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Magnesium in PDB 8gsr: Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)

Protein crystallography data

The structure of Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form), PDB code: 8gsr was solved by S.Fukuhara, Y.Watanabe, S.Watanabe, H.Nishiwaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.07 / 1.73
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 64.217, 66.412, 75.202, 90.15, 91.8, 104.94
R / Rfree (%) 16.8 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) (pdb code 8gsr). 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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form), PDB code: 8gsr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 8gsr

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Magnesium binding site 1 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:14.6
occ:1.00
 OE1 A:GLU121 1.9 17.4 1.0
OD2 A:ASP150 2.0 15.1 1.0
OE2 A:GLU119 2.1 18.4 1.0
O A:HOH633 2.1 27.6 1.0
O A:HOH456 2.1 14.9 1.0
O A:HOH632 2.3 28.2 1.0
CD A:GLU121 3.0 14.7 1.0
CG A:ASP150 3.1 17.1 1.0
CD A:GLU119 3.3 17.0 1.0
OE2 A:GLU121 3.4 14.7 1.0
CB A:ASP150 3.5 15.7 1.0
NZ A:LYS168 3.8 16.9 1.0
O A:ILE71 3.9 19.7 1.0
O A:HOH430 4.0 22.3 1.0
OE1 A:GLU119 4.1 20.2 1.0
O A:HOH466 4.2 24.9 1.0
OD1 A:ASP150 4.2 16.5 1.0
CG A:GLU121 4.3 13.3 1.0
CB A:GLU119 4.3 18.2 1.0
CG A:GLU119 4.4 14.8 1.0
CA A:GLY237 4.5 16.6 1.0
CZ A:PHE93 4.5 19.5 1.0
CE1 A:PHE93 4.8 20.1 1.0
C A:GLY237 4.8 16.2 1.0
O A:ASP150 4.9 13.5 1.0
CB A:THR238 4.9 17.5 1.0
CE A:LYS168 4.9 17.7 1.0
N A:GLY237 5.0 15.2 1.0
CD1 A:ILE235 5.0 18.5 1.0
CA A:ASP150 5.0 14.5 1.0
N A:THR238 5.0 15.2 1.0

Magnesium binding site 2 out of 8 in 8gsr

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Magnesium binding site 2 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:19.1
occ:1.00
 OE1 B:GLU121 2.0 21.9 1.0
OD2 B:ASP150 2.0 18.0 1.0
O B:HOH482 2.1 20.9 1.0
O B:HOH559 2.1 31.8 1.0
O B:HOH532 2.1 28.5 1.0
OE2 B:GLU119 2.1 22.5 1.0
CD B:GLU121 3.0 19.7 1.0
CG B:ASP150 3.1 21.4 1.0
CD B:GLU119 3.4 24.0 1.0
OE2 B:GLU121 3.4 19.2 1.0
CB B:ASP150 3.5 17.8 1.0
NZ B:LYS168 3.6 20.7 1.0
O B:HOH436 3.9 23.9 1.0
O B:ILE71 3.9 22.8 1.0
O B:HOH522 4.1 30.8 1.0
OE1 B:GLU119 4.1 25.8 1.0
OD1 B:ASP150 4.1 18.3 1.0
CG B:GLU121 4.3 19.9 1.0
CB B:GLU119 4.4 20.7 1.0
CG B:GLU119 4.4 21.8 1.0
CA B:GLY237 4.5 17.7 1.0
CZ B:PHE93 4.5 24.6 1.0
C B:GLY237 4.8 22.3 1.0
CE B:LYS168 4.8 20.4 1.0
N B:GLY237 4.9 19.1 1.0
O B:ASP150 4.9 18.2 1.0
CE1 B:PHE93 5.0 28.1 1.0

Magnesium binding site 3 out of 8 in 8gsr

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Magnesium binding site 3 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:28.9
occ:1.00
 O B:HOH409 2.1 30.8 1.0
O B:HOH420 2.1 33.7 1.0
O B:HOH517 2.2 33.3 1.0
O B:HOH497 2.2 33.8 1.0
O B:HOH583 4.0 37.6 1.0
O B:HOH534 4.1 39.8 1.0
OD1 B:ASN22 4.1 33.4 1.0
OE1 B:GLU55 4.1 33.6 1.0
O B:HOH680 4.3 37.0 1.0
O B:HOH570 4.3 36.2 1.0
OE2 B:GLU55 4.4 34.0 1.0
O B:GLY21 4.4 31.5 1.0
O B:HOH633 4.5 39.9 1.0
CD B:GLU55 4.7 30.2 1.0

Magnesium binding site 4 out of 8 in 8gsr

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Magnesium binding site 4 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:15.6
occ:1.00
 OE1 C:GLU121 2.0 16.8 1.0
OD2 C:ASP150 2.0 16.6 1.0
O C:HOH428 2.1 16.3 1.0
O C:HOH621 2.1 26.8 1.0
OE2 C:GLU119 2.1 18.9 1.0
O C:HOH569 2.3 25.6 1.0
CD C:GLU121 3.0 15.4 1.0
CG C:ASP150 3.1 18.7 1.0
CD C:GLU119 3.3 18.1 1.0
OE2 C:GLU121 3.4 14.2 1.0
CB C:ASP150 3.5 13.1 1.0
NZ C:LYS168 3.7 15.8 1.0
O C:ILE71 3.8 19.2 1.0
O C:HOH494 4.0 23.9 1.0
OE1 C:GLU119 4.1 23.4 1.0
OD1 C:ASP150 4.2 17.4 1.0
CG C:GLU121 4.3 13.7 1.0
CB C:GLU119 4.3 18.2 1.0
CG C:GLU119 4.4 16.7 1.0
CA C:GLY237 4.6 16.8 1.0
CZ C:PHE93 4.7 26.7 1.0
O C:HOH670 4.7 28.2 1.0
CE C:LYS168 4.9 17.4 1.0
C C:GLY237 4.9 18.0 1.0
CD1 C:ILE235 4.9 19.1 1.0
O C:ASP150 4.9 15.6 1.0
N C:GLY237 5.0 16.8 1.0
CE1 C:PHE93 5.0 26.4 1.0
CA C:ASP150 5.0 13.7 1.0

Magnesium binding site 5 out of 8 in 8gsr

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Magnesium binding site 5 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:36.8
occ:1.00
 O C:HOH729 2.2 39.9 1.0
O C:HOH704 4.2 36.0 1.0
O C:HOH715 4.3 32.1 1.0
O C:HOH643 4.3 35.8 1.0

Magnesium binding site 6 out of 8 in 8gsr

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Magnesium binding site 6 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:29.0
occ:1.00
 O C:HOH487 2.0 28.4 1.0
O C:HOH475 2.1 29.5 1.0
O C:HOH440 2.1 24.3 1.0
O C:HOH429 2.2 28.8 1.0
O C:HOH441 2.2 27.8 1.0
OD1 C:ASP191 3.7 26.8 1.0
O C:HOH654 3.8 37.3 1.0
OD2 C:ASP191 4.1 30.0 1.0
O C:HOH681 4.1 27.5 1.0
CG C:ASP191 4.2 25.9 1.0
OE2 C:GLU264 4.2 20.1 1.0
O C:HOH703 4.3 30.1 1.0
OE1 C:GLU264 4.3 26.1 1.0
OD2 C:ASP193 4.5 31.2 1.0
O C:ASP191 4.6 24.3 1.0
O C:HOH461 4.7 41.4 1.0
CD C:GLU264 4.7 28.1 1.0
ND2 C:ASN207 4.7 21.6 1.0
OD1 C:ASP193 4.9 23.9 1.0

Magnesium binding site 7 out of 8 in 8gsr

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Magnesium binding site 7 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:26.8
occ:1.00
 O D:HOH1237 2.0 29.2 1.0
OE2 D:GLU135 4.3 32.5 1.0
O D:HOH1393 4.4 29.2 1.0
O D:HOH1420 4.4 44.7 1.0
O D:HOH1224 4.4 44.8 1.0
OD1 D:ASP136 4.4 44.7 1.0
O D:HOH1342 4.5 40.1 1.0

Magnesium binding site 8 out of 8 in 8gsr

Go back to Magnesium Binding Sites List in 8gsr
Magnesium binding site 8 out of 8 in the Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form)


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 L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase From Sphingomonas Sp. (Apo-Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:19.4
occ:1.00
 OD2 D:ASP150 1.9 19.2 1.0
OE2 D:GLU121 1.9 21.0 1.0
O D:HOH1347 2.0 28.2 1.0
O D:HOH1241 2.1 19.0 1.0
OE1 D:GLU119 2.2 23.2 1.0
O D:HOH1340 2.2 33.7 1.0
CD D:GLU121 3.0 18.3 1.0
CG D:ASP150 3.0 16.4 1.0
CD D:GLU119 3.4 23.5 1.0
OE1 D:GLU121 3.4 18.3 1.0
CB D:ASP150 3.4 18.5 1.0
O D:HOH1302 3.8 31.5 1.0
NZ D:LYS168 3.8 21.5 1.0
O D:ILE71 3.9 21.8 1.0
O D:HOH1215 4.0 20.4 1.0
OD1 D:ASP150 4.1 18.3 1.0
OE2 D:GLU119 4.1 25.0 1.0
CG D:GLU121 4.3 19.5 1.0
CB D:GLU119 4.4 21.8 1.0
CG D:GLU119 4.5 22.1 1.0
CZ D:PHE93 4.5 23.6 1.0
CA D:GLY237 4.6 20.7 1.0
O D:ASP150 4.9 19.6 1.0
CE D:LYS168 4.9 20.3 1.0
CE1 D:PHE93 4.9 23.2 1.0
CD1 D:ILE235 4.9 20.7 1.0
CA D:ASP150 4.9 18.8 1.0
C D:GLY237 5.0 20.6 1.0
N D:GLY237 5.0 19.1 1.0

Reference:

S.Fukuhara, S.Watanabe, Y.Watanabe, H.Nishiwaki. Crystal Structure of L-2,4-Diketo-3-Deoxyrhamnonate Hydrolase Involved in the Nonphosphorylated L-Rhamnose Pathway From Bacteria. Biochemistry V. 62 524 2023.
ISSN: ISSN 0006-2960
PubMed: 36563174
DOI: 10.1021/ACS.BIOCHEM.2C00596
Page generated: Fri Oct 4 03:55:33 2024

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