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Nickel in PDB 6lh7: Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals

Enzymatic activity of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals

All present enzymatic activity of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals:
3.4.11.18;

Protein crystallography data

The structure of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals, PDB code: 6lh7 was solved by V.Pillalamarri, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.23 / 1.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.702, 50.293, 131.684, 90.00, 97.24, 90.00
R / Rfree (%) 15.2 / 17.7

Other elements in 6lh7:

The structure of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals (pdb code 6lh7). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals, PDB code: 6lh7:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in 6lh7

Go back to Nickel Binding Sites List in 6lh7
Nickel binding site 1 out of 4 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:21.7
occ:0.40
 O A:HOH528 1.8 23.1 0.4
OD1 A:ASP107 2.1 15.6 0.6
OD2 A:ASP107 2.1 14.1 0.4
OD1 A:ASP118 2.3 18.6 1.0
OE1 A:GLU252 2.4 21.0 1.0
OD1 A:ASP107 2.5 17.0 0.4
CG A:ASP107 2.6 13.7 0.4
CG A:ASP118 2.9 15.7 1.0
OD2 A:ASP118 3.0 19.6 1.0
CG A:ASP107 3.0 15.6 0.6
NI A:NI302 3.2 34.3 0.4
OD2 A:ASP107 3.3 18.2 0.6
CD A:GLU252 3.4 16.1 1.0
O A:HOH470 3.7 14.9 1.0
O A:HOH437 3.7 12.7 0.6
OE2 A:GLU252 3.7 17.5 1.0
OG1 A:THR109 4.0 18.3 1.0
CB A:ASP107 4.1 11.0 0.4
CB A:ASP118 4.3 12.7 1.0
N A:THR119 4.3 8.4 1.0
CB A:ASP107 4.4 11.9 0.6
O A:THR119 4.4 10.0 1.0
O A:HOH454 4.6 18.7 1.0
O A:ILE108 4.6 11.8 1.0
C A:THR119 4.7 8.9 1.0
OE1 A:GLU220 4.7 22.5 1.0
CG A:GLU252 4.7 11.9 1.0
C A:ASP118 4.7 9.2 1.0
CA A:ASP118 4.8 10.6 1.0
CA A:ASP107 4.9 9.8 0.4
CA A:ASP107 4.9 9.8 0.6
CA A:THR119 5.0 8.4 1.0
O A:HOH425 5.0 25.9 0.5
CZ A:PHE194 5.0 19.1 1.0

Nickel binding site 2 out of 4 in 6lh7

Go back to Nickel Binding Sites List in 6lh7
Nickel binding site 2 out of 4 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:34.3
occ:0.40
 O A:HOH437 1.2 12.7 0.6
OD2 A:ASP118 2.1 19.6 1.0
O A:HOH528 2.3 23.1 0.4
OE2 A:GLU220 2.4 16.3 1.0
OE2 A:GLU252 2.5 17.5 1.0
CD A:GLU252 3.1 16.1 1.0
CD A:GLU220 3.1 17.7 1.0
NE2 A:HIS188 3.1 19.1 1.0
OE1 A:GLU252 3.2 21.0 1.0
CG A:ASP118 3.2 15.7 1.0
NI A:NI301 3.2 21.7 0.4
OE1 A:GLU220 3.3 22.5 1.0
OD1 A:ASP118 3.8 18.6 1.0
OG1 A:THR218 3.9 11.3 1.0
CD2 A:HIS188 3.9 16.9 1.0
CE1 A:HIS188 4.0 16.8 1.0
CZ A:PHE194 4.0 19.1 1.0
CG2 A:THR218 4.1 11.1 1.0
CB A:THR218 4.2 10.0 1.0
CB A:ASP118 4.3 12.7 1.0
CG A:GLU252 4.5 11.9 1.0
CG A:GLU220 4.5 13.5 1.0
CE1 A:PHE194 4.5 20.2 1.0
OD2 A:ASP107 4.9 14.1 0.4
O A:HOH425 4.9 25.9 0.5
CE2 A:PHE194 5.0 20.4 1.0

Nickel binding site 3 out of 4 in 6lh7

Go back to Nickel Binding Sites List in 6lh7
Nickel binding site 3 out of 4 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:27.2
occ:0.40
 OD2 B:ASP107 2.1 16.0 0.4
OD1 B:ASP107 2.2 14.8 0.6
OD1 B:ASP118 2.4 20.3 1.0
OE1 B:GLU252 2.4 21.8 1.0
O B:HOH434 2.5 37.2 1.0
OD1 B:ASP107 2.6 16.2 0.4
CG B:ASP107 2.7 14.1 0.4
CG B:ASP118 3.0 18.3 1.0
OD2 B:ASP118 3.0 24.1 1.0
CG B:ASP107 3.1 16.3 0.6
CD B:GLU252 3.4 17.9 1.0
OD2 B:ASP107 3.4 19.4 0.6
NI B:NI302 3.5 30.8 0.4
O B:HOH455 3.6 19.5 1.0
OE2 B:GLU252 3.7 19.2 1.0
OG1 B:THR109 4.1 18.6 1.0
CB B:ASP107 4.2 12.2 0.4
CB B:ASP118 4.4 14.3 1.0
O B:THR119 4.4 11.7 1.0
CB B:ASP107 4.5 12.9 0.6
N B:THR119 4.5 9.7 1.0
O B:HOH447 4.5 24.3 1.0
OE1 B:GLU220 4.6 23.9 1.0
O B:HOH439 4.8 28.9 0.8
CG B:GLU252 4.8 13.6 1.0
O B:ILE108 4.8 12.4 1.0
C B:THR119 4.8 9.9 1.0
C B:ASP118 4.8 11.6 1.0
CA B:ASP118 4.9 12.4 1.0
CZ B:PHE194 4.9 20.9 1.0

Nickel binding site 4 out of 4 in 6lh7

Go back to Nickel Binding Sites List in 6lh7
Nickel binding site 4 out of 4 in the Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Vibrio Cholerae Methionine Aminopeptidase with Partially Occupied Metals within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:30.8
occ:0.40
 OD2 B:ASP118 2.6 24.1 1.0
OE2 B:GLU220 2.6 20.0 1.0
NE2 B:HIS188 2.7 19.8 1.0
OE1 B:GLU220 3.1 23.9 1.0
CD B:GLU220 3.3 20.0 1.0
O B:HOH434 3.3 37.2 1.0
OE2 B:GLU252 3.5 19.2 1.0
NI B:NI301 3.5 27.2 0.4
CZ B:PHE194 3.6 20.9 1.0
CD2 B:HIS188 3.7 18.8 1.0
CG B:ASP118 3.7 18.3 1.0
CE1 B:HIS188 3.7 18.8 1.0
OE1 B:GLU252 3.9 21.8 1.0
CD B:GLU252 4.0 17.9 1.0
CE2 B:PHE194 4.2 22.9 1.0
OD1 B:ASP118 4.2 20.3 1.0
OG1 B:THR218 4.3 13.7 1.0
CE1 B:PHE194 4.4 19.3 1.0
CG B:GLU220 4.7 16.2 1.0
CG2 B:THR218 4.8 15.1 1.0
CG B:HIS188 4.8 17.0 1.0
ND1 B:HIS188 4.8 17.9 1.0
CB B:THR218 4.9 13.5 1.0
CB B:ASP118 4.9 14.3 1.0

Reference:

V.Pillalamarri, C.G.Reddy, S.C.Bala, A.Jangam, V.V.Kutty, A.Addlagatta. Methionine Aminopeptidases with Short Sequence Inserts Within the Catalytic Domain Are Differentially Inhibited: Structural and Biochemical Studies of Three Proteins From Vibrio Spp. Eur.J.Med.Chem. V. 209 12883 2020.
ISSN: ISSN 0223-5234
PubMed: 33035924
DOI: 10.1016/J.EJMECH.2020.112883
Page generated: Thu Oct 10 08:38:39 2024

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