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Nickel in PDB 1ztc: Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution

Protein crystallography data

The structure of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution, PDB code: 1ztc was solved by Joint Center For Structural Genomics (Jcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.60 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.783, 127.343, 152.224, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.8

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution (pdb code 1ztc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution, PDB code: 1ztc:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in 1ztc

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Nickel binding site 1 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:65.1
occ:1.00
OD2 A:ASP162 2.2 51.5 1.0
NE2 A:HIS199 2.2 43.7 1.0
NE2 A:HIS74 2.2 46.5 1.0
O A:HOH425 2.5 40.5 1.0
O A:HOH387 2.6 50.0 1.0
OD1 A:ASP162 2.8 60.3 1.0
OD2 A:ASP73 2.9 56.0 1.0
CG A:ASP162 2.9 49.7 1.0
CD2 A:HIS74 3.0 43.3 1.0
CE1 A:HIS199 3.2 43.5 1.0
CD2 A:HIS199 3.2 47.5 1.0
CE1 A:HIS74 3.4 47.5 1.0
NI A:NI302 3.6 59.9 1.0
O A:HOH402 3.7 62.6 1.0
O A:HOH306 3.8 43.0 1.0
CG A:ASP73 3.8 51.8 1.0
OD1 A:ASP73 4.0 52.2 1.0
CG A:HIS74 4.2 45.9 1.0
ND1 A:HIS199 4.3 48.7 1.0
CE1 A:HIS69 4.3 46.3 1.0
CG A:HIS199 4.3 44.4 1.0
CB A:ASP162 4.3 45.3 1.0
O A:HOH435 4.4 62.2 1.0
ND1 A:HIS74 4.4 46.6 1.0
NE2 A:HIS69 4.4 46.3 1.0
CB A:PRO198 4.8 44.4 1.0
CG A:PRO198 5.0 43.3 1.0

Nickel binding site 2 out of 8 in 1ztc

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Nickel binding site 2 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:59.9
occ:1.00
NE2 A:HIS69 2.2 46.3 1.0
O A:HOH425 2.2 40.5 1.0
ND1 A:HIS71 2.2 57.8 1.0
NE2 A:HIS140 2.3 52.3 1.0
OD2 A:ASP162 2.3 51.5 1.0
O A:HOH306 2.4 43.0 1.0
CE1 A:HIS71 3.0 61.5 1.0
CE1 A:HIS69 3.1 46.3 1.0
CD2 A:HIS69 3.1 43.8 1.0
CD2 A:HIS140 3.2 48.5 1.0
CE1 A:HIS140 3.2 48.5 1.0
CG A:HIS71 3.2 59.0 1.0
CG A:ASP162 3.4 49.7 1.0
NI A:NI301 3.6 65.1 1.0
CB A:HIS71 3.7 49.0 1.0
CB A:ASP162 3.8 45.3 1.0
O A:HOH387 3.9 50.0 1.0
NE2 A:HIS71 4.1 66.2 1.0
ND1 A:HIS69 4.2 44.9 1.0
CG A:HIS69 4.3 44.7 1.0
CD2 A:HIS71 4.3 66.9 1.0
O A:HOH402 4.3 62.6 1.0
ND1 A:HIS140 4.3 51.9 1.0
CG A:HIS140 4.4 47.5 1.0
NE2 A:HIS74 4.4 46.5 1.0
OD1 A:ASP162 4.5 60.3 1.0
CD2 A:HIS74 4.5 43.3 1.0
OD1 A:ASP73 4.8 52.2 1.0

Nickel binding site 3 out of 8 in 1ztc

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Nickel binding site 3 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:65.7
occ:1.00
NE2 B:HIS199 2.2 49.7 1.0
OD2 B:ASP162 2.2 52.9 1.0
NE2 B:HIS74 2.2 45.7 1.0
O B:HOH402 2.5 51.6 1.0
OD1 B:ASP162 2.7 55.0 1.0
O B:HOH336 2.8 67.5 1.0
CG B:ASP162 2.9 48.1 1.0
OD2 B:ASP73 2.9 52.5 1.0
CD2 B:HIS74 3.1 46.7 1.0
CD2 B:HIS199 3.1 47.6 1.0
CE1 B:HIS199 3.2 44.0 1.0
CE1 B:HIS74 3.3 47.9 1.0
O B:HOH403 3.3 67.6 1.0
NI B:NI302 3.5 59.3 1.0
CG B:ASP73 3.8 51.6 1.0
O B:HOH305 3.8 42.8 1.0
OD1 B:ASP73 4.0 51.3 1.0
CG B:HIS74 4.3 46.0 1.0
CG B:HIS199 4.3 48.2 1.0
ND1 B:HIS199 4.3 48.8 1.0
CB B:ASP162 4.4 46.6 1.0
ND1 B:HIS74 4.4 46.0 1.0
CE1 B:HIS69 4.4 45.6 1.0
NE2 B:HIS69 4.4 44.2 1.0
CB B:PRO198 4.8 44.7 1.0

Nickel binding site 4 out of 8 in 1ztc

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Nickel binding site 4 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni302

b:59.3
occ:1.00
ND1 B:HIS71 2.2 57.7 1.0
NE2 B:HIS69 2.2 44.2 1.0
OD2 B:ASP162 2.2 52.9 1.0
NE2 B:HIS140 2.3 51.7 1.0
O B:HOH402 2.3 51.6 1.0
O B:HOH305 2.6 42.8 1.0
CE1 B:HIS71 3.0 63.2 1.0
CD2 B:HIS69 3.1 41.7 1.0
CE1 B:HIS69 3.2 45.6 1.0
CD2 B:HIS140 3.2 48.3 1.0
CG B:HIS71 3.2 56.0 1.0
CE1 B:HIS140 3.3 45.7 1.0
CG B:ASP162 3.3 48.1 1.0
NI B:NI301 3.5 65.7 1.0
CB B:HIS71 3.7 46.8 1.0
CB B:ASP162 3.8 46.6 1.0
NE2 B:HIS71 4.1 68.4 1.0
O B:HOH336 4.1 67.5 1.0
CG B:HIS69 4.2 45.1 1.0
CD2 B:HIS71 4.2 66.5 1.0
ND1 B:HIS69 4.3 48.4 1.0
NE2 B:HIS74 4.3 45.7 1.0
O B:HOH403 4.3 67.6 1.0
OD1 B:ASP162 4.3 55.0 1.0
CG B:HIS140 4.3 47.5 1.0
ND1 B:HIS140 4.3 48.5 1.0
CD2 B:HIS74 4.5 46.7 1.0
OD1 B:ASP73 4.8 51.3 1.0

Nickel binding site 5 out of 8 in 1ztc

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Nickel binding site 5 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni301

b:65.0
occ:1.00
OD2 C:ASP162 2.2 51.6 1.0
NE2 C:HIS199 2.3 48.6 1.0
NE2 C:HIS74 2.3 41.5 1.0
O C:HOH393 2.4 47.7 1.0
OD1 C:ASP162 2.8 56.3 1.0
CG C:ASP162 2.8 49.1 1.0
O C:HOH361 2.9 64.9 1.0
OD2 C:ASP73 2.9 50.5 1.0
CD2 C:HIS74 3.1 48.3 1.0
CD2 C:HIS199 3.2 46.6 1.0
CE1 C:HIS199 3.2 44.3 1.0
CE1 C:HIS74 3.4 44.1 1.0
NI C:NI302 3.5 59.7 1.0
CG C:ASP73 3.9 51.5 1.0
O C:HOH305 3.9 45.0 1.0
OD1 C:ASP73 4.0 49.2 1.0
CE1 C:HIS69 4.3 48.1 1.0
CB C:ASP162 4.3 47.1 1.0
ND1 C:HIS199 4.3 49.6 1.0
NE2 C:HIS69 4.3 44.1 1.0
CG C:HIS199 4.4 45.6 1.0
CG C:HIS74 4.4 41.6 1.0
ND1 C:HIS74 4.5 45.0 1.0
CB C:PRO198 4.8 44.0 1.0
CG C:PRO198 5.0 43.3 1.0

Nickel binding site 6 out of 8 in 1ztc

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Nickel binding site 6 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni302

b:59.7
occ:1.00
NE2 C:HIS69 2.1 44.1 1.0
ND1 C:HIS71 2.2 57.6 1.0
OD2 C:ASP162 2.3 51.6 1.0
NE2 C:HIS140 2.3 48.9 1.0
O C:HOH393 2.4 47.7 1.0
O C:HOH305 2.5 45.0 1.0
CE1 C:HIS71 3.0 62.3 1.0
CD2 C:HIS69 3.1 43.7 1.0
CE1 C:HIS69 3.2 48.1 1.0
CD2 C:HIS140 3.2 49.0 1.0
CG C:HIS71 3.3 56.5 1.0
CE1 C:HIS140 3.3 43.3 1.0
CG C:ASP162 3.3 49.1 1.0
NI C:NI301 3.5 65.0 1.0
CB C:HIS71 3.7 48.0 1.0
CB C:ASP162 3.8 47.1 1.0
NE2 C:HIS71 4.1 66.3 1.0
O C:HOH361 4.2 64.9 1.0
CG C:HIS69 4.2 44.0 1.0
ND1 C:HIS69 4.2 48.7 1.0
CD2 C:HIS71 4.3 66.3 1.0
NE2 C:HIS74 4.3 41.5 1.0
ND1 C:HIS140 4.4 48.8 1.0
CG C:HIS140 4.4 47.5 1.0
OD1 C:ASP162 4.4 56.3 1.0
CD2 C:HIS74 4.6 48.3 1.0
OD1 C:ASP73 4.8 49.2 1.0

Nickel binding site 7 out of 8 in 1ztc

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Nickel binding site 7 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni301

b:65.3
occ:1.00
OD2 D:ASP162 2.2 50.0 1.0
NE2 D:HIS199 2.2 45.8 1.0
NE2 D:HIS74 2.3 45.2 1.0
O D:HOH399 2.4 49.1 1.0
O D:HOH409 2.5 55.8 1.0
OD1 D:ASP162 2.7 56.2 1.0
CG D:ASP162 2.8 48.8 1.0
OD2 D:ASP73 2.9 54.0 1.0
CD2 D:HIS74 3.1 43.9 1.0
CD2 D:HIS199 3.1 48.1 1.0
CE1 D:HIS199 3.2 44.3 1.0
CE1 D:HIS74 3.3 47.3 1.0
NI D:NI302 3.5 58.6 1.0
O D:HOH306 3.8 45.9 1.0
CG D:ASP73 3.9 52.1 1.0
OD1 D:ASP73 4.1 52.6 1.0
CG D:HIS74 4.3 44.0 1.0
CG D:HIS199 4.3 45.5 1.0
CB D:ASP162 4.3 45.6 1.0
ND1 D:HIS199 4.3 46.9 1.0
CE1 D:HIS69 4.3 47.8 1.0
ND1 D:HIS74 4.4 44.3 1.0
NE2 D:HIS69 4.4 41.5 1.0
O D:HOH382 4.6 61.2 1.0
CB D:PRO198 4.7 44.6 1.0
CG D:PRO198 5.0 42.3 1.0

Nickel binding site 8 out of 8 in 1ztc

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Nickel binding site 8 out of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni302

b:58.6
occ:1.00
ND1 D:HIS71 2.2 56.1 1.0
NE2 D:HIS69 2.2 41.5 1.0
OD2 D:ASP162 2.3 50.0 1.0
NE2 D:HIS140 2.3 51.5 1.0
O D:HOH399 2.4 49.1 1.0
O D:HOH306 2.5 45.9 1.0
CE1 D:HIS71 3.0 61.5 1.0
CE1 D:HIS69 3.1 47.8 1.0
CD2 D:HIS69 3.1 44.7 1.0
CE1 D:HIS140 3.2 47.6 1.0
CD2 D:HIS140 3.3 50.3 1.0
CG D:HIS71 3.3 57.6 1.0
CG D:ASP162 3.3 48.8 1.0
NI D:NI301 3.5 65.3 1.0
CB D:HIS71 3.7 47.0 1.0
CB D:ASP162 3.8 45.6 1.0
O D:HOH409 3.9 55.8 1.0
NE2 D:HIS71 4.2 65.7 1.0
ND1 D:HIS69 4.3 47.7 1.0
CG D:HIS69 4.3 44.3 1.0
NE2 D:HIS74 4.3 45.2 1.0
ND1 D:HIS140 4.3 49.1 1.0
CD2 D:HIS71 4.3 65.6 1.0
CG D:HIS140 4.4 46.9 1.0
OD1 D:ASP162 4.4 56.2 1.0
CD2 D:HIS74 4.5 43.9 1.0
OD1 D:ASP73 4.8 52.6 1.0

Reference:

Joint Center For Structural Genomics (Jcsg), Joint Center For Structural Genomics (Jcsg). N/A N/A.
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