Atomistry » Magnesium » PDB 4pjk-4pyk » 4ptn
Atomistry »
  Magnesium »
    PDB 4pjk-4pyk »
      4ptn »

Magnesium in PDB 4ptn: Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde

Protein crystallography data

The structure of Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde, PDB code: 4ptn was solved by P.Manoj Kumar, V.Baskar, S.Manicka, S.Krishnaswamy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.94 / 1.99
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 141.200, 155.070, 55.400, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde (pdb code 4ptn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde, PDB code: 4ptn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 1 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


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 Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:12.1
occ:0.75
 MG A:MG404 0.0 12.1 0.8
MG A:MG404 1.2 11.8 0.2
O A:GXV403 2.0 13.5 0.2
O A:HOH532 2.1 17.9 0.5
C2 A:GXV403 2.9 13.9 0.2
C1 A:GXV403 3.0 20.0 0.5
C1 A:GXV403 3.2 14.1 0.2
O A:HOH526 3.2 16.2 1.0
O A:HOH524 3.2 15.6 1.0
O A:GXV403 3.4 14.1 0.5
N A:GLY57 3.4 12.3 1.0
C A:GXV403 3.5 20.4 0.5
C A:GXV403 3.5 14.2 0.2
CA A:GLY57 3.6 14.1 1.0
C2 A:GXV403 3.6 19.2 0.5
CG A:PRO20 3.6 12.4 1.0
CB A:PRO20 3.9 12.1 1.0
O1 A:GXV403 4.0 25.2 0.5
O2 A:GXV403 4.2 13.7 0.2
CB A:ALA221 4.3 16.8 1.0
O2 A:GXV403 4.5 16.9 0.5
C A:SER56 4.5 11.9 1.0
O1 A:GXV403 4.5 14.2 0.2
CB A:SER56 4.5 12.3 1.0
CA A:ALA221 4.6 16.6 1.0
N A:ALA221 4.6 15.3 1.0
C A:GLY57 4.9 13.3 1.0
NZ A:LYS174 4.9 13.3 1.0
CA A:SER56 4.9 11.5 1.0
N A:SER56 5.0 12.2 1.0

Magnesium binding site 2 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 2 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


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 Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:11.8
occ:0.25
 MG A:MG404 0.0 11.8 0.2
MG A:MG404 1.2 12.1 0.8
O A:GXV403 1.9 13.5 0.2
O A:HOH524 2.1 15.6 1.0
O A:HOH532 2.5 17.9 0.5
N A:GLY57 2.8 12.3 1.0
C2 A:GXV403 3.2 13.9 0.2
CB A:PRO20 3.4 12.1 1.0
CA A:GLY57 3.5 14.1 1.0
O A:GXV403 3.5 14.1 0.5
CG A:PRO20 3.6 12.4 1.0
C1 A:GXV403 3.7 20.0 0.5
O A:HOH526 3.7 16.2 1.0
C1 A:GXV403 3.8 14.1 0.2
CB A:SER56 3.8 12.3 1.0
N A:SER56 3.9 12.2 1.0
C A:SER56 3.9 11.9 1.0
C2 A:GXV403 3.9 19.2 0.5
CA A:SER56 4.1 11.5 1.0
OH A:TYR145 4.1 17.2 1.0
NZ A:LYS174 4.4 13.3 1.0
C A:GXV403 4.4 20.4 0.5
C A:GXV403 4.5 14.2 0.2
OG A:SER56 4.6 11.9 1.0
C A:GLY55 4.6 12.3 1.0
C A:GLY57 4.7 13.3 1.0
O1 A:GXV403 4.7 25.2 0.5
CE A:LYS174 4.7 11.5 1.0
N A:GLY58 4.9 14.1 1.0
CA A:PRO20 4.9 12.7 1.0
O1 A:GXV403 5.0 14.2 0.2

Magnesium binding site 3 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 3 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


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 Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:9.6
occ:0.90
 MG B:MG407 0.0 9.6 0.9
MG B:MG407 1.1 12.0 0.1
O B:GXV406 2.0 16.0 0.5
C2 B:GXV406 3.0 15.3 0.5
N B:GLY57 3.1 10.5 1.0
O B:HOH508 3.1 10.6 1.0
C1 B:GXV406 3.2 17.7 0.5
O B:HOH549 3.2 17.6 1.0
O B:GXV406 3.5 19.6 0.5
CA B:GLY57 3.5 11.2 1.0
C B:GXV406 3.5 17.0 0.5
C1 B:GXV406 3.5 25.5 0.5
C2 B:GXV406 3.6 22.8 0.5
CG B:PRO20 3.7 8.8 1.0
CB B:PRO20 3.8 9.0 1.0
O1 B:GXV406 3.8 27.2 0.5
CB B:SER56 4.2 12.0 1.0
C B:SER56 4.2 11.5 1.0
N B:SER56 4.5 11.2 1.0
CA B:SER56 4.5 11.6 1.0
O2 B:GXV406 4.5 14.8 0.5
O1 B:GXV406 4.6 18.4 0.5
CB B:ALA221 4.6 13.7 1.0
C B:GLY57 4.8 10.7 1.0
OH B:TYR145 4.8 10.3 1.0
NZ B:LYS174 4.9 11.2 1.0
CA B:ALA221 4.9 11.8 1.0
C B:GXV406 4.9 24.8 0.5
O B:PRO20 4.9 8.1 1.0
N B:ALA221 5.0 11.0 1.0

Magnesium binding site 4 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 4 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


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 Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg407

b:12.0
occ:0.10
 MG B:MG407 0.0 12.0 0.1
MG B:MG407 1.1 9.6 0.9
O B:GXV406 2.0 16.0 0.5
O B:HOH508 2.1 10.6 1.0
N B:GLY57 2.9 10.5 1.0
C2 B:GXV406 3.1 15.3 0.5
CB B:PRO20 3.4 9.0 1.0
O B:GXV406 3.5 19.6 0.5
N B:SER56 3.6 11.2 1.0
CA B:GLY57 3.7 11.2 1.0
CB B:SER56 3.7 12.0 1.0
CG B:PRO20 3.7 8.8 1.0
C1 B:GXV406 3.7 17.7 0.5
O B:HOH549 3.9 17.6 1.0
C B:SER56 3.9 11.5 1.0
CA B:SER56 3.9 11.6 1.0
C2 B:GXV406 3.9 22.8 0.5
OH B:TYR145 3.9 10.3 1.0
C1 B:GXV406 4.2 25.5 0.5
C B:GXV406 4.3 17.0 0.5
NZ B:LYS174 4.3 11.2 1.0
C B:GLY55 4.4 10.7 1.0
OG B:SER56 4.4 11.2 1.0
O1 B:GXV406 4.5 27.2 0.5
CE B:LYS174 4.6 9.7 1.0
CA B:GLY55 4.8 11.0 1.0
C B:GLY57 4.8 10.7 1.0
CA B:PRO20 4.9 8.4 1.0
N B:GLY58 5.0 11.1 1.0
O1 B:GXV406 5.0 18.4 0.5

Magnesium binding site 5 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 5 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:9.5
occ:0.75
 MG C:MG405 0.0 9.5 0.8
MG C:MG405 1.3 11.8 0.2
O C:GXV404 2.0 11.6 0.2
C2 C:GXV404 3.0 12.7 0.2
C1 C:GXV404 3.0 20.9 0.5
O1 C:GXV404 3.1 21.6 0.5
C1 C:GXV404 3.1 13.2 0.2
O C:HOH540 3.2 18.5 1.0
O C:HOH528 3.3 15.5 1.0
C2 C:GXV404 3.4 19.9 0.5
O C:GXV404 3.4 15.9 0.5
N C:GLY57 3.4 11.6 1.0
CA C:GLY57 3.6 13.8 1.0
CG C:PRO20 3.6 12.3 1.0
CB C:PRO20 3.9 11.4 1.0
O1 C:GXV404 3.9 13.6 0.2
O C:HOH622 4.0 43.5 1.0
CB C:ALA221 4.3 14.3 1.0
O2 C:GXV404 4.3 12.3 0.2
C C:GXV404 4.3 13.5 0.2
C C:GXV404 4.4 21.7 0.5
C C:SER56 4.5 12.1 1.0
CB C:SER56 4.6 12.7 1.0
CA C:ALA221 4.6 14.5 1.0
N C:ALA221 4.6 14.8 1.0
O2 C:GXV404 4.7 18.3 0.5
C C:GLY57 4.9 12.9 1.0
NZ C:LYS174 4.9 12.7 1.0
CA C:SER56 5.0 12.3 1.0
O C:PRO20 5.0 12.4 1.0
N C:SER56 5.0 12.6 1.0

Magnesium binding site 6 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 6 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg405

b:11.8
occ:0.25
 MG C:MG405 0.0 11.8 0.2
MG C:MG405 1.3 9.5 0.8
O C:GXV404 2.0 11.6 0.2
O C:HOH528 2.1 15.5 1.0
N C:GLY57 2.9 11.6 1.0
O C:HOH622 3.1 43.5 1.0
C2 C:GXV404 3.3 12.7 0.2
CB C:PRO20 3.4 11.4 1.0
O C:GXV404 3.5 15.9 0.5
CA C:GLY57 3.5 13.8 1.0
CG C:PRO20 3.6 12.3 1.0
C2 C:GXV404 3.7 19.9 0.5
O C:HOH540 3.8 18.5 1.0
CB C:SER56 3.9 12.7 1.0
C1 C:GXV404 3.9 20.9 0.5
N C:SER56 3.9 12.6 1.0
C1 C:GXV404 3.9 13.2 0.2
C C:SER56 4.0 12.1 1.0
OH C:TYR145 4.1 14.4 1.0
O1 C:GXV404 4.1 21.6 0.5
CA C:SER56 4.1 12.3 1.0
NZ C:LYS174 4.2 12.7 1.0
O1 C:GXV404 4.6 13.6 0.2
C C:GLY55 4.6 11.9 1.0
OG C:SER56 4.6 12.4 1.0
CE C:LYS174 4.6 12.0 1.0
C C:GLY57 4.7 12.9 1.0
CA C:PRO20 4.9 12.4 1.0
N C:GLY58 4.9 11.6 1.0
O C:PRO20 5.0 12.4 1.0

Magnesium binding site 7 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 7 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:10.2
occ:0.90
 MG D:MG404 0.0 10.2 0.9
MG D:MG404 1.2 15.2 0.1
O D:GXV403 2.0 16.9 0.5
C2 D:GXV403 3.0 16.4 0.5
O D:HOH528 3.2 15.0 1.0
O D:HOH543 3.2 17.2 1.0
N D:GLY57 3.2 11.3 1.0
C1 D:GXV403 3.2 17.6 0.5
O D:HOH643 3.4 72.8 1.0
C D:GXV403 3.5 16.2 0.5
C1 D:GXV403 3.5 26.1 0.5
CG D:PRO20 3.5 12.7 1.0
CA D:GLY57 3.5 11.4 1.0
O D:GXV403 3.6 18.0 0.5
CB D:PRO20 3.7 12.2 1.0
C2 D:GXV403 3.7 22.4 0.5
O1 D:GXV403 3.8 26.5 0.5
CB D:SER56 4.3 12.9 1.0
C D:SER56 4.3 11.4 1.0
CB D:ALA221 4.5 17.1 1.0
O1 D:GXV403 4.6 18.9 0.5
N D:SER56 4.7 11.3 1.0
CA D:SER56 4.7 11.2 1.0
O2 D:GXV403 4.7 14.4 0.5
CA D:ALA221 4.8 14.3 1.0
N D:ALA221 4.8 13.5 1.0
C D:GLY57 4.9 11.9 1.0
NZ D:LYS174 4.9 14.1 1.0
OH D:TYR145 4.9 11.1 1.0
O D:PRO20 4.9 12.5 1.0
C D:GXV403 4.9 26.8 0.5

Magnesium binding site 8 out of 8 in 4ptn

Go back to Magnesium Binding Sites List in 4ptn
Magnesium binding site 8 out of 8 in the Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Yage, A Kdg Aldolase Protein in Complex with Magnesium Cation Coordinated L-Glyceraldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg404

b:15.2
occ:0.10
 MG D:MG404 0.0 15.2 0.1
MG D:MG404 1.2 10.2 0.9
O D:GXV403 2.0 16.9 0.5
O D:HOH528 2.1 15.0 1.0
N D:GLY57 2.8 11.3 1.0
C2 D:GXV403 3.2 16.4 0.5
O D:HOH643 3.4 72.8 1.0
CB D:SER56 3.5 12.9 1.0
CA D:GLY57 3.5 11.4 1.0
N D:SER56 3.6 11.3 1.0
O D:GXV403 3.7 18.0 0.5
CB D:PRO20 3.7 12.2 1.0
C D:SER56 3.7 11.4 1.0
CA D:SER56 3.8 11.2 1.0
C1 D:GXV403 3.8 17.6 0.5
OH D:TYR145 3.8 11.1 1.0
CG D:PRO20 3.9 12.7 1.0
O D:HOH543 4.0 17.2 1.0
C2 D:GXV403 4.0 22.4 0.5
C1 D:GXV403 4.2 26.1 0.5
OG D:SER56 4.2 11.8 1.0
NZ D:LYS174 4.3 14.1 1.0
C D:GXV403 4.4 16.2 0.5
C D:GLY55 4.4 10.4 1.0
O1 D:GXV403 4.5 26.5 0.5
CE D:LYS174 4.7 12.4 1.0
C D:GLY57 4.8 11.9 1.0
CA D:GLY55 4.8 10.8 1.0
O D:SER56 4.9 11.2 1.0
N D:GLY58 4.9 12.1 1.0
O1 D:GXV403 4.9 18.9 0.5

Reference:

S.Manicka, Y.Peleg, T.Unger, S.Albeck, O.Dym, H.M.Greenblatt, G.Bourenkov, V.Lamzin, S.Krishnaswamy, J.L.Sussman. Crystal Structure of Yage, A Putative Dhdps-Like Protein From Escherichia Coli K12. Proteins V. 71 2102 2008.
ISSN: ISSN 0887-3585
PubMed: 18361457
DOI: 10.1002/PROT.22023
Page generated: Tue Aug 20 01:39:12 2024

Last articles

Cl in 7TAZ
Cl in 7TAY
Cl in 7TAV
Cl in 7T8P
Cl in 7T9W
Cl in 7T96
Cl in 7T94
Cl in 7T8K
Cl in 7T8L
Cl in 7T80
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy