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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Aug 11 22:08:49 2025

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