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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: Mon Jan 25 16:00:30 2021

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