Atomistry » Magnesium » PDB 5ds5-5e75 » 5e4r
Atomistry »
  Magnesium »
    PDB 5ds5-5e75 »
      5e4r »

Magnesium in PDB 5e4r: Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd

Enzymatic activity of Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd

All present enzymatic activity of Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd:
1.1.1.86;

Protein crystallography data

The structure of Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd, PDB code: 5e4r was solved by J.K.B.Cahn, S.Brinkmann-Chen, A.R.Buller, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 103.88 / 1.94
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 103.882, 103.882, 142.074, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd (pdb code 5e4r). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd, PDB code: 5e4r:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5e4r

Go back to Magnesium Binding Sites List in 5e4r
Magnesium binding site 1 out of 2 in the Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd


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 Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg502

b:16.4
occ:1.00
O11 A:40E504 2.0 17.4 1.0
O A:HOH683 2.0 19.6 1.0
OD2 A:ASP191 2.1 19.2 1.0
O2 A:40E504 2.1 17.7 1.0
OE1 A:GLU195 2.1 17.4 1.0
O A:HOH775 2.1 19.3 1.0
C2 A:40E504 2.6 21.1 1.0
C1 A:40E504 2.7 19.4 1.0
CG A:ASP191 3.1 16.4 1.0
CD A:GLU195 3.1 17.5 1.0
OD1 A:ASP191 3.4 20.1 1.0
OE2 A:GLU195 3.4 18.0 1.0
MG A:MG503 3.7 20.8 1.0
N3 A:40E504 3.9 27.5 1.0
O A:HOH638 3.9 23.1 1.0
O12 A:40E504 4.0 19.4 1.0
OG A:SER399 4.1 19.3 1.0
O A:HOH615 4.4 18.6 1.0
CB A:ASP191 4.4 16.7 1.0
CG A:GLU195 4.5 19.4 1.0
O A:HOH675 4.5 21.7 1.0
NE2 A:HIS108 4.5 23.5 1.0
O2D A:NAP501 4.5 20.0 1.0
CE1 A:HIS108 4.5 22.2 1.0
O A:ASP191 4.6 15.6 1.0
CD2 A:HIS108 4.7 22.1 1.0
CB A:ALA402 4.7 18.6 1.0
ND1 A:HIS108 4.7 22.8 1.0
C A:ASP191 4.8 17.1 1.0
CG A:HIS108 4.8 20.5 1.0
CB A:GLU195 4.8 17.9 1.0
C4 A:40E504 4.9 28.5 1.0
N1N A:NAP501 5.0 20.9 1.0

Magnesium binding site 2 out of 2 in 5e4r

Go back to Magnesium Binding Sites List in 5e4r
Magnesium binding site 2 out of 2 in the Crystal Structure of Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd


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 Domain-Duplicated Synthetic Class II Ketol-Acid Reductoisomerase 2IA_KARI-Dd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg503

b:20.8
occ:1.00
O2 A:40E504 2.0 17.7 1.0
OD1 A:ASP191 2.0 20.1 1.0
O A:HOH627 2.0 26.7 1.0
O A:HOH675 2.0 21.7 1.0
O A:HOH601 2.3 38.2 1.0
O A:HOH638 2.3 23.1 1.0
C2 A:40E504 2.8 21.1 1.0
N3 A:40E504 3.0 27.5 1.0
CG A:ASP191 3.1 16.4 1.0
OD2 A:ASP191 3.5 19.2 1.0
MG A:MG502 3.7 16.4 1.0
NZ A:LYS131 3.8 28.7 1.0
OE1 A:GLU378 3.9 24.2 1.0
OE1 A:GLU374 4.1 33.5 1.0
OE2 A:GLU378 4.1 27.0 1.0
O A:HOH615 4.2 18.6 1.0
OE2 A:GLU374 4.2 29.5 1.0
OE1 A:GLU195 4.2 17.4 1.0
C1 A:40E504 4.2 19.4 1.0
CB A:ASP191 4.3 16.7 1.0
O A:HOH775 4.3 19.3 1.0
C4 A:40E504 4.4 28.5 1.0
CD A:GLU378 4.5 23.7 1.0
O A:PRO130 4.5 15.7 1.0
C5N A:NAP501 4.6 22.4 1.0
CE A:LYS131 4.6 26.9 1.0
CD A:GLU374 4.6 33.6 1.0
C4N A:NAP501 4.7 24.0 1.0
CA A:ASP191 4.7 15.8 1.0
O11 A:40E504 4.7 17.4 1.0
O A:ASP191 4.8 15.6 1.0
C41 A:40E504 4.9 28.4 1.0
CD A:LYS131 4.9 22.0 1.0
C42 A:40E504 4.9 31.4 1.0

Reference:

J.K.Cahn, S.Brinkmann-Chen, A.R.Buller, F.H.Arnold. Artificial Domain Duplication Replicates Evolutionary History of Ketol-Acid Reductoisomerases. Protein Sci. V. 25 1241 2016.
ISSN: ESSN 1469-896X
PubMed: 26644020
DOI: 10.1002/PRO.2852
Page generated: Mon Dec 14 20:13:45 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