Atomistry » Manganese » PDB 6oe2-6q9f » 6ph9
Atomistry »
  Manganese »
    PDB 6oe2-6q9f »
      6ph9 »

Manganese in PDB 6ph9: Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

Enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex

All present enzymatic activity of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex:
3.6.1.54;

Protein crystallography data

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9 was solved by J.Cho, P.Zhou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.90 / 1.92
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 105.990, 105.990, 52.570, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 19.9

Other elements in 6ph9:

The structure of Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex (pdb code 6ph9). 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 Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex, PDB code: 6ph9:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 1 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:33.5
occ:1.00
OD1 A:ASP8 1.9 32.7 1.0
O A:HOH415 2.2 35.3 1.0
NE2 A:HIS10 2.3 35.4 1.0
NE2 A:HIS197 2.3 37.1 1.0
OD2 A:ASP41 2.5 30.9 1.0
CG A:ASP8 2.8 28.4 1.0
CE1 A:HIS197 3.1 40.0 1.0
CE1 A:HIS10 3.2 40.6 1.0
CD2 A:HIS10 3.3 37.4 1.0
CD2 A:HIS197 3.3 35.2 1.0
CB A:ASP8 3.3 28.0 1.0
MN A:MN302 3.4 30.1 1.0
CG A:ASP41 3.5 30.7 1.0
CB A:ASP41 3.6 26.5 1.0
O A:HOH436 3.7 43.2 1.0
OD2 A:ASP8 3.9 34.7 1.0
CA A:ASP8 3.9 23.3 1.0
O A:HIS195 4.0 33.1 1.0
CA A:HIS195 4.2 35.6 1.0
ND1 A:HIS197 4.3 42.4 1.0
ND1 A:HIS10 4.3 38.8 1.0
CG A:HIS10 4.4 33.5 1.0
CG A:HIS197 4.4 38.5 1.0
CE1 A:HIS114 4.5 31.2 1.0
C A:HIS195 4.5 34.4 1.0
OD1 A:ASP41 4.6 31.2 1.0
NE2 A:HIS114 4.7 29.6 1.0
N A:HIS195 4.7 27.8 1.0
C A:ASP8 4.9 26.1 1.0
N A:ASP8 4.9 24.4 1.0
ND1 A:HIS195 4.9 33.4 1.0
OD1 A:ASN79 4.9 35.5 1.0

Manganese binding site 2 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 2 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:30.1
occ:1.00
O A:HOH415 1.9 35.3 1.0
OD1 A:ASN79 2.0 35.5 1.0
OD2 A:ASP41 2.1 30.9 1.0
NE2 A:HIS114 2.2 29.6 1.0
ND1 A:HIS195 2.3 33.4 1.0
CE1 A:HIS114 3.0 31.2 1.0
CG A:ASP41 3.1 30.7 1.0
CG A:ASN79 3.2 34.5 1.0
CE1 A:HIS195 3.2 40.6 1.0
CG A:HIS195 3.3 35.1 1.0
CD2 A:HIS114 3.3 31.6 1.0
O A:HOH436 3.4 43.2 1.0
MN A:MN301 3.4 33.5 1.0
CA A:HIS195 3.5 35.6 1.0
OD1 A:ASP41 3.6 31.2 1.0
CB A:HIS195 3.6 30.6 1.0
OD1 A:ASP8 3.7 32.7 1.0
ND2 A:ASN79 3.9 34.4 1.0
ND1 A:HIS114 4.1 28.9 1.0
O A:HIS195 4.2 33.1 1.0
N A:ASN79 4.3 30.7 1.0
CB A:ASP41 4.3 26.5 1.0
CB A:ASN79 4.3 29.8 1.0
NE2 A:HIS195 4.3 37.6 1.0
CG A:HIS114 4.3 28.4 1.0
C A:HIS195 4.4 34.4 1.0
CD2 A:HIS195 4.4 35.0 1.0
N A:HIS195 4.5 27.8 1.0
CG A:ASP8 4.8 28.4 1.0
CA A:ASN79 4.9 33.8 1.0

Manganese binding site 3 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 3 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:43.7
occ:0.81
O A:HOH584 2.3 51.8 1.0
O A:HOH520 2.4 40.5 1.0
O A:HOH596 2.5 42.3 1.0
O A:HOH459 2.6 39.0 1.0
O A:HOH578 2.6 36.1 1.0
O A:HOH547 2.8 41.4 0.5
OD1 A:ASP34 4.4 30.7 1.0
O A:HOH547 4.5 46.2 0.5
O A:ALA33 4.5 31.5 1.0
O A:HOH507 4.5 43.0 1.0
O A:GLN32 4.7 40.3 1.0
O A:GLY70 4.7 28.8 1.0

Manganese binding site 4 out of 4 in 6ph9

Go back to Manganese Binding Sites List in 6ph9
Manganese binding site 4 out of 4 in the Crystal Structure of the Klebsiella Pneumoniae Lpxh-Lipid X Complex


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 the Klebsiella Pneumoniae Lpxh-Lipid X Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:42.2
occ:0.27
O A:HOH544 2.1 57.3 1.0
O A:HOH497 2.4 40.2 1.0
O A:HOH511 2.5 43.2 1.0
NZ A:LYS227 3.9 41.5 1.0
O A:HOH552 4.3 53.2 1.0
OE1 A:GLU234 4.4 32.7 1.0
OE2 A:GLU234 4.6 35.8 1.0
CE A:LYS227 4.8 39.9 1.0
O A:HOH527 4.8 47.9 1.0
CD A:GLU234 4.9 33.3 1.0

Reference:

J.Cho, M.Lee, C.Cochrane, C.Webster, B.Fenton, J.Zhao, J.Hong, P.Zhao. Structural Basis of the Udp-Diacylglucosamine Pyrophosphohydrolase Lpxh Inhibition By Sulfonyl Piperazine Antibiotics Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1912876117
Page generated: Sun Oct 6 05:51:04 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy