Atomistry » Manganese » PDB 4dky-4ee1 » 4eay
Atomistry »
  Manganese »
    PDB 4dky-4ee1 »
      4eay »

Manganese in PDB 4eay: Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate

Enzymatic activity of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate

All present enzymatic activity of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate:
4.2.1.8;

Protein crystallography data

The structure of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate, PDB code: 4eay was solved by X.Qiu, Y.Zhu, Y.Yuan, Y.Zhang, H.Liu, Y.Gao, M.Teng, L.Niu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 159.470, 238.580, 54.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 23.6

Other elements in 4eay:

The structure of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate (pdb code 4eay). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate, PDB code: 4eay:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese binding site 1 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:13.9
occ:1.00
 O1B A:CS2402 2.0 37.7 1.0
ND1 A:HIS298 2.1 15.7 1.0
NE2 A:HIS233 2.3 16.2 1.0
O2 A:CS2402 2.3 35.6 1.0
OD2 A:ASP351 2.4 19.3 1.0
SG A:CYS271 2.4 15.6 1.0
C1 A:CS2402 2.9 36.1 1.0
CG A:HIS298 3.1 15.5 1.0
CE1 A:HIS298 3.1 15.2 1.0
C2 A:CS2402 3.2 36.1 1.0
CE1 A:HIS233 3.2 16.5 1.0
CD2 A:HIS233 3.3 18.1 1.0
CB A:CYS271 3.3 17.2 1.0
CG A:ASP351 3.4 18.5 1.0
CB A:HIS298 3.4 15.2 1.0
OD1 A:ASP351 3.7 19.1 1.0
OG A:SER274 4.1 17.6 1.0
O1A A:CS2402 4.1 34.2 1.0
NE2 A:HIS298 4.2 15.2 1.0
CD2 A:HIS298 4.3 16.6 1.0
NE A:ARG300 4.3 15.3 1.0
ND1 A:HIS233 4.3 18.5 1.0
NH2 A:ARG300 4.3 16.1 1.0
CG A:HIS233 4.4 17.8 1.0
CA A:CYS271 4.5 17.4 1.0
C3 A:CS2402 4.5 36.5 1.0
CB A:ASP351 4.6 17.9 1.0
C5 A:CS2402 4.7 33.4 1.0
CZ A:ARG300 4.8 15.5 1.0
C4 A:CS2402 4.9 34.5 1.0
CA A:HIS298 4.9 15.6 1.0

Manganese binding site 2 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese binding site 2 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn403

b:13.2
occ:1.00
 ND1 B:HIS298 2.1 16.2 1.0
NE2 B:HIS233 2.2 17.2 1.0
O2 B:CS2402 2.3 42.2 1.0
SG B:CYS271 2.3 15.2 1.0
O1B B:CS2402 2.3 46.6 1.0
OD2 B:ASP351 2.5 21.3 1.0
CE1 B:HIS233 3.0 19.1 1.0
C1 B:CS2402 3.0 44.8 1.0
CG B:HIS298 3.1 16.1 1.0
CE1 B:HIS298 3.1 15.1 1.0
C2 B:CS2402 3.2 43.9 1.0
CD2 B:HIS233 3.3 18.5 1.0
CB B:CYS271 3.3 17.6 1.0
CB B:HIS298 3.4 16.4 1.0
CG B:ASP351 3.4 20.9 1.0
OD1 B:ASP351 3.8 22.8 1.0
ND1 B:HIS233 4.2 19.6 1.0
O1A B:CS2402 4.2 45.2 1.0
NE2 B:HIS298 4.2 16.1 1.0
CD2 B:HIS298 4.2 17.4 1.0
OG B:SER274 4.2 20.5 1.0
NE B:ARG300 4.3 14.7 1.0
CG B:HIS233 4.3 19.3 1.0
NH2 B:ARG300 4.4 17.0 1.0
CA B:CYS271 4.5 17.9 1.0
C3 B:CS2402 4.5 42.5 1.0
CB B:ASP351 4.6 18.5 1.0
CZ B:ARG300 4.8 16.8 1.0
C5 B:CS2402 4.9 39.1 1.0
CA B:HIS298 4.9 17.0 1.0
C4 B:CS2402 4.9 40.5 1.0

Manganese binding site 3 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese binding site 3 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:21.6
occ:1.00
 ND1 C:HIS298 2.0 21.3 1.0
NE2 C:HIS233 2.2 24.2 1.0
SG C:CYS271 2.3 20.3 1.0
OD2 C:ASP351 2.5 26.0 1.0
CE1 C:HIS298 3.0 21.4 1.0
CG C:HIS298 3.0 20.2 1.0
CE1 C:HIS233 3.1 24.7 1.0
CD2 C:HIS233 3.3 23.9 1.0
CG C:ASP351 3.3 24.4 1.0
CB C:CYS271 3.4 22.8 1.0
CB C:HIS298 3.4 20.4 1.0
OD1 C:ASP351 3.6 25.6 1.0
NE2 C:HIS298 4.1 20.7 1.0
NH2 C:ARG300 4.1 23.2 1.0
CD2 C:HIS298 4.1 20.7 1.0
OG C:SER274 4.2 26.4 1.0
ND1 C:HIS233 4.3 26.3 1.0
NE C:ARG300 4.3 22.4 1.0
CG C:HIS233 4.4 25.0 1.0
CA C:CYS271 4.6 22.4 1.0
CB C:ASP351 4.6 22.8 1.0
CZ C:ARG300 4.7 22.7 1.0
CA C:HIS298 4.9 20.0 1.0
NH2 C:ARG349 5.0 23.4 1.0

Manganese binding site 4 out of 4 in 4eay

Go back to Manganese Binding Sites List in 4eay
Manganese binding site 4 out of 4 in the Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structures of Mannonate Dehydratase From Escherichia Coli Strain K12 Complexed with D-Mannonate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:29.1
occ:1.00
 ND1 D:HIS298 2.1 28.2 1.0
NE2 D:HIS233 2.2 30.7 1.0
SG D:CYS271 2.3 25.3 1.0
OD2 D:ASP351 2.5 30.6 1.0
CE1 D:HIS298 3.0 28.8 1.0
CG D:HIS298 3.1 27.1 1.0
CE1 D:HIS233 3.2 29.7 1.0
CD2 D:HIS233 3.3 30.8 1.0
CG D:ASP351 3.3 29.2 1.0
CB D:HIS298 3.4 26.6 1.0
CB D:CYS271 3.4 28.5 1.0
OD1 D:ASP351 3.5 32.0 1.0
OG D:SER274 4.1 29.3 1.0
NH2 D:ARG300 4.1 28.0 1.0
NE2 D:HIS298 4.2 29.3 1.0
CD2 D:HIS298 4.2 28.3 1.0
ND1 D:HIS233 4.3 32.6 1.0
NE D:ARG300 4.3 25.1 1.0
CG D:HIS233 4.4 31.9 1.0
CB D:ASP351 4.6 26.9 1.0
CA D:CYS271 4.6 28.0 1.0
CZ D:ARG300 4.7 26.7 1.0
CA D:HIS298 4.9 26.8 1.0

Reference:

X.Qiu, Y.Tao, Y.Zhu, Y.Yuan, Y.Zhang, H.Liu, Y.Gao, M.Teng, L.Niu. Structural Insights Into Decreased Enzymatic Activity Induced By An Insert Sequence in Mannonate Dehydratase From Gram Negative Bacterium. J.Struct.Biol. V. 180 327 2012.
ISSN: ISSN 1047-8477
PubMed: 22796868
DOI: 10.1016/J.JSB.2012.06.013
Page generated: Sat Oct 5 19:16:08 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy