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Nickel in PDB 7cl4: The Crystal Structure of Kanj in Complex with N-Oxalylglycine

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

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

Protein crystallography data

The structure of The Crystal Structure of Kanj in Complex with N-Oxalylglycine, PDB code: 7cl4 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) 47.17 / 2.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.472, 185.663, 109.638, 90, 93.93, 90
R / Rfree (%) 18.6 / 21.1

Nickel Binding Sites:

The binding sites of Nickel atom in the The Crystal Structure of Kanj in Complex with N-Oxalylglycine (pdb code 7cl4). 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 N-Oxalylglycine, PDB code: 7cl4:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6;

Nickel binding site 1 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 1 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:38.9
occ:1.00
 O2' A:OGA302 1.9 49.1 1.0
NE2 A:HIS132 2.1 31.8 1.0
NE2 A:HIS219 2.1 36.7 1.0
OD1 A:ASP134 2.2 39.4 1.0
O1 A:OGA302 2.3 44.4 1.0
O A:HOH409 2.4 42.9 1.0
C2 A:OGA302 2.7 50.1 1.0
C1 A:OGA302 2.9 47.5 1.0
CD2 A:HIS132 3.0 31.4 1.0
CE1 A:HIS219 3.1 36.8 1.0
CG A:ASP134 3.1 37.8 1.0
CD2 A:HIS219 3.1 38.3 1.0
CE1 A:HIS132 3.1 32.4 1.0
OD2 A:ASP134 3.3 38.3 1.0
N1 A:OGA302 4.0 52.4 1.0
O2 A:OGA302 4.2 45.3 1.0
ND1 A:HIS219 4.2 37.8 1.0
CG A:HIS132 4.2 32.3 1.0
ND1 A:HIS132 4.2 31.9 1.0
CG A:HIS219 4.2 37.7 1.0
CB A:ASP134 4.5 36.2 1.0
C4 A:OGA302 4.5 52.4 1.0
OE1 A:GLN129 4.8 38.8 1.0
CA A:ASP134 4.9 35.7 1.0
NH2 A:ARG213 4.9 47.2 1.0
N A:ASP134 5.0 35.0 1.0

Nickel binding site 2 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 2 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:34.6
occ:1.00
 O2' B:OGA302 2.0 42.5 1.0
O2 B:OGA302 2.1 40.2 1.0
NE2 B:HIS219 2.1 28.7 1.0
NE2 B:HIS132 2.2 27.4 1.0
OD1 B:ASP134 2.2 34.7 1.0
O B:HOH449 2.4 36.7 1.0
C2 B:OGA302 2.6 44.9 1.0
C1 B:OGA302 2.7 43.8 1.0
CG B:ASP134 3.1 32.6 1.0
CE1 B:HIS219 3.1 28.3 1.0
CD2 B:HIS219 3.1 28.6 1.0
CD2 B:HIS132 3.1 27.5 1.0
CE1 B:HIS132 3.2 28.7 1.0
OD2 B:ASP134 3.2 33.2 1.0
N1 B:OGA302 3.9 43.6 1.0
O1 B:OGA302 4.0 42.8 1.0
ND1 B:HIS219 4.2 28.1 1.0
CG B:HIS219 4.2 28.7 1.0
CG B:HIS132 4.3 28.7 1.0
ND1 B:HIS132 4.3 29.1 1.0
CB B:ASP134 4.5 31.8 1.0
C4 B:OGA302 4.6 42.0 1.0
O B:HOH511 4.7 44.3 1.0
OE1 B:GLN129 4.8 34.9 1.0
NH2 B:ARG213 4.9 37.1 1.0
CA B:ASP134 4.9 32.6 1.0

Nickel binding site 3 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 3 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:33.6
occ:1.00
 O C:HOH401 2.0 29.4 1.0
O1 C:OGA302 2.0 34.3 1.0
NE2 C:HIS219 2.0 29.9 1.0
NE2 C:HIS132 2.1 29.0 1.0
O2' C:OGA302 2.1 39.5 1.0
OD1 C:ASP134 2.3 31.0 1.0
C2 C:OGA302 2.7 39.9 1.0
C1 C:OGA302 2.8 40.2 1.0
CD2 C:HIS219 3.0 30.0 1.0
CE1 C:HIS219 3.0 30.3 1.0
CD2 C:HIS132 3.1 29.2 1.0
CE1 C:HIS132 3.1 30.0 1.0
CG C:ASP134 3.1 31.5 1.0
OD2 C:ASP134 3.3 32.1 1.0
N1 C:OGA302 4.0 42.4 1.0
O2 C:OGA302 4.0 40.2 1.0
O C:HOH474 4.1 43.4 1.0
ND1 C:HIS219 4.1 29.6 1.0
CG C:HIS219 4.1 29.6 1.0
ND1 C:HIS132 4.2 30.7 1.0
CG C:HIS132 4.2 30.0 1.0
CB C:ASP134 4.5 31.0 1.0
C4 C:OGA302 4.5 40.2 1.0
OE1 C:GLN129 4.7 31.8 1.0
NH2 C:ARG213 4.9 36.4 1.0
CA C:ASP134 4.9 31.7 1.0
N C:ASP134 5.0 30.8 1.0

Nickel binding site 4 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 4 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:31.8
occ:1.00
 O2 D:OGA302 2.1 32.0 1.0
NE2 D:HIS219 2.1 29.6 1.0
O D:HOH407 2.1 29.5 1.0
O2' D:OGA302 2.1 39.0 1.0
NE2 D:HIS132 2.1 26.2 1.0
OD1 D:ASP134 2.3 29.2 1.0
C2 D:OGA302 2.8 36.2 1.0
C1 D:OGA302 2.8 35.9 1.0
CD2 D:HIS219 3.1 29.6 1.0
CD2 D:HIS132 3.1 26.8 1.0
CE1 D:HIS219 3.1 29.2 1.0
CE1 D:HIS132 3.1 27.5 1.0
CG D:ASP134 3.1 28.7 1.0
OD2 D:ASP134 3.3 29.2 1.0
O1 D:OGA302 4.0 36.3 1.0
N1 D:OGA302 4.0 39.0 1.0
ND1 D:HIS219 4.2 29.9 1.0
CG D:HIS219 4.2 30.0 1.0
ND1 D:HIS132 4.2 28.1 1.0
CG D:HIS132 4.2 28.3 1.0
CB D:ASP134 4.5 29.2 1.0
C4 D:OGA302 4.6 38.9 1.0
OE1 D:GLN129 4.7 31.8 1.0
NH2 D:ARG213 4.9 36.3 1.0
CA D:ASP134 4.9 30.3 1.0

Nickel binding site 5 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 5 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:38.8
occ:1.00
 O2' E:OGA302 2.0 40.3 1.0
NE2 E:HIS219 2.1 34.1 1.0
NE2 E:HIS132 2.1 32.8 1.0
OD1 E:ASP134 2.2 40.4 1.0
O E:HOH401 2.2 34.3 1.0
O2 E:OGA302 2.2 44.0 1.0
C2 E:OGA302 2.8 41.9 1.0
C1 E:OGA302 2.9 44.5 1.0
CE1 E:HIS219 3.0 33.4 1.0
CG E:ASP134 3.1 40.2 1.0
CD2 E:HIS219 3.1 34.1 1.0
CD2 E:HIS132 3.1 33.8 1.0
CE1 E:HIS132 3.1 32.9 1.0
OD2 E:ASP134 3.2 41.9 1.0
N1 E:OGA302 4.0 42.0 1.0
ND1 E:HIS219 4.1 33.0 1.0
O1 E:OGA302 4.2 42.2 1.0
CG E:HIS219 4.2 34.1 1.0
ND1 E:HIS132 4.2 33.1 1.0
CG E:HIS132 4.2 33.4 1.0
O E:HOH439 4.4 48.2 1.0
CB E:ASP134 4.5 39.5 1.0
C4 E:OGA302 4.6 43.3 1.0
OE1 E:GLN129 4.8 37.4 1.0
NH2 E:ARG213 4.8 41.7 1.0
CA E:ASP134 4.9 39.1 1.0
N E:ASP134 5.0 37.5 1.0

Nickel binding site 6 out of 6 in 7cl4

Go back to Nickel Binding Sites List in 7cl4
Nickel binding site 6 out of 6 in the The Crystal Structure of Kanj in Complex with 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 N-Oxalylglycine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ni301

b:44.0
occ:1.00
 O2' F:OGA302 2.0 51.1 1.0
NE2 F:HIS219 2.1 42.0 1.0
NE2 F:HIS132 2.1 41.5 1.0
OD1 F:ASP134 2.2 41.2 1.0
O F:HOH401 2.3 31.9 1.0
O1 F:OGA302 2.4 43.7 1.0
C2 F:OGA302 2.8 49.7 1.0
C1 F:OGA302 3.0 48.5 1.0
CE1 F:HIS219 3.0 40.9 1.0
CG F:ASP134 3.0 40.6 1.0
CD2 F:HIS132 3.1 41.8 1.0
CD2 F:HIS219 3.1 42.2 1.0
CE1 F:HIS132 3.1 42.3 1.0
OD2 F:ASP134 3.2 42.0 1.0
N1 F:OGA302 4.0 51.2 1.0
ND1 F:HIS219 4.1 41.6 1.0
CG F:HIS219 4.2 42.5 1.0
O2 F:OGA302 4.2 46.9 1.0
CG F:HIS132 4.2 43.0 1.0
ND1 F:HIS132 4.2 43.7 1.0
O F:HOH437 4.3 43.2 1.0
CB F:ASP134 4.5 39.2 1.0
C4 F:OGA302 4.7 51.7 1.0
OE1 F:GLN129 4.8 42.2 1.0
NH2 F:ARG213 4.8 47.4 1.0
CA F:ASP134 4.9 40.0 1.0
N F:ASP134 5.0 40.2 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 09:07:54 2024

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