Atomistry » Nickel » PDB 6z8o-7err » 7cl3
Atomistry »
  Nickel »
    PDB 6z8o-7err »
      7cl3 »

Nickel in PDB 7cl3: The Crystal Structure of Kanj in Complex with Kanamycin B

Enzymatic activity of The Crystal Structure of Kanj in Complex with Kanamycin B

All present enzymatic activity of The Crystal Structure of Kanj in Complex with Kanamycin B:
1.14.11.37;

Protein crystallography data

The structure of The Crystal Structure of Kanj in Complex with Kanamycin B, PDB code: 7cl3 was solved by Y.Kitayama, A.Miyanaga, F.Kudo, T.Eguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.06 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.289, 184.514, 109.543, 90, 93.99, 90
R / Rfree (%) 19.4 / 21.7

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Kanj in Complex with Kanamycin B (pdb code 7cl3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 6 binding sites of Nickel where determined in the The Crystal Structure of Kanj in Complex with Kanamycin B, PDB code: 7cl3:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:78.0
occ:1.00
 NE2 A:HIS219 2.3 38.1 1.0
NE2 A:HIS132 2.4 37.8 1.0
O A:HOH456 2.5 50.2 1.0
OD1 A:ASP134 2.7 37.4 1.0
CE1 A:HIS219 3.2 37.9 1.0
CE1 A:HIS132 3.3 37.0 1.0
CD2 A:HIS219 3.3 38.3 1.0
CD2 A:HIS132 3.4 37.9 1.0
CG A:ASP134 3.5 38.4 1.0
OD2 A:ASP134 3.7 41.2 1.0
O A:HOH446 3.9 41.9 1.0
ND1 A:HIS219 4.3 38.7 1.0
CG A:HIS219 4.4 37.9 1.0
C2 A:9CS303 4.4 40.5 1.0
ND1 A:HIS132 4.4 37.5 1.0
O2 A:SO4302 4.5 77.3 1.0
CG A:HIS132 4.5 37.8 1.0
OE1 A:GLN129 4.6 40.6 1.0
CB A:ASP134 4.9 37.2 1.0

Nickel binding site 2 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 2 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:53.2
occ:1.00
 NE2 B:HIS219 2.2 35.2 1.0
O B:HOH495 2.3 49.8 1.0
NE2 B:HIS132 2.3 32.8 1.0
O B:HOH441 2.3 52.2 1.0
OD1 B:ASP134 2.4 38.9 1.0
O B:HOH409 2.6 43.5 1.0
CE1 B:HIS219 3.0 34.9 1.0
CD2 B:HIS132 3.2 32.0 1.0
CD2 B:HIS219 3.3 34.8 1.0
CE1 B:HIS132 3.3 33.4 1.0
CG B:ASP134 3.3 33.7 1.0
OD2 B:ASP134 3.4 33.9 1.0
O B:HOH481 4.0 54.7 1.0
ND1 B:HIS219 4.1 34.8 1.0
CG B:HIS219 4.3 35.4 1.0
ND1 B:HIS132 4.4 34.8 1.0
CG B:HIS132 4.4 33.4 1.0
O3 B:SO4302 4.4 59.2 1.0
CB B:ASP134 4.7 34.7 1.0
C2 B:9CS303 4.7 71.5 1.0
OE1 B:GLN129 4.8 46.2 1.0
NH2 B:ARG213 5.0 41.2 1.0

Nickel binding site 3 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 3 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:66.2
occ:1.00
 NE2 C:HIS132 2.3 35.8 1.0
O C:HOH424 2.4 39.8 1.0
NE2 C:HIS219 2.4 41.9 1.0
OD1 C:ASP134 2.5 37.4 1.0
CE1 C:HIS219 3.2 40.6 1.0
CE1 C:HIS132 3.3 35.0 1.0
CD2 C:HIS132 3.3 35.5 1.0
CG C:ASP134 3.4 36.0 1.0
CD2 C:HIS219 3.4 39.8 1.0
OD2 C:ASP134 3.6 37.2 1.0
O C:HOH449 4.2 41.6 1.0
ND1 C:HIS219 4.4 38.7 1.0
O2 C:SO4302 4.4 78.2 1.0
ND1 C:HIS132 4.4 36.5 1.0
C2 C:9CS303 4.4 48.1 1.0
CG C:HIS132 4.4 36.0 1.0
CG C:HIS219 4.5 38.3 1.0
OE1 C:GLN129 4.6 40.0 1.0
CB C:ASP134 4.8 36.0 1.0
N6 C:9CS303 4.9 47.1 1.0
O7 C:9CS303 5.0 48.5 1.0

Nickel binding site 4 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 4 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:67.9
occ:1.00
 NE2 D:HIS132 2.3 35.9 1.0
NE2 D:HIS219 2.3 40.1 1.0
O D:HOH442 2.4 56.5 1.0
OD1 D:ASP134 2.4 39.1 1.0
O D:HOH426 2.5 48.7 1.0
CE1 D:HIS219 3.1 38.7 1.0
CD2 D:HIS132 3.2 36.3 1.0
CE1 D:HIS132 3.2 36.8 1.0
CG D:ASP134 3.3 38.8 1.0
CD2 D:HIS219 3.4 39.2 1.0
OD2 D:ASP134 3.5 41.3 1.0
O4 D:SO4302 4.1 97.7 1.0
ND1 D:HIS219 4.2 39.6 1.0
ND1 D:HIS132 4.3 38.8 1.0
CG D:HIS132 4.3 38.1 1.0
CG D:HIS219 4.4 40.3 1.0
C2 D:9CS303 4.6 67.8 1.0
OE1 D:GLN129 4.6 45.7 1.0
O7 D:9CS303 4.7 76.0 1.0
CB D:ASP134 4.7 37.7 1.0

Nickel binding site 5 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 5 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:65.7
occ:1.00
 NE2 E:HIS132 2.3 36.7 1.0
NE2 E:HIS219 2.4 42.0 1.0
OD1 E:ASP134 2.4 42.6 1.0
O E:HOH427 2.5 55.3 1.0
CE1 E:HIS219 3.1 41.8 1.0
CD2 E:HIS132 3.2 36.9 1.0
CE1 E:HIS132 3.2 36.5 1.0
CG E:ASP134 3.4 44.2 1.0
CD2 E:HIS219 3.4 43.1 1.0
OD2 E:ASP134 3.6 45.3 1.0
O E:HOH423 4.2 52.8 1.0
ND1 E:HIS219 4.3 42.6 1.0
O4 E:SO4302 4.3 81.8 1.0
C2 E:9CS303 4.3 59.9 1.0
ND1 E:HIS132 4.3 37.2 1.0
CG E:HIS132 4.3 37.4 1.0
CG E:HIS219 4.4 43.4 1.0
OE1 E:GLN129 4.6 40.8 1.0
CB E:ASP134 4.8 43.9 1.0
N6 E:9CS303 4.8 58.1 1.0

Nickel binding site 6 out of 6 in 7cl3

Go back to Nickel Binding Sites List in 7cl3
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of The Crystal Structure of Kanj in Complex with Kanamycin B within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni301

b:75.9
occ:1.00
 NE2 F:HIS132 2.3 54.1 1.0
NE2 F:HIS219 2.5 52.0 1.0
OD1 F:ASP134 2.5 47.8 1.0
O F:HOH406 2.5 38.2 1.0
CD2 F:HIS132 3.3 57.4 1.0
CE1 F:HIS132 3.3 54.3 1.0
CE1 F:HIS219 3.3 53.8 1.0
CG F:ASP134 3.4 47.1 1.0
CD2 F:HIS219 3.5 51.9 1.0
OD2 F:ASP134 3.6 45.9 1.0
C2 F:9CS303 4.1 50.5 1.0
O1 F:SO4302 4.3 83.5 1.0
ND1 F:HIS132 4.4 58.1 1.0
CG F:HIS132 4.4 58.5 1.0
ND1 F:HIS219 4.5 52.9 1.0
N6 F:9CS303 4.5 49.6 1.0
CG F:HIS219 4.6 54.4 1.0
OE1 F:GLN129 4.6 56.6 1.0
O7 F:9CS303 4.7 53.4 1.0
CB F:ASP134 4.8 45.9 1.0
C3 F:9CS303 4.9 49.6 1.0
C1 F:9CS303 5.0 50.2 1.0

Reference:

T.Eguchi, F.Kudo, Y.Kitayama, A.Miyanaga, M.Numakura. Stepwise Post-Glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis. Chembiochem 2021.
ISSN: ESSN 1439-7633
PubMed: 33403742
DOI: 10.1002/CBIC.202000839
Page generated: Thu Oct 10 09:07:53 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