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Manganese in PDB 1vha: Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase

Enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase

All present enzymatic activity of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase, PDB code: 1vha was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.55 / 2.35
Space group I 41
Cell size a, b, c (Å), α, β, γ (°) 104.715, 104.715, 195.864, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 28.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase (pdb code 1vha). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase, PDB code: 1vha:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 1vha

Go back to Manganese Binding Sites List in 1vha
Manganese binding site 1 out of 5 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn169

b:52.9
occ:0.50
 O A:HOH210 2.3 41.9 1.0
OD2 A:ASP9 2.4 33.2 0.8
O B:HOH210 3.0 56.9 1.0
OD1 A:ASP9 3.5 26.5 0.1
CG A:ASP9 3.5 28.3 0.8
OE2 B:GLU136 3.7 35.4 1.0
O A:VAL10 3.8 23.3 1.0
OD1 A:ASP9 3.9 28.1 0.8
OG1 B:THR133 4.1 38.8 1.0
O A:HOH211 4.2 45.2 1.0
O B:THR134 4.4 32.1 1.0
N A:VAL10 4.4 23.7 1.0
CG A:ASP9 4.5 26.2 0.1
CD B:GLU136 4.6 33.1 1.0
CG B:GLU136 4.7 32.1 1.0
CB A:ASP9 4.7 26.6 1.0
O A:HOH201 4.8 50.8 1.0
C A:VAL10 4.8 24.8 1.0
CA A:ASP9 5.0 25.3 1.0

Manganese binding site 2 out of 5 in 1vha

Go back to Manganese Binding Sites List in 1vha
Manganese binding site 2 out of 5 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn169

b:54.2
occ:0.50
 O C:HOH216 2.6 36.7 1.0
OE2 C:GLU136 3.1 27.5 1.0
OD1 B:ASP9 3.2 40.2 1.0
O B:VAL10 3.2 25.2 1.0
CD C:GLU136 3.8 27.9 1.0
O B:HOH202 4.0 47.4 1.0
CG C:GLU136 4.0 22.7 1.0
CG B:ASP9 4.0 36.8 1.0
OD2 B:ASP9 4.2 37.8 1.0
N B:VAL10 4.3 24.9 1.0
C B:VAL10 4.3 23.4 1.0
O C:THR134 4.4 27.1 1.0
OG1 C:THR133 4.5 33.9 1.0
O B:HOH174 4.6 31.6 1.0
CA B:VAL10 4.9 22.6 1.0
OE1 C:GLU136 4.9 25.2 1.0

Manganese binding site 3 out of 5 in 1vha

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Manganese binding site 3 out of 5 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn169

b:64.4
occ:0.50
 OD1 C:ASP9 2.8 33.5 1.0
OE2 A:GLU136 3.3 29.9 1.0
O C:VAL10 3.4 22.1 1.0
O C:HOH174 3.8 39.6 1.0
CG C:ASP9 3.8 31.7 1.0
CD A:GLU136 4.0 27.8 1.0
OD2 C:ASP9 4.2 32.0 1.0
CG A:GLU136 4.3 22.6 1.0
N C:VAL10 4.4 23.1 1.0
C C:VAL10 4.5 22.9 1.0
O A:THR134 4.6 24.0 1.0
OG1 A:THR133 4.7 33.8 1.0
O C:HOH201 4.8 41.6 1.0
OG1 A:THR134 5.0 32.5 1.0

Manganese binding site 4 out of 5 in 1vha

Go back to Manganese Binding Sites List in 1vha
Manganese binding site 4 out of 5 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn169

b:62.0
occ:0.50
 OD2 D:ASP9 2.4 34.5 0.5
O D:HOH202 2.6 46.2 1.0
CG D:ASP9 3.3 33.5 0.5
OD1 D:ASP9 3.4 33.5 0.5
O D:VAL10 3.6 34.2 1.0
OE1 E:GLU136 3.7 38.0 1.0
O D:HOH203 3.7 63.2 1.0
CE1 D:HIS35 4.1 61.9 1.0
OD1 D:ASP9 4.2 35.9 0.5
NE2 D:HIS35 4.2 62.4 1.0
N D:VAL10 4.4 34.2 1.0
CD2 D:HIS43 4.4 53.9 1.0
OG1 E:THR133 4.5 36.9 1.0
CG D:ASP9 4.5 37.8 0.5
CD E:GLU136 4.6 35.1 1.0
CB D:ASP9 4.6 35.0 1.0
O D:HOH204 4.7 54.5 1.0
C D:VAL10 4.7 33.7 1.0
O E:HOH172 4.7 40.1 1.0
CG E:GLU136 4.8 34.5 1.0
O E:THR134 4.9 30.5 1.0

Manganese binding site 5 out of 5 in 1vha

Go back to Manganese Binding Sites List in 1vha
Manganese binding site 5 out of 5 in the Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn169

b:55.2
occ:0.50
 O F:HOH204 2.5 41.8 1.0
OD1 F:ASP9 2.6 25.7 0.3
O F:VAL10 3.0 26.8 1.0
OE2 D:GLU136 3.1 33.9 1.0
CG F:ASP9 3.4 25.3 0.3
OD2 F:ASP9 3.6 22.9 0.3
CD D:GLU136 3.8 34.7 1.0
O F:HOH205 3.9 57.0 1.0
CG D:GLU136 4.0 31.7 1.0
N F:VAL10 4.1 28.8 1.0
OD2 F:ASP9 4.1 27.8 0.7
O D:HOH174 4.1 34.0 1.0
C F:VAL10 4.1 27.9 1.0
NE2 F:HIS35 4.4 55.6 1.0
CE1 F:HIS35 4.4 55.2 1.0
O D:THR134 4.4 29.6 1.0
CA F:VAL10 4.7 27.2 1.0
OG1 D:THR133 4.7 38.8 1.0
CB F:ASP9 4.7 27.6 1.0
OE1 D:GLU136 4.8 30.3 1.0
CG F:ASP9 4.8 29.3 0.7
CD2 F:HIS43 5.0 43.4 1.0

Reference:

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541
Page generated: Sat Aug 16 09:17:14 2025

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