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Magnesium in PDB 6z9j: Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant

Enzymatic activity of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant

All present enzymatic activity of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant:
4.1.2.4;

Protein crystallography data

The structure of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant, PDB code: 6z9j was solved by J.Paakkonen, N.Hakulinen, J.Rouvinen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.30 / 1.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.504, 52.811, 80.675, 90.00, 111.23, 90.00
R / Rfree (%) 15.9 / 18.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant (pdb code 6z9j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant, PDB code: 6z9j:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6z9j

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Magnesium binding site 1 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:27.6
occ:1.00
 O B:HOH534 1.9 35.3 1.0
O A:HOH518 2.0 32.6 1.0
O B:HOH538 2.0 36.5 1.0
O B:HOH514 2.1 32.0 1.0
O A:HOH573 2.1 30.9 1.0
NE2 A:HIS78 2.1 26.7 1.0
CD2 A:HIS78 3.0 33.4 1.0
CE1 A:HIS78 3.2 36.1 1.0
OE2 B:GLU27 3.9 55.4 1.0
O B:HOH545 4.1 23.9 1.0
CG A:HIS78 4.2 31.0 1.0
O B:HOH410 4.2 37.2 1.0
OE1 B:GLU27 4.2 24.7 1.0
ND1 A:HIS78 4.2 28.7 1.0
OD2 B:ASP26 4.3 29.4 1.0
O A:HOH681 4.3 39.1 1.0
CD B:GLU27 4.5 42.9 1.0
O B:HOH432 4.9 41.0 1.0
CD A:PRO77 4.9 19.4 1.0
CG B:ASP26 5.0 27.6 1.0

Magnesium binding site 2 out of 9 in 6z9j

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Magnesium binding site 2 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:32.0
occ:1.00
 O A:HOH668 2.0 41.8 1.0
O A:HOH605 2.0 23.8 1.0
O A:HOH469 2.3 37.4 1.0
O A:HOH599 4.0 34.5 1.0
O A:HOH430 4.1 24.5 1.0
NZ A:LYS126 4.1 24.8 1.0
O A:HOH484 4.3 25.8 1.0
O A:HOH450 4.4 18.4 1.0
CA A:GLY162 4.9 19.2 1.0

Magnesium binding site 3 out of 9 in 6z9j

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Magnesium binding site 3 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:62.8
occ:1.00
 O A:HOH515 2.0 45.5 1.0
O A:HOH686 2.5 63.2 1.0
O A:HOH615 2.7 39.3 1.0
O A:LYS37 3.9 24.9 1.0
N A:PRO39 4.1 23.3 1.0
CA A:PRO39 4.1 26.3 1.0
C A:THR38 4.3 18.7 1.0
O A:THR38 4.3 23.9 1.0
O A:HOH538 4.4 41.5 1.0
CB A:PRO39 4.5 34.6 1.0
O A:HOH496 4.5 41.2 1.0
CD A:PRO39 4.5 26.4 1.0
C A:LYS37 4.8 22.0 1.0
CA A:THR38 5.0 19.9 1.0

Magnesium binding site 4 out of 9 in 6z9j

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Magnesium binding site 4 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:43.5
occ:1.00
 O A:HOH543 2.1 40.7 1.0
O B:HOH604 2.2 37.1 1.0
O B:HOH660 2.3 34.9 1.0
O B:HOH410 2.3 37.2 1.0
O A:HOH452 2.4 45.4 1.0
O B:HOH421 2.5 40.2 1.0
O A:PHE76 3.5 18.8 1.0
OD1 B:ASP26 3.7 24.1 1.0
O A:HOH429 3.8 20.7 1.0
OD2 B:ASP26 3.9 29.4 1.0
O A:HOH508 4.1 19.0 1.0
CG B:ASP26 4.2 27.6 1.0
O B:HOH574 4.4 27.2 1.0
O A:HOH593 4.4 42.5 1.0
O A:HOH573 4.5 30.9 1.0
O A:HOH602 4.5 22.8 1.0
OE2 A:GLU89 4.6 25.1 1.0
O B:HOH545 4.6 23.9 1.0
O A:HOH440 4.6 44.8 1.0
C A:PHE76 4.7 18.6 1.0
O B:HOH432 4.8 41.0 1.0

Magnesium binding site 5 out of 9 in 6z9j

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Magnesium binding site 5 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg305

b:35.2
occ:1.00
 O A:HOH483 2.0 38.3 1.0
O A:HOH425 2.1 47.2 1.0
O A:HOH509 2.2 28.4 1.0
O A:HOH461 2.2 28.3 1.0
O A:HOH608 3.9 43.5 1.0
OE2 A:GLU148 4.0 33.7 1.0
OE1 A:GLU148 4.2 34.0 1.0
OE1 A:GLU187 4.2 26.7 1.0
OE2 A:GLU187 4.3 24.9 1.0
O A:HOH576 4.3 30.6 1.0
CD A:GLU148 4.5 37.8 1.0
CD A:GLU187 4.7 31.3 1.0
O A:HOH423 4.9 35.1 1.0

Magnesium binding site 6 out of 9 in 6z9j

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Magnesium binding site 6 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg306

b:58.5
occ:1.00
 O B:HOH415 2.2 39.2 1.0
O A:HOH445 2.2 46.8 1.0
O B:HOH616 2.3 44.5 1.0
O B:HOH425 2.5 48.4 1.0
O A:HOH578 3.3 41.9 1.0
O A:ASP22 3.3 34.8 1.0
O A:HOH409 3.5 34.7 1.0
CA A:ASP22 3.8 24.3 1.0
O B:HOH592 3.9 40.4 1.0
O B:ASP22 3.9 31.0 1.0
C A:ASP22 4.0 31.4 1.0
O B:ASP24 4.1 20.1 1.0
CB A:ASP22 4.1 39.6 1.0
NH2 B:ARG51 4.2 23.5 1.0
OD1 A:ASP22 4.2 55.0 1.0
O B:HOH574 4.3 27.2 1.0
O A:HOH652 4.4 49.1 1.0
CG A:ASP22 4.6 63.7 1.0
NH2 A:ARG51 4.7 26.0 1.0

Magnesium binding site 7 out of 9 in 6z9j

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Magnesium binding site 7 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:26.4
occ:1.00
 OD1 B:ASP81 2.0 21.3 1.0
O B:HOH441 2.0 28.2 1.0
O B:HOH576 2.1 21.8 1.0
O B:HOH573 2.1 30.1 1.0
CG B:ASP81 3.0 26.2 1.0
OD2 B:ASP81 3.3 27.3 1.0
O B:HOH602 3.7 47.5 1.0
O A:HOH405 4.1 31.4 1.0
O B:HOH664 4.3 26.3 1.0
CB B:ASP81 4.4 13.8 1.0
O B:HOH584 4.4 21.8 1.0
C B:ASP81 4.5 18.0 1.0
N B:ASP81 4.6 17.3 1.0
NZ A:LYS58 4.6 48.4 1.0
N B:ASP82 4.7 17.6 1.0
CA B:ASP81 4.7 17.6 1.0
O B:ASP81 4.7 18.9 1.0
O A:HOH564 5.0 43.1 1.0

Magnesium binding site 8 out of 9 in 6z9j

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Magnesium binding site 8 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:31.9
occ:1.00
 O B:HOH566 1.9 35.5 1.0
NE2 B:HIS78 2.1 21.4 0.4
O A:HOH535 2.1 32.9 1.0
O A:HOH453 2.2 28.8 1.0
O B:HOH581 2.2 34.2 1.0
O A:HOH476 2.3 33.8 1.0
CE1 B:HIS78 3.0 35.3 0.4
CD2 B:HIS78 3.1 30.3 0.4
O A:HOH533 3.9 25.5 1.0
OE2 A:GLU27 4.0 48.9 1.0
ND1 B:HIS78 4.1 17.4 0.4
CG B:HIS78 4.2 19.5 0.4
O B:HOH676 4.2 40.9 1.0
OE1 A:GLU27 4.2 27.1 1.0
O A:HOH404 4.3 39.8 1.0
OD2 A:ASP26 4.5 30.3 1.0
CD A:GLU27 4.6 36.6 1.0

Magnesium binding site 9 out of 9 in 6z9j

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Magnesium binding site 9 out of 9 in the Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Escherichia Coli D-2-Deoxyribose-5-Phosphate Aldolase - N21K Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:52.6
occ:1.00
 O A:HOH404 2.2 39.8 1.0
O B:HOH495 2.2 48.7 1.0
O B:HOH411 2.3 39.5 1.0
O A:HOH589 2.3 50.7 1.0
O A:HOH412 2.3 44.3 1.0
O A:HOH660 2.5 39.5 1.0
O B:PHE76 3.4 18.4 1.0
OD2 A:ASP26 3.8 30.3 1.0
OD1 A:ASP26 3.8 26.3 1.0
O B:HOH439 3.9 23.0 1.0
O B:HOH485 4.0 20.8 1.0
CG A:ASP26 4.2 41.3 1.0
NE2 B:HIS78 4.3 30.5 0.6
O B:HOH581 4.4 34.2 1.0
CD2 B:HIS78 4.5 29.1 0.6
O B:HOH586 4.5 40.4 1.0
C B:PHE76 4.6 17.6 1.0
OE2 B:GLU89 4.7 24.7 1.0
O A:HOH549 4.7 34.0 1.0
O A:HOH533 4.8 25.5 1.0

Reference:

S.Voutilainen, M.Heinonen, M.Andberg, E.Jokinen, H.Maaheimo, J.Paakkonen, N.Hakulinen, J.Rouvinen, H.Lahdesmaki, S.Kaski, J.Rousu, M.Penttila, A.Koivula. Substrate Specificity of 2-Deoxy-D-Ribose 5-Phosphate Aldolase (Dera) Assessed By Different Protein Engineering and Machine Learning Methods. Appl.Microbiol.Biotechnol. V. 104 10515 2020.
ISSN: ESSN 1432-0614
PubMed: 33147349
DOI: 10.1007/S00253-020-10960-X
Page generated: Wed Oct 2 02:13:04 2024

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