Atomistry » Magnesium » PDB 8d9r-8diq » 8dht
Atomistry »
  Magnesium »
    PDB 8d9r-8diq »
      8dht »

Magnesium in PDB 8dht: Crystal Structure of A Typeiii Rubisco

Enzymatic activity of Crystal Structure of A Typeiii Rubisco

All present enzymatic activity of Crystal Structure of A Typeiii Rubisco:
4.1.1.39;

Protein crystallography data

The structure of Crystal Structure of A Typeiii Rubisco, PDB code: 8dht was solved by H.Qingqiu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.38 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.329, 116.206, 83.285, 90, 96.32, 90
R / Rfree (%) 14.4 / 17.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Typeiii Rubisco (pdb code 8dht). 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 A Typeiii Rubisco, PDB code: 8dht:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8dht

Go back to Magnesium Binding Sites List in 8dht
Magnesium binding site 1 out of 4 in the Crystal Structure of A Typeiii Rubisco


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 A Typeiii Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:14.8
occ:1.00
O3 A:3PG503 2.0 18.6 1.0
OD1 A:ASP188 2.0 15.8 1.0
OE1 A:GLU189 2.1 13.7 1.0
OQ2 A:KCX186 2.1 14.9 1.0
O2 A:3PG502 2.2 16.1 1.0
O2 A:3PG503 2.2 14.9 1.0
C1 A:3PG503 2.8 15.7 1.0
C2 A:3PG503 2.8 19.6 1.0
C1 A:3PG502 3.1 16.0 1.0
CD A:GLU189 3.2 15.9 1.0
CX A:KCX186 3.2 14.9 1.0
CG A:ASP188 3.2 18.2 1.0
O1 A:3PG502 3.5 16.7 1.0
OQ1 A:KCX186 3.6 17.1 1.0
OE2 A:GLU189 3.6 15.0 1.0
ND2 C:ASN108 3.8 14.2 1.0
OD2 A:ASP188 3.9 21.1 1.0
NZ A:LYS160 3.9 15.8 1.0
N A:GLU189 3.9 13.4 1.0
NE2 A:HIS278 4.0 15.1 1.0
NZ A:LYS162 4.0 21.8 1.0
O1 A:3PG503 4.0 19.6 1.0
C3 A:3PG503 4.1 18.0 1.0
CA A:ASP188 4.3 15.5 1.0
NZ A:KCX186 4.3 13.2 1.0
CB A:ASP188 4.3 12.5 1.0
C2 A:3PG502 4.3 20.5 1.0
CG A:GLU189 4.5 15.9 1.0
CB A:GLU189 4.6 14.2 1.0
CG1 A:VAL158 4.7 14.6 1.0
C A:ASP188 4.7 15.2 1.0
CD2 A:HIS278 4.7 13.5 1.0
O1P A:3PG503 4.8 14.2 1.0
CE1 A:HIS278 4.8 13.9 1.0
CG2 A:VAL158 4.9 13.7 1.0
CA A:GLU189 4.9 12.6 1.0
CE A:LYS162 5.0 19.8 1.0

Magnesium binding site 2 out of 4 in 8dht

Go back to Magnesium Binding Sites List in 8dht
Magnesium binding site 2 out of 4 in the Crystal Structure of A Typeiii Rubisco


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 A Typeiii Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg501

b:15.8
occ:1.00
O3 B:3PG503 2.0 19.7 1.0
OD1 B:ASP188 2.0 17.2 1.0
OE1 B:GLU189 2.1 16.6 1.0
OQ1 B:KCX186 2.1 14.4 1.0
O1 B:3PG503 2.2 20.0 1.0
O1 B:3PG502 2.2 16.6 1.0
C1 B:3PG503 2.8 17.2 1.0
C2 B:3PG503 2.8 23.7 1.0
C1 B:3PG502 3.1 20.7 1.0
CD B:GLU189 3.2 19.5 1.0
CX B:KCX186 3.2 16.6 1.0
CG B:ASP188 3.2 16.8 1.0
O2 B:3PG502 3.5 19.2 1.0
OE2 B:GLU189 3.6 19.4 1.0
OQ2 B:KCX186 3.6 16.1 1.0
NZ B:LYS160 3.9 20.8 1.0
NZ B:LYS162 3.9 17.1 1.0
NE2 B:HIS278 3.9 15.1 1.0
OD2 B:ASP188 3.9 23.6 1.0
N B:GLU189 3.9 13.9 1.0
O2 B:3PG503 4.0 23.3 1.0
C3 B:3PG503 4.1 20.3 1.0
CA B:ASP188 4.2 13.0 1.0
CB B:ASP188 4.3 13.6 1.0
NZ B:KCX186 4.3 14.2 1.0
C2 B:3PG502 4.4 19.6 1.0
CG B:GLU189 4.4 16.3 1.0
CB B:GLU189 4.6 12.2 1.0
CG1 B:VAL158 4.6 13.8 1.0
C B:ASP188 4.6 13.6 1.0
CD2 B:HIS278 4.7 15.3 1.0
CE1 B:HIS278 4.8 15.2 1.0
O1P B:3PG503 4.8 18.5 1.0
CG2 B:VAL158 4.9 12.9 1.0
CA B:GLU189 4.9 14.2 1.0

Magnesium binding site 3 out of 4 in 8dht

Go back to Magnesium Binding Sites List in 8dht
Magnesium binding site 3 out of 4 in the Crystal Structure of A Typeiii Rubisco


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 A Typeiii Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg501

b:16.6
occ:1.00
OD1 C:ASP188 2.0 18.2 1.0
O3 C:3PG503 2.0 21.0 1.0
OE1 C:GLU189 2.1 16.8 1.0
OQ2 C:KCX186 2.1 18.1 1.0
O2 C:3PG502 2.1 20.1 1.0
O2 C:3PG503 2.2 20.9 1.0
C1 C:3PG503 2.8 19.3 1.0
C2 C:3PG503 2.8 20.9 1.0
C1 C:3PG502 3.1 21.5 1.0
CD C:GLU189 3.2 20.2 1.0
CG C:ASP188 3.2 18.7 1.0
CX C:KCX186 3.2 18.4 1.0
O1 C:3PG502 3.5 20.6 1.0
OE2 C:GLU189 3.6 19.4 1.0
OQ1 C:KCX186 3.6 17.8 1.0
ND2 A:ASN108 3.8 16.9 1.0
OD2 C:ASP188 3.9 22.7 1.0
NZ C:LYS160 3.9 17.8 1.0
O1 C:3PG503 4.0 23.4 1.0
N C:GLU189 4.0 14.6 1.0
NE2 C:HIS278 4.0 16.2 1.0
NZ C:LYS162 4.0 19.1 1.0
C3 C:3PG503 4.1 22.6 1.0
CA C:ASP188 4.3 11.8 1.0
CB C:ASP188 4.3 12.6 1.0
C2 C:3PG502 4.3 20.1 1.0
NZ C:KCX186 4.3 17.0 1.0
CG C:GLU189 4.5 16.6 1.0
CG1 C:VAL158 4.6 15.2 1.0
CB C:GLU189 4.7 16.4 1.0
C C:ASP188 4.7 16.3 1.0
CD2 C:HIS278 4.8 15.9 1.0
O1P C:3PG503 4.8 18.7 1.0
CE1 C:HIS278 4.8 16.0 1.0
CG2 C:VAL158 4.9 13.8 1.0
CE C:LYS162 4.9 22.9 1.0
CA C:GLU189 5.0 14.8 1.0
CG A:ASN108 5.0 17.5 1.0

Magnesium binding site 4 out of 4 in 8dht

Go back to Magnesium Binding Sites List in 8dht
Magnesium binding site 4 out of 4 in the Crystal Structure of A Typeiii Rubisco


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 A Typeiii Rubisco within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg501

b:15.4
occ:1.00
O3 D:3PG503 2.0 15.1 1.0
OD1 D:ASP188 2.1 16.0 1.0
OE1 D:GLU189 2.1 15.7 1.0
OQ2 D:KCX186 2.1 16.0 1.0
O1 D:3PG502 2.2 16.1 1.0
O2 D:3PG503 2.2 16.5 1.0
C1 D:3PG503 2.8 13.8 1.0
C2 D:3PG503 2.8 16.6 1.0
C1 D:3PG502 3.1 16.5 1.0
CD D:GLU189 3.2 16.6 1.0
CX D:KCX186 3.2 14.9 1.0
CG D:ASP188 3.3 16.3 1.0
O2 D:3PG502 3.5 16.4 1.0
OQ1 D:KCX186 3.6 14.9 1.0
OE2 D:GLU189 3.7 16.3 1.0
NZ D:LYS160 3.9 14.2 1.0
NE2 D:HIS278 3.9 15.8 1.0
OD2 D:ASP188 3.9 19.2 1.0
N D:GLU189 4.0 12.4 1.0
O1 D:3PG503 4.0 18.1 1.0
NZ D:LYS162 4.0 17.2 1.0
C3 D:3PG503 4.1 16.4 1.0
CA D:ASP188 4.3 13.0 1.0
C2 D:3PG502 4.3 17.6 1.0
NZ D:KCX186 4.3 12.2 1.0
CB D:ASP188 4.3 13.6 1.0
CG D:GLU189 4.5 15.3 1.0
C D:ASP188 4.7 13.1 1.0
CB D:GLU189 4.7 14.9 1.0
CG1 D:VAL158 4.7 13.4 1.0
CD2 D:HIS278 4.7 13.0 1.0
CE1 D:HIS278 4.7 15.4 1.0
O1P D:3PG503 4.8 14.1 1.0
CG2 D:VAL158 4.9 12.9 1.0
CA D:GLU189 4.9 11.8 1.0
CE D:LYS162 5.0 19.2 1.0

Reference:

Q.Huang, D.M.E.Szebenyi. Crystal Structure of A Type III Rubisco in Complex with Its Product 3-Phosphoglycerate. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36151846
DOI: 10.1002/PROT.26431
Page generated: Fri Oct 4 00:43:00 2024

Last articles

Sr in 3BNQ
Sr in 2X53
Sr in 2SPT
Sr in 2QJY
Sr in 2XRM
Sr in 2WOH
Sr in 2RIO
Sr in 2PN4
Sr in 2QJP
Sr in 2HMP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy