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Magnesium in PDB 5gue: Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens

Enzymatic activity of Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens

All present enzymatic activity of Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens:
4.2.3.146;

Protein crystallography data

The structure of Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens, PDB code: 5gue was solved by T.Tomita, S.-Y.Kim, T.Ozaki, A.Yoshida, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.15 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 58.698, 100.373, 108.937, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens (pdb code 5gue). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens, PDB code: 5gue:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5gue

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Magnesium binding site 1 out of 4 in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens


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 COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:34.9
occ:1.00
 O A:HOH561 1.9 32.4 1.0
OE2 A:GLU228 2.0 32.4 1.0
O2B A:GGS401 2.0 52.9 1.0
O1A A:GGS401 2.0 58.6 1.0
OD1 A:ASN220 2.3 30.3 1.0
OG A:SER224 2.3 27.2 1.0
CD A:GLU228 3.0 32.9 1.0
CB A:SER224 3.2 26.7 1.0
CG A:ASN220 3.3 26.2 1.0
PA A:GGS401 3.3 59.8 1.0
PB A:GGS401 3.4 56.4 1.0
OE1 A:GLU228 3.4 30.9 1.0
O3A A:GGS401 3.6 57.9 1.0
O A:HOH566 3.7 37.5 1.0
ND2 A:ASN220 3.8 28.4 1.0
O A:ASN220 4.0 22.1 1.0
O A:HOH547 4.0 50.6 1.0
NH1 A:ARG177 4.1 24.9 1.0
O1B A:GGS401 4.2 56.6 1.0
CG A:GLU228 4.2 32.2 1.0
OD1 A:ASP221 4.3 21.2 1.0
S1 A:GGS401 4.4 62.1 1.0
C A:ASN220 4.4 20.6 1.0
O2A A:GGS401 4.4 62.1 1.0
O3B A:GGS401 4.4 56.4 1.0
CA A:SER224 4.6 26.1 1.0
CB A:ASN220 4.6 21.4 1.0
CA A:ASP221 4.7 21.2 1.0
N A:ASP221 4.8 20.2 1.0

Magnesium binding site 2 out of 4 in 5gue

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Magnesium binding site 2 out of 4 in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens


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 COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:39.1
occ:1.00
 O1A B:GGS401 2.0 64.5 1.0
O B:HOH526 2.0 30.7 1.0
O2B B:GGS401 2.1 62.0 1.0
OE2 B:GLU228 2.1 34.0 1.0
OD1 B:ASN220 2.1 31.3 1.0
OG B:SER224 2.5 27.4 1.0
CD B:GLU228 3.1 33.0 1.0
CG B:ASN220 3.2 25.5 1.0
PA B:GGS401 3.3 66.3 1.0
CB B:SER224 3.3 26.9 1.0
PB B:GGS401 3.4 64.0 1.0
OE1 B:GLU228 3.5 33.6 1.0
O3A B:GGS401 3.6 65.1 1.0
ND2 B:ASN220 3.8 28.6 1.0
O B:HOH597 3.8 38.0 1.0
NH1 B:ARG177 4.0 25.7 1.0
O B:ASN220 4.1 21.9 1.0
S1 B:GGS401 4.2 68.8 1.0
O B:HOH638 4.2 67.7 1.0
OD1 B:ASP221 4.3 22.2 1.0
O1B B:GGS401 4.4 63.3 1.0
O3B B:GGS401 4.4 62.7 1.0
CG B:GLU228 4.4 34.6 1.0
C B:ASN220 4.4 21.1 1.0
O2A B:GGS401 4.5 68.0 1.0
CB B:ASN220 4.5 21.9 1.0
CA B:SER224 4.7 26.4 1.0
N B:ASP221 4.7 20.7 1.0
CA B:ASP221 4.8 21.3 1.0

Magnesium binding site 3 out of 4 in 5gue

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Magnesium binding site 3 out of 4 in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens


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 COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg402

b:35.7
occ:1.00
 O C:HOH551 2.0 33.0 1.0
O2B C:GGS401 2.0 54.8 1.0
OE2 C:GLU228 2.0 35.5 1.0
O1A C:GGS401 2.1 59.4 1.0
OD1 C:ASN220 2.2 33.8 1.0
OG C:SER224 2.4 27.8 1.0
CD C:GLU228 3.0 35.1 1.0
CG C:ASN220 3.2 27.8 1.0
CB C:SER224 3.2 25.7 1.0
PA C:GGS401 3.3 60.8 1.0
PB C:GGS401 3.3 58.5 1.0
OE1 C:GLU228 3.4 34.4 1.0
O3A C:GGS401 3.5 59.1 1.0
ND2 C:ASN220 3.6 30.5 1.0
O C:HOH606 3.8 39.0 1.0
NH1 C:ARG177 4.0 21.6 1.0
O C:ASN220 4.0 21.8 1.0
O1B C:GGS401 4.1 58.2 1.0
O C:HOH629 4.2 50.5 1.0
S1 C:GGS401 4.2 60.9 1.0
CG C:GLU228 4.3 34.8 1.0
OD1 C:ASP221 4.4 20.7 1.0
C C:ASN220 4.4 20.8 1.0
O3B C:GGS401 4.4 57.4 1.0
O2A C:GGS401 4.5 62.8 1.0
CB C:ASN220 4.5 22.4 1.0
CA C:SER224 4.7 25.7 1.0
N C:ASP221 4.8 19.5 1.0
CA C:ASP221 4.8 20.3 1.0

Magnesium binding site 4 out of 4 in 5gue

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Magnesium binding site 4 out of 4 in the Crystal Structure of COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens


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 COTB2 (Ggspp/MG2+-Bound Form) From Streptomyces Melanosporofaciens within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg402

b:35.2
occ:1.00
 O2B D:GGS401 2.0 64.2 1.0
OE2 D:GLU228 2.0 34.9 1.0
O D:HOH527 2.1 30.8 1.0
O1A D:GGS401 2.1 66.3 1.0
OD1 D:ASN220 2.2 30.6 1.0
OG D:SER224 2.5 28.8 1.0
CD D:GLU228 3.0 33.2 1.0
CG D:ASN220 3.2 26.2 1.0
CB D:SER224 3.3 27.1 1.0
PA D:GGS401 3.3 68.3 1.0
PB D:GGS401 3.4 66.4 1.0
OE1 D:GLU228 3.4 32.3 1.0
O3A D:GGS401 3.5 67.3 1.0
ND2 D:ASN220 3.7 27.4 1.0
O D:HOH560 3.8 37.2 1.0
NH1 D:ARG177 4.0 26.6 1.0
O D:ASN220 4.1 22.2 1.0
O D:HOH625 4.1 62.8 1.0
S1 D:GGS401 4.2 69.7 1.0
O1B D:GGS401 4.3 66.1 1.0
CG D:GLU228 4.3 34.0 1.0
O3B D:GGS401 4.4 65.4 1.0
OD1 D:ASP221 4.4 20.8 1.0
C D:ASN220 4.4 21.0 1.0
CB D:ASN220 4.5 21.2 1.0
O2A D:GGS401 4.6 70.1 1.0
CA D:SER224 4.7 26.8 1.0
N D:ASP221 4.8 21.0 1.0
CA D:ASP221 4.8 22.0 1.0
NH2 D:ARG227 5.0 53.4 1.0

Reference:

T.Tomita, S.-Y.Kim, K.Teramoto, A.Meguro, T.Ozaki, A.Yoshida, Y.Motoyoshi, N.Mori, K.Ishigami, H.Watanabe, M.Nishiyama, T.Kuzuyama. Structural Insights Into the COTB2-Catalyzed Cyclization of Geranylgeranyl Diphosphate to the Diterpene Cyclooctat-9-En-7-Ol Acs Chem. Biol. V. 12 1621 2017.
ISSN: ESSN 1554-8937
PubMed: 28463490
DOI: 10.1021/ACSCHEMBIO.7B00154
Page generated: Mon Dec 14 20:25:19 2020

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