Atomistry » Manganese » PDB 1uvj-1vzx » 1vha
Atomistry »
  Manganese »
    PDB 1uvj-1vzx »
      1vha »

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

Go back to Manganese Binding Sites List in 1vha
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 Oct 5 12:49:00 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy