG B:ASP213 2.9 49.1 1.0
PB B:ANP501 3.7 65.5 1.0
O B:HOH675 3.9 48.0 1.0
N3B B:ANP501 4.0 72.1 1.0
MG B:MG502 4.2 40.5 1.0
OD2 B:ASP195 4.4 39.5 1.0
CB B:ASP213 4.4 52.1 1.0
NZ B:LYS104 4.4 40.1 1.0
O2G B:ANP501 4.5 1.0 1.0
O1B B:ANP501 4.6 57.7 1.0
O3A B:ANP501 4.8 46.7 1.0
O2A B:ANP501 4.9 38.1 1.0

Magnesium binding site 3 out of 4 in 5ckw

Go back to Magnesium Binding Sites List in 5ckw
Magnesium binding site 3 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:79.8
occ:1.00
O2B A:ANP501 2.0 0.1 1.0
OD1 A:ASN200 2.3 83.6 1.0
O A:HOH648 2.6 60.0 1.0
O3A A:ANP501 2.8 0.9 1.0
PB A:ANP501 2.9 0.5 1.0
CG A:ASN200 3.2 71.9 1.0
OD2 A:ASP213 3.4 87.9 1.0
ND2 A:ASN200 3.5 66.5 1.0
O A:GLY199 3.7 67.8 1.0
N3B A:ANP501 3.8 0.2 1.0
PA A:ANP501 3.9 91.8 1.0
O5' A:ANP501 4.0 97.6 1.0
CG A:ASP213 4.1 78.2 1.0
O1B A:ANP501 4.1 0.5 1.0
O2G A:ANP501 4.4 0.6 1.0
O1A A:ANP501 4.5 90.9 1.0
C A:GLY199 4.5 69.8 1.0
CB A:ASP213 4.5 77.0 1.0
C5' A:ANP501 4.6 94.3 1.0
CB A:ASN200 4.6 65.6 1.0
PG A:ANP501 4.8 0.5 1.0
OD1 A:ASP213 4.9 74.7 1.0
NZ A:LYS197 4.9 62.0 1.0
CA A:ASN200 4.9 69.0 1.0
O A:HOH618 5.0 69.3 1.0

Magnesium binding site 4 out of 4 in 5ckw

Go back to Magnesium Binding Sites List in 5ckw
Magnesium binding site 4 out of 4 in the Crystal Structure of LEGK4_AMPPNP Kinase


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 LEGK4_AMPPNP Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:77.5
occ:1.00
OD2 A:ASP213 2.8 87.9 1.0
OD1 A:ASP213 2.8 74.7 1.0
O1B A:ANP501 3.0 0.5 1.0
O A:HOH603 3.0 65.3 1.0
CG A:ASP213 3.2 78.2 1.0
OD2 A:ASP195 3.4 89.5 1.0
OG A:SER216 3.7 83.5 1.0
PB A:ANP501 4.1 0.5 1.0
O2B A:ANP501 4.1 0.1 1.0
CG A:ASP195 4.2 77.8 1.0
CB A:ASP195 4.5 69.6 1.0
N A:GLY215 4.6 81.2 1.0
CB A:ASP213 4.6 77.0 1.0
CA A:GLY215 4.7 82.6 1.0
ND2 A:ASN200 4.8 66.5 1.0
O3A A:ANP501 4.8 0.9 1.0
CB A:SER216 4.8 87.7 1.0
O A:TRP228 4.8 80.1 1.0
N A:SER216 4.9 81.4 1.0
O A:ASP213 4.9 82.4 1.0
C A:GLY215 5.0 86.6 1.0

Reference:

A.Flayhan, C.Berge, N.Bailo, P.Doublet, R.Bayliss, L.Terradot. The Structure of Legionella Pneumophila LEGK4 Type Four Secretion System (T4SS) Effector Reveals A Novel Dimeric Eukaryotic-Like Kinase. Sci Rep V. 5 14602 2015.
ISSN: ESSN 2045-2322
PubMed: 26419332
DOI: 10.1038/SREP14602
Page generated: Mon Dec 14 20:07:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy