Nickel in PDB 6l7f: Metallo Beta-Lactamase Fold Protein (Camp Free)

Protein crystallography data

The structure of Metallo Beta-Lactamase Fold Protein (Camp Free), PDB code: 6l7f was solved by K.-Y.Lee, D.-G.Kim, B.-J.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.82 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.952, 120.752, 186.485, 90, 90, 90
R / Rfree (%) 19.7 / 24.8

Other elements in 6l7f:

The structure of Metallo Beta-Lactamase Fold Protein (Camp Free) also contains other interesting chemical elements:

Zinc (Zn) 12 atoms
Caesium (Cs) 6 atoms

Nickel Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Nickel atom in the Metallo Beta-Lactamase Fold Protein (Camp Free) (pdb code 6l7f). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 12 binding sites of Nickel where determined in the Metallo Beta-Lactamase Fold Protein (Camp Free), PDB code: 6l7f:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 1 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:43.3
occ:0.50
ZN A:ZN306 0.0 33.7 0.5
O A:HOH436 1.8 52.3 1.0
NE2 A:HIS110 2.0 27.2 1.0
NE2 A:HIS48 2.2 23.3 1.0
ND1 A:HIS50 2.3 28.2 1.0
OD2 A:ASP144 2.7 31.7 1.0
CD2 A:HIS110 3.0 30.4 1.0
CE1 A:HIS110 3.0 29.6 1.0
CE1 A:HIS48 3.1 25.8 1.0
CD2 A:HIS48 3.2 25.2 1.0
CG A:HIS50 3.2 30.9 1.0
NI A:NI304 3.2 39.6 0.5
ZN A:ZN305 3.2 38.7 0.5
CE1 A:HIS50 3.3 31.1 1.0
CB A:HIS50 3.5 29.5 1.0
O A:HOH497 3.5 43.9 1.0
CG A:ASP144 3.6 28.6 1.0
O C:HOH467 3.7 32.4 1.0
CB A:ASP144 3.8 27.2 1.0
CG A:HIS110 4.1 28.2 1.0
ND1 A:HIS110 4.1 30.3 1.0
NE2 A:HIS53 4.2 31.5 1.0
CD2 A:HIS53 4.2 32.3 1.0
ND1 A:HIS48 4.2 25.1 1.0
CG A:HIS48 4.3 23.4 1.0
OD1 A:ASP52 4.3 35.1 1.0
CD2 A:HIS50 4.4 29.7 1.0
NE2 A:HIS50 4.4 26.9 1.0
OD1 A:ASP144 4.6 29.0 1.0
O A:SER111 4.7 28.6 1.0
OD2 A:ASP52 4.9 33.8 1.0
CA A:HIS50 4.9 29.4 1.0

Nickel binding site 2 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 2 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni304

b:39.6
occ:0.50
ZN A:ZN305 0.0 38.7 0.5
O A:HOH436 2.0 52.3 1.0
OD2 A:ASP144 2.1 31.7 1.0
NE2 A:HIS195 2.2 32.9 1.0
OD2 A:ASP52 2.3 33.8 1.0
NE2 A:HIS53 2.3 31.5 1.0
O A:HOH497 2.7 43.9 1.0
CG A:ASP144 3.1 28.6 1.0
CD2 A:HIS53 3.1 32.3 1.0
CE1 A:HIS195 3.1 31.5 1.0
CD2 A:HIS195 3.1 28.1 1.0
CG A:ASP52 3.2 32.7 1.0
ZN A:ZN306 3.2 33.7 0.5
NI A:NI301 3.2 43.3 0.5
OD1 A:ASP52 3.3 35.1 1.0
OD1 A:ASP144 3.4 29.0 1.0
CE1 A:HIS53 3.4 30.1 1.0
ND1 A:HIS195 4.2 32.7 1.0
CG A:HIS195 4.3 30.7 1.0
OE1 A:GLN8 4.3 37.2 1.0
NE2 A:HIS48 4.3 23.3 1.0
CE1 A:HIS48 4.3 25.8 1.0
CG A:HIS53 4.3 31.0 1.0
CB A:ASP144 4.4 27.2 1.0
ND1 A:HIS53 4.5 28.4 1.0
CB A:ASP52 4.5 34.7 1.0
NE2 A:HIS110 4.6 27.2 1.0
CD A:GLN8 4.9 31.9 1.0
CE1 A:HIS110 4.9 29.6 1.0

Nickel binding site 3 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 3 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:45.4
occ:0.50
ZN B:ZN304 0.0 34.2 0.5
O B:HOH404 2.0 79.2 1.0
NE2 B:HIS110 2.2 31.5 1.0
OD2 B:ASP144 2.2 30.0 1.0
NE2 B:HIS48 2.3 34.6 1.0
ND1 B:HIS50 2.4 37.5 1.0
O B:HOH474 3.0 43.6 1.0
ZN B:ZN305 3.0 45.9 0.5
NI B:NI303 3.0 47.6 0.5
CD2 B:HIS110 3.1 26.7 1.0
CE1 B:HIS110 3.2 32.9 1.0
CD2 B:HIS48 3.3 35.5 1.0
CE1 B:HIS48 3.3 30.7 1.0
CG B:ASP144 3.3 28.8 1.0
CE1 B:HIS50 3.3 39.7 1.0
CG B:HIS50 3.4 40.4 1.0
CB B:HIS50 3.6 37.1 1.0
CB B:ASP144 3.9 26.6 1.0
O A:HOH478 3.9 31.0 1.0
NE2 B:HIS53 4.0 41.2 1.0
CD2 B:HIS53 4.1 40.8 1.0
CG B:HIS110 4.2 26.4 1.0
OD1 B:ASP144 4.2 28.6 1.0
ND1 B:HIS110 4.3 32.7 1.0
ND1 B:HIS48 4.4 34.4 1.0
OD1 B:ASP52 4.4 47.9 1.0
CG B:HIS48 4.4 35.3 1.0
NE2 B:HIS50 4.4 33.7 1.0
CD2 B:HIS50 4.5 37.6 1.0
OD2 B:ASP52 4.7 46.6 1.0
O B:SER111 4.8 29.8 1.0
CE1 B:HIS53 5.0 37.8 1.0
NE2 B:HIS195 5.0 31.9 1.0
CG B:ASP52 5.0 43.6 1.0

Nickel binding site 4 out of 12 in 6l7f

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Nickel binding site 4 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni303

b:47.6
occ:0.50
ZN B:ZN305 0.0 45.9 0.5
NE2 B:HIS195 2.2 31.9 1.0
NE2 B:HIS53 2.3 41.2 1.0
OD2 B:ASP144 2.4 30.0 1.0
O B:HOH404 2.4 79.2 1.0
OD2 B:ASP52 2.4 46.6 1.0
O B:HOH474 2.5 43.6 1.0
ZN B:ZN304 3.0 34.2 0.5
NI B:NI301 3.0 45.4 0.5
CG B:ASP144 3.1 28.8 1.0
CD2 B:HIS53 3.1 40.8 1.0
CD2 B:HIS195 3.2 32.3 1.0
CE1 B:HIS195 3.2 32.4 1.0
OD1 B:ASP144 3.3 28.6 1.0
CG B:ASP52 3.3 43.6 1.0
CE1 B:HIS53 3.4 37.8 1.0
OD1 B:ASP52 3.6 47.9 1.0
NE2 B:HIS48 4.2 34.6 1.0
ND1 B:HIS195 4.3 28.4 1.0
CE1 B:HIS48 4.3 30.7 1.0
CG B:HIS195 4.3 31.4 1.0
CG B:HIS53 4.3 40.2 1.0
ND1 B:HIS53 4.4 35.9 1.0
OE1 B:GLN8 4.5 41.1 1.0
CB B:ASP144 4.5 26.6 1.0
NE2 B:HIS110 4.5 31.5 1.0
CB B:ASP52 4.7 42.5 1.0
CE1 B:HIS110 4.9 32.9 1.0

Nickel binding site 5 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 5 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:39.2
occ:0.50
ZN C:ZN304 0.0 32.8 0.5
O C:HOH404 2.0 39.2 1.0
NE2 C:HIS110 2.1 28.6 1.0
ND1 C:HIS50 2.2 30.6 1.0
NE2 C:HIS48 2.2 22.5 1.0
OD2 C:ASP144 2.4 33.0 1.0
O C:HOH479 3.0 39.1 1.0
CD2 C:HIS48 3.0 26.3 1.0
CD2 C:HIS110 3.0 27.2 1.0
CE1 C:HIS50 3.1 30.9 1.0
NI C:NI303 3.1 45.7 0.5
ZN C:ZN305 3.1 44.2 0.5
CE1 C:HIS110 3.1 28.7 1.0
CG C:HIS50 3.2 31.0 1.0
CE1 C:HIS48 3.3 23.1 1.0
CG C:ASP144 3.4 35.5 1.0
CB C:HIS50 3.5 32.1 1.0
O B:HOH472 3.8 30.2 1.0
CB C:ASP144 3.9 33.5 1.0
NE2 C:HIS53 3.9 35.1 1.0
CD2 C:HIS53 4.0 34.7 1.0
CG C:HIS110 4.2 25.9 1.0
ND1 C:HIS110 4.2 27.6 1.0
CG C:HIS48 4.2 26.1 1.0
NE2 C:HIS50 4.3 28.4 1.0
ND1 C:HIS48 4.3 24.7 1.0
CD2 C:HIS50 4.3 30.4 1.0
OD1 C:ASP52 4.4 39.8 1.0
OD1 C:ASP144 4.4 32.5 1.0
OD2 C:ASP52 4.8 38.1 1.0
O C:SER111 4.9 26.9 1.0
NE2 C:HIS195 4.9 30.6 1.0
CA C:HIS50 4.9 33.3 1.0
CE1 C:HIS53 5.0 32.9 1.0

Nickel binding site 6 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 6 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni303

b:45.7
occ:0.50
ZN C:ZN305 0.0 44.2 0.5
O C:HOH404 2.0 39.2 1.0
NE2 C:HIS195 2.2 30.6 1.0
NE2 C:HIS53 2.2 35.1 1.0
OD2 C:ASP144 2.3 33.0 1.0
OD2 C:ASP52 2.4 38.1 1.0
O C:HOH479 2.6 39.1 1.0
CD2 C:HIS53 3.1 34.7 1.0
NI C:NI301 3.1 39.2 0.5
ZN C:ZN304 3.1 32.8 0.5
CG C:ASP144 3.1 35.5 1.0
CD2 C:HIS195 3.1 31.8 1.0
CE1 C:HIS195 3.2 30.6 1.0
CG C:ASP52 3.2 36.2 1.0
CE1 C:HIS53 3.3 32.9 1.0
OD1 C:ASP144 3.3 32.5 1.0
OD1 C:ASP52 3.5 39.8 1.0
NE2 C:HIS48 4.0 22.5 1.0
OE1 C:GLN8 4.0 37.3 1.0
CE1 C:HIS48 4.2 23.1 1.0
ND1 C:HIS195 4.3 31.4 1.0
CG C:HIS53 4.3 34.8 1.0
CG C:HIS195 4.3 32.4 1.0
ND1 C:HIS53 4.3 32.2 1.0
CB C:ASP144 4.5 33.5 1.0
CB C:ASP52 4.5 36.3 1.0
NE2 C:HIS110 4.7 28.6 1.0
CD C:GLN8 4.8 37.2 1.0
ND1 C:HIS50 4.9 30.6 1.0

Nickel binding site 7 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 7 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:41.8
occ:0.50
ZN D:ZN304 0.0 33.4 0.5
O D:HOH409 2.0 48.0 1.0
NE2 D:HIS110 2.2 29.0 1.0
NE2 D:HIS48 2.3 25.4 1.0
ND1 D:HIS50 2.3 29.3 1.0
OD2 D:ASP144 2.5 38.5 1.0
O D:HOH492 2.9 40.5 1.0
CD2 D:HIS48 3.0 27.7 1.0
CD2 D:HIS110 3.1 35.5 1.0
NI D:NI303 3.2 44.6 0.5
ZN D:ZN305 3.2 43.1 0.5
CG D:HIS50 3.2 31.7 1.0
CE1 D:HIS110 3.3 28.6 1.0
CE1 D:HIS50 3.3 33.8 1.0
CE1 D:HIS48 3.4 25.2 1.0
CG D:ASP144 3.4 36.4 1.0
CB D:HIS50 3.5 31.8 1.0
CB D:ASP144 3.8 35.4 1.0
NE2 D:HIS53 3.9 32.6 1.0
O F:HOH468 3.9 31.3 1.0
CD2 D:HIS53 4.0 39.3 1.0
CG D:HIS48 4.3 26.4 1.0
CG D:HIS110 4.3 32.5 1.0
ND1 D:HIS110 4.3 33.7 1.0
OD1 D:ASP52 4.4 40.4 1.0
ND1 D:HIS48 4.4 27.4 1.0
CD2 D:HIS50 4.4 33.0 1.0
NE2 D:HIS50 4.4 29.7 1.0
OD1 D:ASP144 4.5 38.1 1.0
OD2 D:ASP52 4.8 36.1 1.0
O D:SER111 4.8 29.4 1.0
CE1 D:HIS53 4.8 34.7 1.0
CA D:HIS50 4.9 35.2 1.0

Nickel binding site 8 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 8 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni303

b:44.6
occ:0.50
ZN D:ZN305 0.0 43.1 0.5
O D:HOH409 2.2 48.0 1.0
OD2 D:ASP144 2.2 38.5 1.0
NE2 D:HIS195 2.2 30.7 1.0
NE2 D:HIS53 2.2 32.6 1.0
OD2 D:ASP52 2.4 36.1 1.0
O D:HOH492 2.9 40.5 1.0
CE1 D:HIS195 3.0 30.8 1.0
CD2 D:HIS53 3.1 39.3 1.0
CG D:ASP144 3.1 36.4 1.0
NI D:NI301 3.2 41.8 0.5
ZN D:ZN304 3.2 33.4 0.5
CG D:ASP52 3.3 41.8 1.0
CD2 D:HIS195 3.3 32.4 1.0
CE1 D:HIS53 3.3 34.7 1.0
OD1 D:ASP144 3.4 38.1 1.0
OD1 D:ASP52 3.5 40.4 1.0
OE1 D:GLN8 4.0 41.3 1.0
NE2 D:HIS48 4.1 25.4 1.0
ND1 D:HIS195 4.2 36.0 1.0
CG D:HIS53 4.3 36.5 1.0
CG D:HIS195 4.3 33.4 1.0
ND1 D:HIS53 4.4 32.9 1.0
CE1 D:HIS48 4.4 25.2 1.0
CB D:ASP144 4.5 35.4 1.0
CB D:ASP52 4.6 39.6 1.0
NE2 D:HIS110 4.7 29.0 1.0
CD D:GLN8 4.7 40.4 1.0

Nickel binding site 9 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 9 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni301

b:40.0
occ:0.50
ZN E:ZN305 0.0 32.9 0.5
O E:HOH432 1.9 41.3 1.0
ND1 E:HIS50 2.1 27.7 1.0
NE2 E:HIS110 2.2 27.1 1.0
NE2 E:HIS48 2.2 31.2 1.0
OD2 E:ASP144 2.5 32.1 1.0
CD2 E:HIS110 3.0 29.6 1.0
CE1 E:HIS50 3.1 31.1 1.0
CD2 E:HIS48 3.1 29.1 1.0
NI E:NI304 3.1 42.3 0.5
ZN E:ZN306 3.1 41.1 0.5
O E:HOH492 3.2 37.6 1.0
CG E:HIS50 3.2 30.6 1.0
CE1 E:HIS110 3.2 29.7 1.0
CE1 E:HIS48 3.3 30.9 1.0
CG E:ASP144 3.5 28.6 1.0
CB E:HIS50 3.5 30.3 1.0
O D:HOH493 3.6 32.0 1.0
CB E:ASP144 3.9 28.5 1.0
NE2 E:HIS53 4.1 31.6 1.0
CD2 E:HIS53 4.2 30.6 1.0
CG E:HIS110 4.2 28.3 1.0
NE2 E:HIS50 4.2 28.1 1.0
ND1 E:HIS110 4.3 29.9 1.0
CG E:HIS48 4.3 26.4 1.0
CD2 E:HIS50 4.3 30.8 1.0
ND1 E:HIS48 4.3 26.1 1.0
OD1 E:ASP52 4.4 35.6 1.0
OD1 E:ASP144 4.5 33.2 1.0
O E:SER111 4.7 29.1 1.0
OD2 E:ASP52 4.8 32.3 1.0
CA E:HIS50 4.9 29.1 1.0
CG E:ASP52 5.0 34.5 1.0

Nickel binding site 10 out of 12 in 6l7f

Go back to Nickel Binding Sites List in 6l7f
Nickel binding site 10 out of 12 in the Metallo Beta-Lactamase Fold Protein (Camp Free)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Metallo Beta-Lactamase Fold Protein (Camp Free) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ni304

b:42.3
occ:0.50
ZN E:ZN306 0.0 41.1 0.5
O E:HOH432 1.9 41.3 1.0
OD2 E:ASP144 2.1 32.1 1.0
NE2 E:HIS53 2.3 31.6 1.0
OD2 E:ASP52 2.3 32.3 1.0
CE1 E:HIS195 2.4 30.7 1.0
O E:HOH492 2.9 37.6 1.0
CD2 E:HIS53 3.0 30.6 1.0
CG E:ASP144 3.1 28.6 1.0
ZN E:ZN305 3.1 32.9 0.5
NI E:NI301 3.1 40.0 0.5
NE2 E:HIS195 3.2 27.5 1.0
CG E:ASP52 3.2 34.5 1.0
ND1 E:HIS195 3.3 28.5 1.0
OD1 E:ASP144 3.4 33.2 1.0
CE1 E:HIS53 3.4 34.2 1.0
OD1 E:ASP52 3.5 35.6 1.0
OE1 E:GLN8 4.1 36.7 1.0
NE2 E:HIS48 4.1 31.2 1.0
CG E:HIS53 4.3 32.2 1.0
CE1 E:HIS48 4.3 30.9 1.0
CD2 E:HIS195 4.4 31.2 1.0
CB E:ASP144 4.4 28.5 1.0
ND1 E:HIS53 4.4 30.4 1.0
CG E:HIS195 4.5 30.5 1.0
CB E:ASP52 4.6 33.7 1.0
NE2 E:HIS110 4.6 27.1 1.0
ND1 E:HIS50 4.9 27.7 1.0
CD E:GLN8 4.9 29.3 1.0
CE1 E:HIS110 5.0 29.7 1.0

Reference:

K.-Y.Lee, D.-G.Kim, B.-J.Lee. Metallo Beta-Lactamase Fold Protein To Be Published.
Page generated: Wed Mar 3 15:40:16 2021

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