Atomistry » Magnesium » PDB 4x7w-4xgp » 4xdy
Atomistry »
  Magnesium »
    PDB 4x7w-4xgp »
      4xdy »

Magnesium in PDB 4xdy: Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean

Enzymatic activity of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean

All present enzymatic activity of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean:
1.1.1.86;

Protein crystallography data

The structure of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean, PDB code: 4xdy was solved by J.K.B.Cahn, S.Brinkmann-Chen, F.H.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 102.57 / 1.54
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 49.695, 141.748, 148.598, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean (pdb code 4xdy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean, PDB code: 4xdy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 1 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.9
occ:1.00
 O2 A:HIO406 2.0 17.6 1.0
OE1 A:GLU199 2.0 16.4 1.0
O11 A:HIO406 2.0 17.2 1.0
OD2 A:ASP195 2.1 17.3 1.0
O A:HOH528 2.1 19.1 1.0
O A:HOH647 2.2 15.4 1.0
C2 A:HIO406 2.7 18.7 1.0
C1 A:HIO406 2.8 16.8 1.0
CD A:GLU199 3.1 17.4 1.0
CG A:ASP195 3.1 16.8 1.0
OE2 A:GLU199 3.4 17.7 1.0
OD1 A:ASP195 3.5 20.0 1.0
MG A:MG402 3.6 17.1 1.0
N3 A:HIO406 3.9 20.7 1.0
O B:HOH539 3.9 19.2 1.0
O12 A:HIO406 4.1 19.2 1.0
O A:HOH534 4.2 17.7 1.0
OG B:SER256 4.2 17.0 1.0
NE2 A:HIS112 4.3 21.9 1.0
CE1 A:HIS112 4.3 22.2 1.0
CB A:ASP195 4.4 19.2 1.0
CG A:GLU199 4.5 17.2 1.0
O A:HOH527 4.5 20.2 1.0
O2D A:NAI403 4.5 19.2 1.0
ND1 A:HIS112 4.5 18.0 1.0
CD2 A:HIS112 4.5 22.3 1.0
O A:ASP195 4.6 17.4 1.0
O3 A:HIO406 4.6 25.5 1.0
CB B:ALA259 4.7 17.5 1.0
CG A:HIS112 4.7 19.7 1.0
C A:ASP195 4.8 17.1 1.0
CB A:GLU199 4.8 17.5 1.0
C4 A:HIO406 5.0 23.3 1.0

Magnesium binding site 2 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 2 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.1
occ:1.00
 OD1 A:ASP195 2.0 20.0 1.0
O3 A:HIO406 2.0 25.5 1.0
O2 A:HIO406 2.0 17.6 1.0
O B:HOH539 2.1 19.2 1.0
O B:HOH540 2.2 18.7 1.0
O A:HOH527 2.2 20.2 1.0
N3 A:HIO406 2.7 20.7 1.0
C2 A:HIO406 2.7 18.7 1.0
CG A:ASP195 3.0 16.8 1.0
OD2 A:ASP195 3.5 17.3 1.0
MG A:MG401 3.6 13.9 1.0
OE1 A:GLU199 4.0 16.4 1.0
OE1 B:GLU235 4.0 20.4 1.0
NZ A:LYS135 4.0 20.0 1.0
C4 A:HIO406 4.1 23.3 1.0
OE2 B:GLU235 4.1 22.2 1.0
OE2 B:GLU231 4.1 20.8 1.0
C1 A:HIO406 4.2 16.8 1.0
OE1 B:GLU231 4.2 19.4 1.0
O A:HOH534 4.2 17.7 1.0
CB A:ASP195 4.3 19.2 1.0
O A:HOH647 4.4 15.4 1.0
C41 A:HIO406 4.4 24.1 1.0
CD B:GLU235 4.5 22.4 1.0
CE A:LYS135 4.6 21.5 1.0
O11 A:HIO406 4.6 17.2 1.0
O A:ASP195 4.6 17.4 1.0
CA A:ASP195 4.6 18.4 1.0
CD B:GLU231 4.6 18.5 1.0
O A:PRO134 4.7 19.7 1.0
C5N A:NAI403 4.8 24.2 1.0
C42 A:HIO406 4.8 23.7 1.0
C4N A:NAI403 4.9 24.1 1.0
C A:ASP195 5.0 17.1 1.0

Magnesium binding site 3 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 3 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:34.2
occ:1.00
 O A:HOH623 1.9 35.0 1.0
O A:HOH665 2.1 32.9 1.0
O A:HOH533 2.1 23.8 1.0
OD1 A:ASN257 2.1 20.5 1.0
O A:HOH630 2.1 34.7 1.0
CG A:ASN257 3.3 18.7 1.0
ND2 A:ASN257 3.9 18.6 1.0
OE1 A:GLU260 4.0 24.5 1.0
NH2 B:ARG310 4.1 27.1 1.0
O A:GLU253 4.1 19.1 1.0
O A:ILE255 4.2 16.5 1.0
N A:ASN257 4.3 16.2 1.0
O B:HOH553 4.4 18.6 1.0
O A:ALA252 4.4 20.6 1.0
CB A:ASN257 4.4 16.9 1.0
CA A:ASN257 4.5 15.1 1.0
O1A B:NAI404 4.5 20.5 1.0
O B:HOH640 4.6 33.2 1.0
C A:SER256 4.8 16.2 1.0
C A:GLU253 4.8 20.4 1.0
O B:HOH557 4.8 17.8 1.0
O B:HOH570 4.9 29.1 1.0
O A:HOH565 5.0 26.2 1.0
CA A:GLU253 5.0 20.6 1.0

Magnesium binding site 4 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 4 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:14.2
occ:1.00
 OD2 B:ASP195 2.0 16.9 1.0
O11 B:HIO401 2.1 15.4 1.0
OE1 B:GLU199 2.1 15.1 1.0
O2 B:HIO401 2.1 15.6 1.0
O B:HOH536 2.2 17.1 1.0
O B:HOH537 2.2 17.4 1.0
C2 B:HIO401 2.8 17.1 1.0
C1 B:HIO401 2.8 16.3 1.0
CD B:GLU199 3.1 17.2 1.0
CG B:ASP195 3.1 14.8 1.0
OE2 B:GLU199 3.4 17.5 1.0
OD1 B:ASP195 3.5 15.0 1.0
MG B:MG403 3.7 15.3 1.0
O A:HOH525 3.9 17.9 1.0
N3 B:HIO401 4.0 19.4 1.0
O12 B:HIO401 4.0 15.8 1.0
O B:HOH544 4.2 19.4 1.0
NE2 B:HIS112 4.2 18.6 1.0
CE1 B:HIS112 4.3 18.2 1.0
OG A:SER256 4.3 15.8 1.0
O B:HOH682 4.3 45.4 1.0
CB B:ASP195 4.4 14.8 1.0
O2D B:NAI404 4.4 17.9 1.0
O B:HOH538 4.5 17.6 1.0
ND1 B:HIS112 4.5 18.1 1.0
CG B:GLU199 4.5 16.2 1.0
CD2 B:HIS112 4.5 18.5 1.0
O B:ASP195 4.5 15.0 1.0
O3 B:HIO401 4.5 21.6 1.0
CB A:ALA259 4.6 16.9 1.0
CG B:HIS112 4.6 17.0 1.0
C B:ASP195 4.7 15.4 1.0
CB B:GLU199 4.9 16.9 1.0

Magnesium binding site 5 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 5 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:15.3
occ:1.00
 OD1 B:ASP195 2.0 15.0 1.0
O3 B:HIO401 2.0 21.6 1.0
O2 B:HIO401 2.0 15.6 1.0
O A:HOH526 2.0 16.3 1.0
O B:HOH538 2.1 17.6 1.0
O A:HOH525 2.2 17.9 1.0
C2 B:HIO401 2.8 17.1 1.0
N3 B:HIO401 2.9 19.4 1.0
CG B:ASP195 3.0 14.8 1.0
OD2 B:ASP195 3.4 16.9 1.0
MG B:MG402 3.7 14.2 1.0
NZ B:LYS135 3.9 18.9 1.0
O B:HOH682 3.9 45.4 1.0
OE1 A:GLU235 4.0 17.7 1.0
OE1 B:GLU199 4.1 15.1 1.0
OE2 A:GLU235 4.1 18.1 1.0
OE2 A:GLU231 4.2 17.1 1.0
O B:HOH544 4.2 19.4 1.0
OE1 A:GLU231 4.2 17.4 1.0
C4 B:HIO401 4.2 19.2 1.0
CB B:ASP195 4.3 14.8 1.0
C1 B:HIO401 4.3 16.3 1.0
O B:HOH537 4.5 17.4 1.0
CD A:GLU235 4.5 17.0 1.0
CE B:LYS135 4.5 18.7 1.0
O B:PRO134 4.6 17.9 1.0
CA B:ASP195 4.6 14.9 1.0
O B:ASP195 4.6 15.0 1.0
O11 B:HIO401 4.6 15.4 1.0
CD A:GLU231 4.7 16.4 1.0
C41 B:HIO401 4.7 21.0 1.0
C5N B:NAI404 4.7 20.3 1.0
C4N B:NAI404 4.9 19.8 1.0
C42 B:HIO401 4.9 19.9 1.0
C B:ASP195 5.0 15.4 1.0
CA B:LYS135 5.0 15.6 1.0

Magnesium binding site 6 out of 6 in 4xdy

Go back to Magnesium Binding Sites List in 4xdy
Magnesium binding site 6 out of 6 in the Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Nadh-Preferring Ketol-Acid Reductoisomerase From An Uncultured Archean within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg405

b:34.3
occ:1.00
 O A:HOH625 1.9 35.6 1.0
O B:HOH694 2.0 37.2 1.0
OD1 B:ASN257 2.1 20.7 1.0
O B:HOH649 2.1 31.3 1.0
O B:HOH551 2.1 26.0 1.0
CG B:ASN257 3.2 20.4 1.0
ND2 B:ASN257 3.8 22.9 1.0
O B:GLU253 4.0 20.5 1.0
OE1 B:GLU260 4.1 23.0 1.0
O B:ILE255 4.1 17.8 1.0
NH2 A:ARG310 4.3 31.2 1.0
N B:ASN257 4.3 19.0 1.0
O A:HOH531 4.3 23.3 1.0
O B:ALA252 4.4 19.1 1.0
O1A A:NAI403 4.4 23.4 1.0
CB B:ASN257 4.5 20.8 1.0
CA B:ASN257 4.5 18.3 1.0
C B:GLU253 4.8 20.2 1.0
C B:SER256 4.8 18.0 1.0
O A:HOH544 4.8 19.8 1.0
O A:HOH557 4.9 27.9 1.0
CA B:GLU253 5.0 22.6 1.0

Reference:

J.K.Cahn, S.Brinkmann-Chen, T.Spatzal, J.A.Wiig, A.R.Buller, O.Einsle, Y.Hu, M.W.Ribbe, F.H.Arnold. Cofactor Specificity Motifs and the Induced Fit Mechanism in Class I Ketol-Acid Reductoisomerases. Biochem.J. 2015.
ISSN: ESSN 1470-8728
PubMed: 25849365
DOI: 10.1042/BJ20150183
Page generated: Mon Dec 14 19:46:19 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