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Manganese in PDB 3vyl: Structure of L-Ribulose 3-Epimerase

Protein crystallography data

The structure of Structure of L-Ribulose 3-Epimerase, PDB code: 3vyl was solved by K.Uechi, H.Sakuraba, G.Takata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.48 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 202.511, 206.234, 121.975, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 26.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Structure of L-Ribulose 3-Epimerase (pdb code 3vyl). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Structure of L-Ribulose 3-Epimerase, PDB code: 3vyl:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3vyl

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Manganese binding site 1 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:21.1
occ:1.00
 OD2 A:ASP180 2.1 32.0 1.0
OE2 A:GLU147 2.1 24.4 1.0
ND1 A:HIS206 2.2 34.1 1.0
O A:HOH1143 2.4 31.8 1.0
OE2 A:GLU241 2.4 29.2 1.0
OE1 A:GLU241 2.8 34.6 1.0
CD A:GLU241 2.9 30.6 1.0
CE1 A:HIS206 3.0 34.2 1.0
CD A:GLU147 3.1 25.2 1.0
CG A:ASP180 3.2 29.8 1.0
CG A:HIS206 3.3 32.7 1.0
OE1 A:GLU147 3.4 26.4 1.0
CB A:ASP180 3.7 27.6 1.0
CB A:HIS206 3.7 30.9 1.0
NH2 A:ARG212 4.0 34.8 1.0
NE2 A:HIS206 4.1 33.4 1.0
OD1 A:ASP180 4.2 30.6 1.0
O A:HOH1134 4.3 28.1 1.0
CD2 A:HIS206 4.3 32.2 1.0
CD2 A:HIS183 4.3 26.8 1.0
NE2 A:HIS183 4.3 28.3 1.0
CG A:GLU147 4.4 25.6 1.0
NE2 A:HIS178 4.4 30.6 1.0
CG A:GLU241 4.4 29.4 1.0
CE1 A:HIS178 4.5 29.2 1.0
O A:HOH1139 4.9 21.0 1.0

Manganese binding site 2 out of 8 in 3vyl

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Manganese binding site 2 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1001

b:26.3
occ:1.00
 OE2 B:GLU147 1.9 29.6 1.0
OD2 B:ASP180 2.1 32.1 1.0
OE2 B:GLU241 2.1 31.9 1.0
ND1 B:HIS206 2.2 38.2 1.0
O B:HOH1150 2.4 42.0 1.0
CE1 B:HIS206 2.9 38.2 1.0
CD B:GLU147 3.0 31.6 1.0
CD B:GLU241 3.1 33.5 1.0
CG B:ASP180 3.2 29.5 1.0
OE1 B:GLU147 3.3 34.2 1.0
CG B:HIS206 3.3 37.2 1.0
OE1 B:GLU241 3.4 33.5 1.0
CB B:ASP180 3.6 28.3 1.0
CB B:HIS206 3.8 35.0 1.0
O B:HOH1151 4.0 42.8 1.0
NE2 B:HIS206 4.2 38.3 1.0
NH1 B:ARG212 4.2 38.6 1.0
OD1 B:ASP180 4.3 29.8 1.0
NE2 B:HIS183 4.3 28.2 1.0
CG B:GLU147 4.3 30.8 1.0
CD2 B:HIS183 4.3 27.4 1.0
CD2 B:HIS206 4.4 38.0 1.0
CG B:GLU241 4.4 32.4 1.0
NE2 B:HIS178 4.4 27.6 1.0
CE1 B:HIS178 4.6 28.0 1.0
CA B:ASP180 5.0 27.6 1.0

Manganese binding site 3 out of 8 in 3vyl

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Manganese binding site 3 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1001

b:26.2
occ:1.00
 O C:HOH1158 1.9 22.3 1.0
OE1 C:GLU147 2.0 26.8 1.0
ND1 C:HIS206 2.1 28.1 1.0
OD2 C:ASP180 2.1 30.6 1.0
OE2 C:GLU241 2.4 32.2 1.0
CE1 C:HIS206 2.8 28.2 1.0
O C:HOH1145 2.9 27.7 1.0
CD C:GLU147 3.1 28.2 1.0
CG C:HIS206 3.2 28.4 1.0
CG C:ASP180 3.2 27.2 1.0
CD C:GLU241 3.4 31.2 1.0
OE2 C:GLU147 3.5 30.6 1.0
OE1 C:GLU241 3.7 33.8 1.0
CB C:ASP180 3.8 25.3 1.0
CB C:HIS206 3.8 28.1 1.0
NE2 C:HIS206 4.0 27.5 1.0
CD2 C:HIS206 4.3 27.6 1.0
O C:HOH1143 4.3 15.6 1.0
O C:HOH1142 4.3 30.0 1.0
OD1 C:ASP180 4.3 26.5 1.0
NE2 C:HIS183 4.3 26.2 1.0
CD2 C:HIS183 4.4 25.2 1.0
CG C:GLU147 4.4 27.6 1.0
NE2 C:HIS178 4.5 30.1 1.0
CE1 C:HIS178 4.5 29.3 1.0
NH2 C:ARG212 4.6 28.1 1.0
NH1 C:ARG212 4.7 26.7 1.0
CG C:GLU241 4.8 29.0 1.0

Manganese binding site 4 out of 8 in 3vyl

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Manganese binding site 4 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1001

b:22.6
occ:1.00
 OD2 D:ASP180 2.0 27.3 1.0
OE1 D:GLU147 2.0 19.9 1.0
O D:HOH1171 2.0 29.1 1.0
ND1 D:HIS206 2.0 24.5 1.0
OE1 D:GLU241 2.5 31.7 1.0
CE1 D:HIS206 2.9 24.2 1.0
CG D:ASP180 3.1 25.5 1.0
CD D:GLU147 3.1 20.1 1.0
CG D:HIS206 3.2 24.4 1.0
OE2 D:GLU241 3.2 33.2 1.0
CD D:GLU241 3.2 31.4 1.0
OE2 D:GLU147 3.5 20.6 1.0
CB D:ASP180 3.6 23.2 1.0
CB D:HIS206 3.6 24.2 1.0
NH1 D:ARG212 4.0 27.7 1.0
NE2 D:HIS206 4.1 23.8 1.0
OD1 D:ASP180 4.1 25.7 1.0
CD2 D:HIS206 4.2 23.2 1.0
CD2 D:HIS183 4.3 23.6 1.0
O D:HOH1110 4.3 27.3 1.0
NE2 D:HIS183 4.4 24.5 1.0
CG D:GLU147 4.4 20.6 1.0
NE2 D:HIS178 4.4 25.0 1.0
CE1 D:HIS178 4.5 25.4 1.0
O D:HOH1126 4.7 15.7 1.0
CG D:GLU241 4.7 30.7 1.0
CA D:ASP180 4.8 22.1 1.0

Manganese binding site 5 out of 8 in 3vyl

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Manganese binding site 5 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1001

b:33.7
occ:1.00
 OD2 E:ASP180 1.9 35.2 1.0
OE1 E:GLU147 2.0 36.6 1.0
ND1 E:HIS206 2.1 29.4 1.0
OE1 E:GLU241 2.3 44.9 1.0
O E:HOH1113 2.5 42.6 1.0
CE1 E:HIS206 2.9 30.5 1.0
CD E:GLU241 3.0 41.2 1.0
OE2 E:GLU241 3.0 42.4 1.0
CD E:GLU147 3.0 35.8 1.0
CG E:ASP180 3.1 35.8 1.0
CG E:HIS206 3.2 30.3 1.0
OE2 E:GLU147 3.4 36.0 1.0
CB E:HIS206 3.7 30.5 1.0
NH2 E:ARG212 3.7 36.0 1.0
CB E:ASP180 3.8 34.3 1.0
O E:HOH1125 4.1 42.2 1.0
NE2 E:HIS206 4.1 29.2 1.0
OD1 E:ASP180 4.1 36.0 1.0
CD2 E:HIS206 4.3 30.0 1.0
NE2 E:HIS183 4.3 39.2 1.0
NE2 E:HIS178 4.3 34.6 1.0
CG E:GLU147 4.3 35.9 1.0
CE1 E:HIS178 4.4 34.7 1.0
CG E:GLU241 4.4 39.0 1.0
CD2 E:HIS183 4.4 37.8 1.0
O E:HOH1119 4.5 38.3 1.0
CB E:GLU241 4.9 37.9 1.0

Manganese binding site 6 out of 8 in 3vyl

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Manganese binding site 6 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1001

b:41.8
occ:1.00
 OD2 F:ASP180 2.0 47.5 1.0
OE1 F:GLU147 2.1 52.9 1.0
ND1 F:HIS206 2.3 37.4 1.0
OE1 F:GLU241 2.6 51.5 1.0
O F:HOH1104 2.6 38.1 1.0
CE1 F:HIS206 2.9 38.5 1.0
CD F:GLU147 3.0 52.0 1.0
OE2 F:GLU241 3.1 50.3 1.0
CG F:ASP180 3.1 48.8 1.0
CD F:GLU241 3.1 48.2 1.0
OE2 F:GLU147 3.3 54.3 1.0
CG F:HIS206 3.4 39.5 1.0
CB F:ASP180 3.9 47.1 1.0
NH1 F:ARG212 3.9 42.2 1.0
CB F:HIS206 4.0 38.4 1.0
OD1 F:ASP180 4.1 50.1 1.0
NE2 F:HIS206 4.2 37.4 1.0
CG F:GLU147 4.3 52.5 1.0
NE2 F:HIS183 4.3 45.0 1.0
CD2 F:HIS206 4.5 38.7 1.0
CD2 F:HIS183 4.5 44.6 1.0
CG F:GLU241 4.6 46.9 1.0
NE2 F:HIS178 4.7 47.5 1.0
CZ F:ARG212 4.8 40.8 1.0
NH2 F:ARG212 4.9 42.5 1.0
CE1 F:HIS178 4.9 48.5 1.0

Manganese binding site 7 out of 8 in 3vyl

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Manganese binding site 7 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mn1001

b:50.1
occ:1.00
 ND1 G:HIS206 2.0 62.7 1.0
OE1 G:GLU147 2.0 43.1 1.0
OD1 G:ASP180 2.2 62.8 1.0
OE2 G:GLU241 2.4 65.7 1.0
CE1 G:HIS206 2.7 66.8 1.0
CG G:HIS206 2.9 63.8 1.0
CD G:GLU241 3.1 68.8 1.0
CD G:GLU147 3.1 47.0 1.0
OE1 G:GLU241 3.2 71.7 1.0
CG G:ASP180 3.3 57.4 1.0
CB G:HIS206 3.5 61.8 1.0
OE2 G:GLU147 3.5 48.1 1.0
NE2 G:HIS206 3.8 67.5 1.0
CB G:ASP180 3.9 53.2 1.0
NH1 G:ARG212 3.9 49.5 1.0
CD2 G:HIS206 3.9 63.8 1.0
CD2 G:HIS183 4.1 63.8 1.0
NE2 G:HIS183 4.3 64.2 1.0
OD2 G:ASP180 4.3 59.5 1.0
CG G:GLU147 4.4 48.9 1.0
NH2 G:ARG212 4.4 52.3 1.0
CG G:GLU241 4.4 65.6 1.0
CE1 G:HIS178 4.5 48.2 1.0
CZ G:ARG212 4.6 49.2 1.0
NE2 G:HIS178 4.7 50.6 1.0
CA G:HIS206 5.0 57.5 1.0

Manganese binding site 8 out of 8 in 3vyl

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Manganese binding site 8 out of 8 in the Structure of L-Ribulose 3-Epimerase


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Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of L-Ribulose 3-Epimerase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1001

b:43.0
occ:1.00
 OE1 H:GLU147 2.0 44.3 1.0
ND1 H:HIS206 2.2 49.2 1.0
OD2 H:ASP180 2.2 58.4 1.0
OE1 H:GLU241 2.4 58.0 1.0
O H:HOH1109 2.4 41.1 1.0
CE1 H:HIS206 2.9 49.7 1.0
OE2 H:GLU241 3.1 57.9 1.0
CD H:GLU241 3.1 57.9 1.0
CD H:GLU147 3.1 44.6 1.0
CG H:ASP180 3.2 52.7 1.0
CG H:HIS206 3.3 50.4 1.0
OE2 H:GLU147 3.6 46.7 1.0
CB H:ASP180 3.7 50.1 1.0
CB H:HIS206 3.8 50.9 1.0
OD1 H:ASP180 4.1 54.9 1.0
NE2 H:HIS206 4.1 49.6 1.0
NH2 H:ARG212 4.1 47.7 1.0
CD2 H:HIS183 4.2 42.0 1.0
NE2 H:HIS183 4.2 40.9 1.0
CD2 H:HIS206 4.3 49.0 1.0
CG H:GLU147 4.4 45.8 1.0
CG H:GLU241 4.6 55.6 1.0
CE1 H:HIS178 4.6 52.7 1.0
NH1 H:ARG212 4.6 51.4 1.0
NE2 H:HIS178 4.7 54.5 1.0
CZ H:ARG212 4.8 50.2 1.0
CA H:ASP180 4.9 48.2 1.0

Reference:

K.Uechi, H.Sakuraba, A.Yoshihara, K.Morimoto, G.Takata. Structural Insight Into L-Ribulose 3-Epimerase From Mesorhizobium Loti. Acta Crystallogr.,Sect.D V. 69 2330 2013.
ISSN: ISSN 0907-4449
PubMed: 24311575
DOI: 10.1107/S0907444913021665
Page generated: Sat Aug 16 13:16:07 2025

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