Magnesium in PDB 5ocr: Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans

Enzymatic activity of Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans

All present enzymatic activity of Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans:
3.2.1.83;

Protein crystallography data

The structure of Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans, PDB code: 5ocr was solved by M.Czjzek, M.Matard-Mann, G.Michel, A.Jeudy, R.Larocque, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.74 / 1.66
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 40.960, 83.040, 85.710, 72.56, 88.34, 89.48
R / Rfree (%) 16.8 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans (pdb code 5ocr). 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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans, PDB code: 5ocr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5ocr

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Magnesium binding site 1 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.9
occ:1.00
O A:GLY87 2.2 23.6 1.0
O A:GLU51 2.2 19.1 1.0
O A:ASP299 2.4 19.6 1.0
O A:HOH511 2.4 30.5 1.0
OD1 A:ASP299 2.5 24.3 1.0
O A:HOH561 2.6 27.4 1.0
C A:GLY87 3.3 22.5 1.0
C A:GLU51 3.4 19.4 1.0
C A:ASP299 3.4 18.2 1.0
CG A:ASP299 3.6 24.4 1.0
O A:HOH530 3.7 43.6 1.0
CA A:GLY87 3.7 23.0 1.0
CA A:ASP299 3.9 19.3 1.0
CA A:GLU51 4.1 19.5 1.0
OD1 A:ASN53 4.2 37.3 1.0
CB A:ASP299 4.3 20.5 1.0
O A:HOH712 4.3 47.4 1.0
CB A:PHE52 4.4 20.2 1.0
CB A:GLU51 4.4 21.0 1.0
OD2 A:ASP299 4.4 29.2 1.0
N A:PHE52 4.4 19.2 1.0
N A:ILE88 4.5 20.5 1.0
C A:PHE52 4.5 21.3 1.0
N A:TYR300 4.5 17.4 1.0
O A:HOH571 4.6 35.9 1.0
CA A:PHE52 4.6 21.2 1.0
O A:PHE52 4.6 22.6 1.0
CB A:TYR300 4.8 17.5 1.0
CD1 A:ILE88 4.8 25.1 1.0
OE1 A:GLU51 4.9 23.7 1.0
N A:ASN53 4.9 22.9 1.0
CA A:TYR300 4.9 16.8 1.0
CA A:ILE88 4.9 20.4 1.0
CG A:ASN53 4.9 30.5 1.0

Magnesium binding site 2 out of 8 in 5ocr

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Magnesium binding site 2 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:32.2
occ:1.00
O A:PHE52 2.9 22.6 1.0
N A:GLY87 2.9 23.8 1.0
OD1 A:ASN55 3.0 28.7 0.5
O A:ASN53 3.1 25.0 1.0
C A:ASN53 3.4 25.5 1.0
N A:ASN86 3.4 26.0 1.0
CG2 A:ILE84 3.4 23.1 1.0
C A:SER85 3.7 26.0 1.0
CA A:GLY87 3.7 23.0 1.0
O A:HOH620 3.8 25.9 1.0
CA A:ASN53 3.8 25.4 1.0
C A:LYS54 3.8 26.8 1.0
N A:LYS54 3.9 25.0 1.0
C A:ASN86 3.9 25.8 1.0
C A:PHE52 3.9 21.3 1.0
CG A:ASN55 3.9 29.4 0.5
CA A:ASN86 3.9 27.2 0.5
N A:ASN55 3.9 26.1 1.0
CA A:ASN86 4.0 27.4 0.5
O A:LYS54 4.0 25.5 1.0
CA A:SER85 4.0 27.2 1.0
O A:HOH509 4.1 31.8 1.0
N A:SER85 4.1 23.6 1.0
OD1 A:ASN55 4.2 28.6 0.5
CA A:LYS54 4.3 27.0 1.0
O A:SER85 4.3 23.4 1.0
CA A:ASN55 4.3 26.9 0.5
N A:ASN53 4.3 22.9 1.0
C A:ILE84 4.4 24.2 1.0
N A:ILE88 4.4 20.5 1.0
C A:GLY87 4.4 22.5 1.0
CA A:ASN55 4.4 26.5 0.5
O A:ILE84 4.6 23.4 1.0
CB A:ILE84 4.6 22.6 1.0
ND2 A:ASN55 4.7 31.5 0.5
CB A:ASN55 4.7 28.3 0.5
CG A:ASN55 4.8 27.2 0.5

Magnesium binding site 3 out of 8 in 5ocr

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Magnesium binding site 3 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:22.5
occ:1.00
O B:ASP299 2.3 24.0 1.0
O B:GLU51 2.3 23.0 1.0
OD1 B:ASP299 2.3 28.4 1.0
O B:GLY87 2.4 27.3 1.0
O B:HOH610 2.4 37.5 1.0
O B:HOH586 2.6 29.4 1.0
C B:ASP299 3.3 22.1 1.0
C B:GLY87 3.4 25.4 1.0
CG B:ASP299 3.4 29.7 1.0
C B:GLU51 3.4 22.6 1.0
CA B:GLY87 3.7 28.9 1.0
CA B:ASP299 3.9 23.4 1.0
CA B:GLU51 4.2 23.4 1.0
CB B:ASP299 4.3 24.0 1.0
OD2 B:ASP299 4.3 34.6 1.0
OD1 B:ASN53 4.3 40.2 1.0
CB B:PHE52 4.4 23.2 1.0
N B:TYR300 4.5 20.4 1.0
CB B:GLU51 4.5 25.6 1.0
N B:PHE52 4.5 22.2 1.0
N B:ILE88 4.5 24.9 1.0
O B:HOH633 4.6 57.9 1.0
C B:PHE52 4.7 26.7 1.0
CB B:TYR300 4.7 19.8 1.0
O B:PHE52 4.7 26.3 1.0
CD1 B:ILE88 4.8 24.9 1.0
CA B:PHE52 4.8 23.6 1.0
CA B:TYR300 4.8 19.5 1.0
OE1 B:GLU51 4.8 28.0 1.0
CA B:ILE88 4.9 23.3 1.0
CG B:ASN53 4.9 35.3 1.0

Magnesium binding site 4 out of 8 in 5ocr

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Magnesium binding site 4 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:41.2
occ:1.00
OD1 B:ASN55 2.5 28.4 0.5
N B:GLY87 2.7 31.4 1.0
O B:PHE52 2.9 26.3 1.0
O B:ASN53 3.2 35.0 1.0
C B:ASN53 3.4 32.6 1.0
N B:ASN86 3.4 30.3 1.0
CA B:ASN86 3.5 31.5 1.0
C B:ASN86 3.6 31.4 1.0
CG2 B:ILE84 3.6 27.6 1.0
CG B:ASN55 3.6 30.1 0.5
CA B:GLY87 3.6 28.9 1.0
C B:LYS54 3.7 32.9 1.0
N B:ASN55 3.7 31.9 1.0
CA B:ASN53 3.8 32.5 1.0
O B:LYS54 3.8 28.8 1.0
N B:LYS54 3.9 32.1 1.0
C B:PHE52 3.9 26.7 1.0
O B:HOH595 3.9 34.5 1.0
CA B:ASN55 4.0 33.8 0.5
C B:SER85 4.0 30.5 1.0
CA B:ASN55 4.2 34.9 0.5
CA B:LYS54 4.3 32.9 1.0
N B:ASN53 4.3 27.3 1.0
CB B:ASN55 4.4 31.8 0.5
CA B:SER85 4.5 32.5 1.0
C B:GLY87 4.5 25.4 1.0
N B:SER85 4.6 27.8 1.0
O B:SER85 4.6 29.1 1.0
O B:HOH656 4.6 39.9 1.0
N B:ILE88 4.6 24.9 1.0
ND2 B:ASN55 4.7 31.9 0.5
O B:ASN86 4.8 32.2 1.0
CB B:ILE84 4.8 28.1 1.0
C B:ILE84 4.9 28.7 1.0
OD1 B:ASN86 5.0 44.0 1.0

Magnesium binding site 5 out of 8 in 5ocr

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Magnesium binding site 5 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:17.8
occ:1.00
O C:GLY87 2.2 21.4 1.0
O C:GLU51 2.3 22.5 1.0
OD1 C:ASP299 2.3 29.6 1.0
O C:ASP299 2.4 24.2 1.0
O C:HOH608 2.5 27.6 1.0
C C:GLY87 3.3 19.8 1.0
C C:ASP299 3.4 22.6 1.0
C C:GLU51 3.4 22.8 1.0
CG C:ASP299 3.5 30.1 1.0
CA C:GLY87 3.8 20.5 1.0
CA C:ASP299 3.9 21.3 1.0
CA C:GLU51 4.1 22.9 1.0
CB C:ASP299 4.3 24.4 1.0
CB C:GLU51 4.4 25.9 1.0
OD2 C:ASP299 4.4 35.1 1.0
N C:ILE88 4.5 19.8 1.0
N C:PHE52 4.5 21.2 1.0
N C:TYR300 4.6 19.2 1.0
CB C:PHE52 4.6 20.9 1.0
C C:PHE52 4.7 22.2 1.0
CD1 C:ILE88 4.7 18.2 0.5
O C:PHE52 4.7 24.2 1.0
OE1 C:GLU51 4.8 29.5 1.0
CA C:PHE52 4.8 20.4 1.0
CA C:TYR300 4.9 19.3 1.0
CB C:TYR300 4.9 20.3 1.0
CA C:ILE88 4.9 20.0 0.5
CD2 C:PHE52 4.9 22.9 1.0
CA C:ILE88 5.0 19.2 0.5

Magnesium binding site 6 out of 8 in 5ocr

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Magnesium binding site 6 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg404

b:27.4
occ:1.00
O C:PHE52 2.8 24.2 1.0
OD1 C:ASN55 2.8 25.6 1.0
N C:GLY87 2.8 21.0 1.0
CA C:GLY87 3.5 20.5 1.0
C C:ASN53 3.5 23.8 1.0
O C:ASN53 3.6 22.1 1.0
CG2 C:ILE84 3.6 21.1 1.0
N C:ASN86 3.6 23.2 1.0
N C:LYS54 3.7 25.3 1.0
C C:LYS54 3.8 26.7 1.0
C C:PHE52 3.8 22.2 1.0
C C:ASN86 3.8 22.2 1.0
CA C:ASN53 3.9 23.0 1.0
CG C:ASN55 4.0 26.1 1.0
N C:ASN55 4.0 26.2 1.0
CA C:ASN86 4.0 20.8 0.5
CA C:ASN86 4.0 23.0 0.5
CA C:LYS54 4.0 27.6 1.0
O C:LYS54 4.0 24.8 1.0
C C:SER85 4.1 23.9 1.0
N C:ASN53 4.3 23.7 1.0
CA C:ASN55 4.4 27.4 1.0
O C:HOH614 4.4 29.1 1.0
C C:GLY87 4.5 19.8 1.0
CA C:SER85 4.6 24.1 1.0
O C:HOH609 4.6 24.3 1.0
N C:SER85 4.6 22.3 1.0
N C:ILE88 4.6 19.8 1.0
O C:SER85 4.7 21.5 1.0
CB C:ASN55 4.8 27.1 1.0
CB C:ILE84 4.9 21.6 1.0
ND2 C:ASN55 4.9 25.9 1.0
C C:ILE84 5.0 23.0 1.0

Magnesium binding site 7 out of 8 in 5ocr

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Magnesium binding site 7 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:20.3
occ:1.00
O D:ASP299 2.3 22.1 1.0
O D:GLU51 2.3 21.7 1.0
O D:GLY87 2.3 21.8 1.0
O D:HOH589 2.5 27.5 1.0
OD1 D:ASP299 2.5 26.6 1.0
C D:ASP299 3.4 20.4 1.0
C D:GLY87 3.4 21.3 1.0
C D:GLU51 3.4 21.6 1.0
CG D:ASP299 3.5 26.7 1.0
CA D:ASP299 3.8 21.0 1.0
CA D:GLY87 3.9 23.4 1.0
CA D:GLU51 4.1 21.9 1.0
CB D:ASP299 4.3 23.2 1.0
OD2 D:ASP299 4.4 33.6 1.0
CB D:GLU51 4.4 24.1 1.0
N D:PHE52 4.5 22.9 1.0
N D:TYR300 4.5 19.4 1.0
CB D:PHE52 4.5 22.2 1.0
N D:ILE88 4.6 21.9 1.0
CD1 D:ILE88 4.7 21.0 0.5
OE1 D:GLU51 4.8 26.3 1.0
CA D:PHE52 4.8 21.3 1.0
C D:PHE52 4.8 22.8 1.0
CA D:TYR300 4.8 19.1 1.0
CD2 D:PHE52 4.8 22.6 1.0
CB D:TYR300 4.9 19.3 1.0
CA D:ILE88 4.9 21.0 0.5
O D:PHE52 4.9 22.7 1.0
CA D:ILE88 5.0 21.1 0.5

Magnesium binding site 8 out of 8 in 5ocr

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Magnesium binding site 8 out of 8 in the Crystal Structure of the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans


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 the Kappa-Carrageenase ZOBELLIA_236 From Zobellia Galactanivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:35.1
occ:1.00
OD1 D:ASN55 2.5 45.8 1.0
N D:GLY87 2.9 22.4 1.0
N D:ASN86 3.2 24.6 1.0
O D:PHE52 3.3 22.7 1.0
C D:SER85 3.6 25.0 1.0
CA D:GLY87 3.6 23.4 1.0
CG2 D:ILE84 3.7 25.4 1.0
CG D:ASN55 3.7 49.9 1.0
C D:LYS54 3.8 39.8 1.0
N D:ASN55 3.8 40.6 1.0
CA D:SER85 3.9 26.6 1.0
C D:ASN86 3.9 26.4 1.0
O D:ASN53 3.9 23.2 1.0
CA D:ASN86 3.9 25.2 1.0
N D:SER85 4.0 25.7 1.0
O D:LYS54 4.0 44.4 1.0
C D:ASN53 4.1 26.3 1.0
CA D:ASN55 4.3 37.2 1.0
O D:HOH659 4.3 33.0 1.0
C D:ILE84 4.3 26.8 1.0
CA D:LYS54 4.3 35.1 1.0
O D:SER85 4.3 23.4 1.0
O D:ILE84 4.5 28.8 1.0
C D:GLY87 4.5 21.3 1.0
C D:PHE52 4.5 22.8 1.0
N D:ILE88 4.5 21.9 1.0
N D:LYS54 4.5 28.1 1.0
CA D:ASN53 4.6 25.3 0.5
CA D:ASN53 4.6 25.1 0.5
CB D:ASN55 4.6 42.7 1.0
ND2 D:ASN55 4.7 45.0 1.0
CB D:ILE84 4.7 25.0 1.0

Reference:

M.Matard-Mann, T.Bernard, C.Leroux, T.Barbeyron, R.Larocque, A.Prechoux, A.Jeudy, M.Jam, P.Nyvall Collen, G.Michel, M.Czjzek. Structural Insights Into Marine Carbohydrate Degradation By Family GH16 Kappa-Carrageenases. J. Biol. Chem. V. 292 19919 2017.
ISSN: ESSN 1083-351X
PubMed: 29030427
DOI: 10.1074/JBC.M117.808279
Page generated: Mon Dec 14 20:59:22 2020

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