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Nickel in PDB 7cl5: The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine

Enzymatic activity of The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine

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

Protein crystallography data

The structure of The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine, PDB code: 7cl5 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) 49.68 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.083, 184.259, 109.771, 90, 97.68, 90
R / Rfree (%) 19.7 / 21.4

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine (pdb code 7cl5). 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 and N- Oxalylglycine, PDB code: 7cl5:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 7cl5

Go back to Nickel Binding Sites List in 7cl5
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:49.0
occ:1.00
 NE2 A:HIS219 2.1 46.7 1.0
O A:HOH401 2.1 43.7 1.0
O2' A:OGA302 2.1 50.1 1.0
O1 A:OGA302 2.2 48.6 1.0
OD1 A:ASP134 2.2 42.7 1.0
NE2 A:HIS132 2.2 47.8 1.0
C2 A:OGA302 2.8 49.4 1.0
C1 A:OGA302 2.9 49.7 1.0
CE1 A:HIS219 3.0 45.9 1.0
CG A:ASP134 3.0 40.7 1.0
CD2 A:HIS219 3.1 46.8 1.0
CE1 A:HIS132 3.1 47.8 1.0
OD2 A:ASP134 3.2 40.3 1.0
CD2 A:HIS132 3.2 46.6 1.0
N1 A:OGA302 4.0 47.8 1.0
O2 A:OGA302 4.1 49.6 1.0
ND1 A:HIS219 4.1 45.6 1.0
O A:HOH402 4.1 44.2 1.0
CG A:HIS219 4.2 46.5 1.0
ND1 A:HIS132 4.2 47.6 1.0
CG A:HIS132 4.3 46.4 1.0
C2 A:9CS303 4.4 40.2 1.0
CB A:ASP134 4.4 40.5 1.0
C4 A:OGA302 4.6 48.2 1.0
NH2 A:ARG213 4.7 53.5 1.0
OE1 A:GLN129 4.8 43.9 1.0
CA A:ASP134 4.9 41.5 1.0
N A:ASP134 4.9 43.0 1.0
C1 A:9CS303 5.0 40.3 1.0

Nickel binding site 2 out of 6 in 7cl5

Go back to Nickel Binding Sites List in 7cl5
Nickel binding site 2 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:43.3
occ:1.00
 O2' B:OGA302 2.0 45.4 1.0
NE2 B:HIS219 2.1 35.8 1.0
O B:HOH403 2.1 43.6 1.0
NE2 B:HIS132 2.1 35.2 1.0
OD1 B:ASP134 2.2 36.8 1.0
O2 B:OGA302 2.2 46.1 1.0
C2 B:OGA302 2.8 46.1 1.0
C1 B:OGA302 2.9 46.8 1.0
CG B:ASP134 3.0 36.5 1.0
CE1 B:HIS219 3.0 35.8 1.0
CE1 B:HIS132 3.1 35.6 1.0
CD2 B:HIS219 3.1 36.0 1.0
CD2 B:HIS132 3.1 35.3 1.0
OD2 B:ASP134 3.2 36.5 1.0
O B:HOH411 3.9 49.3 1.0
N1 B:OGA302 4.0 45.1 1.0
ND1 B:HIS219 4.1 35.8 1.0
O1 B:OGA302 4.1 47.3 1.0
ND1 B:HIS132 4.2 36.1 1.0
CG B:HIS219 4.2 36.0 1.0
CG B:HIS132 4.2 35.9 1.0
CB B:ASP134 4.4 36.4 1.0
C2 B:9CS303 4.6 44.3 1.0
C4 B:OGA302 4.6 44.1 1.0
NH2 B:ARG213 4.7 38.5 1.0
CA B:ASP134 4.8 36.8 1.0
OE1 B:GLN129 4.8 39.9 1.0
N B:ASP134 4.9 36.5 1.0
O5 B:9CS303 4.9 43.6 1.0

Nickel binding site 3 out of 6 in 7cl5

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Nickel binding site 3 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:39.5
occ:1.00
 O C:HOH403 1.8 41.0 1.0
O1 C:OGA302 2.0 38.0 1.0
NE2 C:HIS219 2.1 34.4 1.0
NE2 C:HIS132 2.1 33.6 1.0
OD1 C:ASP134 2.2 32.6 1.0
O2' C:OGA302 2.2 39.1 1.0
C1 C:OGA302 2.8 38.7 1.0
C2 C:OGA302 2.8 39.3 1.0
CE1 C:HIS219 3.0 34.9 1.0
CG C:ASP134 3.0 32.7 1.0
CE1 C:HIS132 3.1 34.0 1.0
CD2 C:HIS219 3.1 35.2 1.0
CD2 C:HIS132 3.2 34.0 1.0
OD2 C:ASP134 3.2 32.5 1.0
O2 C:OGA302 4.0 38.8 1.0
N1 C:OGA302 4.0 39.5 1.0
O C:HOH414 4.1 36.3 1.0
ND1 C:HIS219 4.1 34.9 1.0
CG C:HIS219 4.2 35.0 1.0
ND1 C:HIS132 4.2 34.9 1.0
CG C:HIS132 4.3 34.9 1.0
CB C:ASP134 4.5 32.9 1.0
C2 C:9CS303 4.5 36.5 1.0
C4 C:OGA302 4.6 40.1 1.0
NH2 C:ARG213 4.7 36.0 1.0
OE1 C:GLN129 4.8 39.1 1.0
CA C:ASP134 4.8 33.9 1.0
N C:ASP134 4.9 33.8 1.0

Nickel binding site 4 out of 6 in 7cl5

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Nickel binding site 4 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:38.3
occ:1.00
 NE2 D:HIS219 2.1 38.6 1.0
O2 D:OGA302 2.1 38.3 1.0
NE2 D:HIS132 2.2 34.2 1.0
OD1 D:ASP134 2.2 34.5 1.0
O2' D:OGA302 2.2 41.2 1.0
O D:HOH410 2.3 45.7 1.0
C2 D:OGA302 2.8 39.8 1.0
C1 D:OGA302 2.8 39.7 1.0
CE1 D:HIS219 3.0 38.7 1.0
CG D:ASP134 3.1 34.6 1.0
CD2 D:HIS219 3.1 38.8 1.0
CE1 D:HIS132 3.1 35.1 1.0
CD2 D:HIS132 3.2 34.6 1.0
OD2 D:ASP134 3.2 35.0 1.0
O D:HOH421 3.8 40.7 1.0
N1 D:OGA302 3.9 39.9 1.0
O1 D:OGA302 4.1 39.1 1.0
ND1 D:HIS219 4.1 39.1 1.0
CG D:HIS219 4.2 39.5 1.0
ND1 D:HIS132 4.2 35.8 1.0
CG D:HIS132 4.3 35.7 1.0
CB D:ASP134 4.5 34.8 1.0
C4 D:OGA302 4.6 40.5 1.0
C2 D:9CS303 4.6 36.4 1.0
OE1 D:GLN129 4.7 35.6 1.0
NH2 D:ARG213 4.8 36.9 1.0
CA D:ASP134 4.9 35.0 1.0
N D:ASP134 4.9 35.0 1.0

Nickel binding site 5 out of 6 in 7cl5

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Nickel binding site 5 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:46.5
occ:1.00
 NE2 E:HIS132 2.1 39.8 1.0
O2' E:OGA302 2.1 49.6 1.0
O E:HOH401 2.1 44.3 1.0
NE2 E:HIS219 2.2 44.5 1.0
OD1 E:ASP134 2.2 43.6 1.0
O2 E:OGA302 2.3 44.9 1.0
C2 E:OGA302 2.8 49.1 1.0
C1 E:OGA302 2.9 47.7 1.0
CE1 E:HIS132 3.0 39.3 1.0
CD2 E:HIS132 3.1 40.0 1.0
CG E:ASP134 3.1 43.5 1.0
CE1 E:HIS219 3.1 44.6 1.0
CD2 E:HIS219 3.2 44.2 1.0
OD2 E:ASP134 3.3 44.0 1.0
N1 E:OGA302 4.0 50.2 1.0
ND1 E:HIS132 4.1 39.2 1.0
O1 E:OGA302 4.2 47.8 1.0
CG E:HIS132 4.2 39.6 1.0
ND1 E:HIS219 4.2 44.6 1.0
CG E:HIS219 4.3 44.3 1.0
C2 E:9CS303 4.4 46.9 1.0
CB E:ASP134 4.5 43.8 1.0
OE1 E:GLN129 4.7 40.6 1.0
C4 E:OGA302 4.7 50.0 1.0
CA E:ASP134 4.9 42.9 1.0
NH2 E:ARG213 4.9 46.4 1.0
N E:ASP134 4.9 42.0 1.0

Nickel binding site 6 out of 6 in 7cl5

Go back to Nickel Binding Sites List in 7cl5
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanj in Complex with Kanamycin B and N- Oxalylglycine


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 and N- Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni301

b:54.7
occ:1.00
 O2' F:OGA302 1.9 66.9 1.0
NE2 F:HIS132 2.1 45.8 1.0
NE2 F:HIS219 2.1 52.3 1.0
OD1 F:ASP134 2.2 46.4 1.0
O F:HOH403 2.2 47.3 1.0
O1 F:OGA302 2.3 61.0 1.0
C2 F:OGA302 2.7 64.4 1.0
C1 F:OGA302 2.9 62.9 1.0
CG F:ASP134 3.0 46.5 1.0
CE1 F:HIS132 3.1 47.1 1.0
CE1 F:HIS219 3.1 51.7 1.0
CD2 F:HIS132 3.1 45.9 1.0
CD2 F:HIS219 3.1 52.6 1.0
OD2 F:ASP134 3.2 46.4 1.0
N1 F:OGA302 4.0 63.2 1.0
O2 F:OGA302 4.1 63.5 1.0
ND1 F:HIS132 4.2 48.0 1.0
ND1 F:HIS219 4.2 51.9 1.0
CG F:HIS132 4.2 46.6 1.0
CG F:HIS219 4.2 52.8 1.0
CB F:ASP134 4.4 47.1 1.0
C2 F:9CS303 4.5 45.9 1.0
C4 F:OGA302 4.5 62.5 1.0
OE1 F:GLN129 4.7 45.0 1.0
NH2 F:ARG213 4.8 54.6 1.0
CA F:ASP134 4.8 46.9 1.0
O5 F:9CS303 4.9 47.0 1.0
N6 F:9CS303 4.9 45.5 1.0
N F:ASP134 4.9 47.2 1.0
C1 F:9CS303 5.0 46.3 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 09:07:59 2024

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